0.016503 0.009528 0.000000 0.000000 0.019056 0.000000 0.000000 0.000000 0.015589 0.000000 0.000000 0.000000 Barabas, O. Nemeth, V. Vertessy, B.G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.000 90.000 120.000 60.594 60.594 64.146 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C9 H16 N3 O13 P3 467.157 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE non-polymer C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking Mg 2 24.305 MAGNESIUM ION non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C9 H13 N2 O8 P 308.182 2'-DEOXYURIDINE 5'-MONOPHOSPHATE DUMP non-polymer C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N N N 75 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N O Y 89 N C Y 90 N C Y 91 N C Y 92 N N Y 93 N C N 94 N O Y 95 N N N 96 R C N 97 N C N 98 S C N 99 N O N 100 N O N 101 R C N 102 N C N 103 N O N 104 S P N 105 N O N 106 N O N 107 N N N 108 R P N 109 N O N 110 N O N 111 N O N 112 N P N 113 N O N 114 N O N 115 N O N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N N N 133 S C N 134 N C N 135 N O N 136 N C N 137 N C N 138 N C N 139 N O N 140 N N N 141 N O N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N N N 153 S C N 154 N C N 155 N O N 156 N C N 157 N C N 158 N C N 159 N O N 160 N O N 161 N O N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N N N 172 N C N 173 N C N 174 N O N 175 N O N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N N N 182 S C N 183 N C N 184 N O N 185 N C Y 186 N C Y 187 N N Y 188 N C Y 189 N C Y 190 N N N 191 N O N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N O N 203 N H N 204 N H N 205 N N N 206 S C N 207 N C N 208 N O N 209 S C N 210 N C N 211 N C N 212 N C N 213 N O N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N N N 228 S C N 229 N C N 230 N O N 231 N C N 232 N C N 233 N C N 234 N C N 235 N O N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N N N 250 S C N 251 N C N 252 N O N 253 N C N 254 N C N 255 N C N 256 N C N 257 N N N 258 N O N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N N N 275 S C N 276 N C N 277 N O N 278 N C N 279 N C N 280 N S N 281 N C N 282 N O N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N MG N 295 N N N 296 S C N 297 N C N 298 N O N 299 N C Y 300 N C Y 301 N C Y 302 N C Y 303 N C Y 304 N C Y 305 N C N 306 N O N 307 N H N 308 N H N 309 N H N 310 N H N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N N N 319 S C N 320 N C N 321 N O N 322 N C N 323 N C N 324 N C N 325 N O N 326 N H N 327 N H N 328 N H N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N N N 336 S C N 337 N C N 338 N O N 339 N C N 340 N O N 341 N O N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N N N 350 S C N 351 N C N 352 N O N 353 R C N 354 N O N 355 N C N 356 N O N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N N N 367 S C N 368 N C N 369 N O N 370 N C Y 371 N C Y 372 N C Y 373 N C Y 374 N N Y 375 N C Y 376 N C Y 377 N C Y 378 N C Y 379 N C N 380 N O N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 390 N H N 391 N H N 392 N H N 393 N N N 394 S C N 395 N C N 396 N O N 397 N C Y 398 N C Y 399 N C Y 400 N C Y 401 N C Y 402 N C Y 403 N C N 404 N O N 405 N O N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N N N 418 N C N 419 N N N 420 N C N 421 N C N 422 N C N 423 N O N 424 N O N 425 R C N 426 N C N 427 S C N 428 R C N 429 N O N 430 N O N 431 N C N 432 N O N 433 N P N 434 N O N 435 N O N 436 N O N 437 N H N 438 N H N 439 N H N 440 N H N 441 N H N 442 N H N 443 N H N 444 N H N 445 N H N 446 N H N 447 N H N 448 N H N 449 N H N 450 N N N 451 S C N 452 N C N 453 N O N 454 N C N 455 N C N 456 N C N 457 N O N 458 N H N 459 N H N 460 N H N 461 N H N 462 N H N 463 N H N 464 N H N 465 N H N 466 N H N 467 N H N 468 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N doub Y 84 N sing Y 85 N sing Y 86 N doub N 87 N sing Y 88 N sing N 89 N sing Y 90 N sing N 91 N sing N 92 N doub Y 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N doub N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N doub N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N doub N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N doub N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing Y 185 N sing Y 186 N doub Y 187 N doub N 188 N sing Y 189 N sing N 190 N sing Y 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N doub N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N doub N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N doub N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N doub N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N doub N 289 N sing N 290 N sing N 291 N sing N 292 N sing Y 293 N doub Y 294 N sing Y 295 N sing N 296 N sing Y 297 N doub N 298 N sing Y 299 N doub N 300 N sing Y 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N doub N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N doub N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N doub N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N doub N 358 N sing N 359 N sing N 360 N sing N 361 N sing Y 362 N doub Y 363 N sing Y 364 N sing N 365 N sing Y 366 N doub Y 367 N sing Y 368 N sing N 369 N sing Y 370 N sing Y 371 N doub N 372 N sing Y 373 N doub N 374 N sing Y 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N doub N 386 N sing N 387 N sing N 388 N sing N 389 N sing Y 390 N doub Y 391 N sing Y 392 N sing N 393 N sing Y 394 N doub N 395 N sing Y 396 N doub N 397 N sing Y 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N doub N 408 N sing N 409 N sing N 410 N sing N 411 N doub N 412 N doub N 413 N sing N 414 N sing N 415 N sing N 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N sing N 421 N sing N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing N 427 N sing N 428 N sing N 429 N sing N 430 N sing N 431 N sing N 432 N doub N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N sing N 440 N sing N 441 N sing N 442 N sing N 443 N doub N 444 N sing N 445 N sing N 446 N sing N 447 N sing N 448 N sing N 449 N sing N 450 N sing N 451 N sing N 452 N sing N 453 N sing N 454 N sing to be published 0353 Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion DK Acta Crystallogr.,Sect.F 1744-3091 62 399 401 16582495 Crystallization and preliminary X-ray studies of dUTPase from Mason-Pfizer monkey retrovirus. 2006 10.2210/pdb3tq3/pdb pdb_00003tq3 100 1 mirrors CCD 2003-11-14 MAR CCD 165 mm Si [111], horizontally focusing SINGLE WAVELENGTH M x-ray 1 0.8124 1.0 X11 EMBL/DESY, HAMBURG 0.8124 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 16155.373 DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE 3.6.1.23 dUTPase (catalytic) domain, UNP residues 608-759 N1K 1 man polymer 308.182 2'-DEOXYURIDINE 5'-MONOPHOSPHATE 1 syn non-polymer 467.157 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE 1 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 99 nat water no no KRVEGPAPGPETSLWGSQLCSSQQKQPISKLTRATPGSAGLDLCSTSHTVLTPEMGPQALSTGIYGPLPPNTFGLILGRS SITMKGLQVYPGVIDNDYTGEIKIMAKAVNNIVTVSQGNRIAQLILLPLIETDNKVQQPYRGQGSFGSSDIY KRVEGPAPGPETSLWGSQLCSSQQKQPISKLTRATPGSAGLDLCSTSHTVLTPEMGPQALSTGIYGPLPPNTFGLILGRS SITMKGLQVYPGVIDNDYTGEIKIMAKAVNNIVTVSQGNRIAQLILLPLIETDNKVQQPYRGQGSFGSSDIY A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n MPMV sample gag-pro 11855 Mason-Pfizer monkey virus 469008 Escherichia coli BL21(DE3) plasmid pET22B 1 2.10 41.55 VAPOR DIFFUSION, HANGING DROP 8.5 PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, vapor diffusion, hanging drop, temperature 293K 293 software citation_author chem_comp_atom chem_comp_bond database_2 diffrn_source pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Refinement description Database references Data collection Database references Derived calculations Refinement description 1 0 2011-10-12 1 1 2017-11-08 1 2 2018-01-24 1 3 2023-09-13 _software.name _citation_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _diffrn_source.pdbx_synchrotron_site _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2011-09-09 REL REL UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE MG MAGNESIUM ION HOH water 2D4L PDB entry 2D4L PDB experimental model UMP 777 2 UMP UMP 777 A DUP 777 3 DUP DUP 153 A MG 1 4 MG MG 154 A HOH 1 5 HOH HOH 155 A HOH 2 5 HOH HOH 156 A HOH 3 5 HOH HOH 157 A HOH 4 5 HOH HOH 158 A HOH 5 5 HOH HOH 159 A HOH 6 5 HOH HOH 160 A HOH 7 5 HOH HOH 161 A HOH 8 5 HOH HOH 162 A HOH 9 5 HOH HOH 163 A HOH 10 5 HOH HOH 164 A HOH 11 5 HOH HOH 165 A HOH 12 5 HOH HOH 166 A HOH 13 5 HOH HOH 167 A HOH 14 5 HOH HOH 168 A HOH 15 5 HOH HOH 169 A HOH 16 5 HOH HOH 170 A HOH 17 5 HOH HOH 171 A HOH 18 5 HOH HOH 172 A HOH 19 5 HOH HOH 173 A HOH 20 5 HOH HOH 174 A HOH 21 5 HOH HOH 175 A HOH 22 5 HOH HOH 176 A HOH 23 5 HOH HOH 177 A HOH 24 5 HOH HOH 178 A HOH 25 5 HOH HOH 179 A HOH 26 5 HOH HOH 180 A HOH 27 5 HOH HOH 181 A HOH 28 5 HOH HOH 182 A HOH 29 5 HOH HOH 183 A HOH 30 5 HOH HOH 184 A HOH 31 5 HOH HOH 185 A HOH 32 5 HOH HOH 186 A HOH 33 5 HOH HOH 187 A HOH 34 5 HOH HOH 188 A HOH 35 5 HOH HOH 189 A HOH 36 5 HOH HOH 190 A HOH 37 5 HOH HOH 191 A HOH 38 5 HOH HOH 192 A HOH 39 5 HOH HOH 193 A HOH 40 5 HOH HOH 194 A HOH 41 5 HOH HOH 195 A HOH 42 5 HOH HOH 196 A HOH 43 5 HOH HOH 197 A HOH 44 5 HOH HOH 198 A HOH 45 5 HOH HOH 199 A HOH 46 5 HOH HOH 200 A HOH 47 5 HOH HOH 201 A HOH 48 5 HOH HOH 202 A HOH 49 5 HOH HOH 203 A HOH 50 5 HOH HOH 204 A HOH 51 5 HOH HOH 205 A HOH 52 5 HOH HOH 206 A HOH 53 5 HOH HOH 207 A HOH 54 5 HOH HOH 208 A HOH 55 5 HOH HOH 209 A HOH 56 5 HOH HOH 210 A HOH 57 5 HOH HOH 211 A HOH 58 5 HOH HOH 212 A HOH 59 5 HOH HOH 213 A HOH 60 5 HOH HOH 214 A HOH 62 5 HOH HOH 215 A HOH 63 5 HOH HOH 216 A HOH 64 5 HOH HOH 217 A HOH 65 5 HOH HOH 218 A HOH 66 5 HOH HOH 219 A HOH 67 5 HOH HOH 220 A HOH 68 5 HOH HOH 221 A HOH 69 5 HOH HOH 222 A HOH 70 5 HOH HOH 223 A HOH 71 5 HOH HOH 224 A HOH 72 5 HOH HOH 225 A HOH 73 5 HOH HOH 226 A HOH 74 5 HOH HOH 227 A HOH 75 5 HOH HOH 228 A HOH 76 5 HOH HOH 229 A HOH 77 5 HOH HOH 230 A HOH 78 5 HOH HOH 231 A HOH 79 5 HOH HOH 232 A HOH 80 5 HOH HOH 233 A HOH 81 5 HOH HOH 234 A HOH 82 5 HOH HOH 235 A HOH 84 5 HOH HOH 236 A HOH 85 5 HOH HOH 237 A HOH 86 5 HOH HOH 238 A HOH 87 5 HOH HOH 239 A HOH 88 5 HOH HOH 240 A HOH 90 5 HOH HOH 241 A HOH 92 5 HOH HOH 242 A HOH 93 5 HOH HOH 243 A HOH 94 5 HOH HOH 244 A HOH 95 5 HOH HOH 245 A HOH 96 5 HOH HOH 246 A HOH 98 5 HOH HOH 247 A HOH 100 5 HOH HOH 248 A HOH 101 5 HOH HOH 249 A HOH 102 5 HOH HOH 250 A HOH 103 5 HOH HOH 251 A HOH 104 5 HOH HOH 252 A HOH 105 5 HOH HOH 253 A n 1 1 A n 2 2 A n 3 3 A n 4 4 A n 5 5 A n 6 6 A n 7 7 A n 8 8 A n 9 9 A n 10 10 A n 11 11 A n 12 12 A n 13 13 A n 14 14 A n 15 15 A n 16 16 A n 17 17 A n 18 18 A n 19 19 A n 20 20 A n 21 21 A n 22 22 A n 23 23 A n 24 24 A LYS 25 n 25 LYS 25 A GLN 26 n 26 GLN 26 A PRO 27 n 27 PRO 27 A ILE 28 n 28 ILE 28 A SER 29 n 29 SER 29 A LYS 30 n 30 LYS 30 A LEU 31 n 31 LEU 31 A THR 32 n 32 THR 32 A ARG 33 n 33 ARG 33 A ALA 34 n 34 ALA 34 A THR 35 n 35 THR 35 A PRO 36 n 36 PRO 36 A GLY 37 n 37 GLY 37 A SER 38 n 38 SER 38 A ALA 39 n 39 ALA 39 A GLY 40 n 40 GLY 40 A LEU 41 n 41 LEU 41 A ASP 42 n 42 ASP 42 A LEU 43 n 43 LEU 43 A CYS 44 n 44 CYS 44 A SER 45 n 45 SER 45 A THR 46 n 46 THR 46 A SER 47 n 47 SER 47 A HIS 48 n 48 HIS 48 A THR 49 n 49 THR 49 A VAL 50 n 50 VAL 50 A LEU 51 n 51 LEU 51 A THR 52 n 52 THR 52 A PRO 53 n 53 PRO 53 A GLU 54 n 54 GLU 54 A MET 55 n 55 MET 55 A GLY 56 n 56 GLY 56 A PRO 57 n 57 PRO 57 A GLN 58 n 58 GLN 58 A ALA 59 n 59 ALA 59 A LEU 60 n 60 LEU 60 A SER 61 n 61 SER 61 A THR 62 n 62 THR 62 A GLY 63 n 63 GLY 63 A ILE 64 n 64 ILE 64 A TYR 65 n 65 TYR 65 A GLY 66 n 66 GLY 66 A PRO 67 n 67 PRO 67 A LEU 68 n 68 LEU 68 A PRO 69 n 69 PRO 69 A PRO 70 n 70 PRO 70 A ASN 71 n 71 ASN 71 A THR 72 n 72 THR 72 A PHE 73 n 73 PHE 73 A GLY 74 n 74 GLY 74 A LEU 75 n 75 LEU 75 A ILE 76 n 76 ILE 76 A LEU 77 n 77 LEU 77 A GLY 78 n 78 GLY 78 A ARG 79 n 79 ARG 79 A SER 80 n 80 SER 80 A SER 81 n 81 SER 81 A ILE 82 n 82 ILE 82 A THR 83 n 83 THR 83 A MET 84 n 84 MET 84 A LYS 85 n 85 LYS 85 A GLY 86 n 86 GLY 86 A LEU 87 n 87 LEU 87 A GLN 88 n 88 GLN 88 A VAL 89 n 89 VAL 89 A TYR 90 n 90 TYR 90 A PRO 91 n 91 PRO 91 A GLY 92 n 92 GLY 92 A VAL 93 n 93 VAL 93 A ILE 94 n 94 ILE 94 A ASP 95 n 95 ASP 95 A ASN 96 n 96 ASN 96 A ASP 97 n 97 ASP 97 A TYR 98 n 98 TYR 98 A THR 99 n 99 THR 99 A GLY 100 n 100 GLY 100 A GLU 101 n 101 GLU 101 A ILE 102 n 102 ILE 102 A LYS 103 n 103 LYS 103 A ILE 104 n 104 ILE 104 A MET 105 n 105 MET 105 A ALA 106 n 106 ALA 106 A LYS 107 n 107 LYS 107 A ALA 108 n 108 ALA 108 A VAL 109 n 109 VAL 109 A ASN 110 n 110 ASN 110 A ASN 111 n 111 ASN 111 A ILE 112 n 112 ILE 112 A VAL 113 n 113 VAL 113 A THR 114 n 114 THR 114 A VAL 115 n 115 VAL 115 A SER 116 n 116 SER 116 A GLN 117 n 117 GLN 117 A GLY 118 n 118 GLY 118 A ASN 119 n 119 ASN 119 A ARG 120 n 120 ARG 120 A ILE 121 n 121 ILE 121 A ALA 122 n 122 ALA 122 A GLN 123 n 123 GLN 123 A LEU 124 n 124 LEU 124 A ILE 125 n 125 ILE 125 A LEU 126 n 126 LEU 126 A LEU 127 n 127 LEU 127 A PRO 128 n 128 PRO 128 A LEU 129 n 129 LEU 129 A ILE 130 n 130 ILE 130 A GLU 131 n 131 GLU 131 A THR 132 n 132 THR 132 A ASP 133 n 133 ASP 133 A ASN 134 n 134 ASN 134 A LYS 135 n 135 LYS 135 A VAL 136 n 136 VAL 136 A GLN 137 n 137 GLN 137 A n 138 138 A n 139 139 A n 140 140 A n 141 141 A n 142 142 A n 143 143 A n 144 144 A n 145 145 A n 146 146 A n 147 147 A n 148 148 A n 149 149 A n 150 150 A n 151 151 A n 152 152 A 1.0541 0.1926 -0.6254 1.1755 0.2064 2.0741 0.0021 -0.0969 -0.1571 0.0372 -0.0005 -0.0088 0.1085 0.1308 -0.0016 -0.0383 0.0035 -0.0079 -0.0712 0.0380 -0.0296 refined 2.4667 58.4802 30.3162 X-RAY DIFFRACTION A 25 A 137 X-RAY DIFFRACTION 1 A 153 A 154 X-RAY DIFFRACTION 1 A 777 A 777 X-RAY DIFFRACTION 1 author_and_software_defined_assembly PISA 3 trimeric 10880 -101 12920 A DUP 153 B C O1A DUP 1_555 A MG 154 D MG MG 1_555 A DUP 153 B C O2G DUP 1_555 86.8 A DUP 153 B C O1A DUP 1_555 A MG 154 D MG MG 1_555 A DUP 153 B C O1B DUP 1_555 88.6 A DUP 153 B C O2G DUP 1_555 A MG 154 D MG MG 1_555 A DUP 153 B C O1B DUP 1_555 87.0 A DUP 153 B C O1A DUP 1_555 A MG 154 D MG MG 1_555 A HOH 226 E O HOH 1_555 96.0 A DUP 153 B C O2G DUP 1_555 A MG 154 D MG MG 1_555 A HOH 226 E O HOH 1_555 84.2 A DUP 153 B C O1B DUP 1_555 A MG 154 D MG MG 1_555 A HOH 226 E O HOH 1_555 169.9 A DUP 153 B C O1A DUP 1_555 A MG 154 D MG MG 1_555 A HOH 230 E O HOH 1_555 176.0 A DUP 153 B C O2G DUP 1_555 A MG 154 D MG MG 1_555 A HOH 230 E O HOH 1_555 91.1 A DUP 153 B C O1B DUP 1_555 A MG 154 D MG MG 1_555 A HOH 230 E O HOH 1_555 87.9 A HOH 226 E O HOH 1_555 A MG 154 D MG MG 1_555 A HOH 230 E O HOH 1_555 87.2 A DUP 153 B C O1A DUP 1_555 A MG 154 D MG MG 1_555 A UMP 777 A B OP1 UMP 1_555 26.8 A DUP 153 B C O2G DUP 1_555 A MG 154 D MG MG 1_555 A UMP 777 A B OP1 UMP 1_555 80.5 A DUP 153 B C O1B DUP 1_555 A MG 154 D MG MG 1_555 A UMP 777 A B OP1 UMP 1_555 62.4 A HOH 226 E O HOH 1_555 A MG 154 D MG MG 1_555 A UMP 777 A B OP1 UMP 1_555 120.8 A HOH 230 E O HOH 1_555 A MG 154 D MG MG 1_555 A UMP 777 A B OP1 UMP 1_555 149.3 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -0.5000000000 -0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_775 -y+2,x-y+2,z crystal symmetry operation 60.5940000000 104.9518866338 0.0000000000 -0.5000000000 0.8660254038 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_575 -x+y,-x+2,z crystal symmetry operation -60.5940000000 104.9518866338 0.0000000000 A N GLN 26 A N GLN 26 A O TYR 65 A O TYR 65 A N LEU 41 A N LEU 41 A O LEU 124 A O LEU 124 A O ILE 125 A O ILE 125 A N LEU 75 A N LEU 75 A N GLY 74 A N GLY 74 A O ILE 94 A O ILE 94 A N THR 49 A N THR 49 A O VAL 115 A O VAL 115 A N LEU 60 A N LEU 60 A O ILE 104 A O ILE 104 A O LYS 107 A O LYS 107 A N GLN 88 A N GLN 88 1 A OE1 GLN 117 A OE1 GLN 117 1 Y 1 A NE2 GLN 117 A NE2 GLN 117 1 Y 1 A CD1 ILE 121 A CD1 ILE 121 1 Y 1 A OE1 GLU 131 A OE1 GLU 131 1 Y 1 A OE2 GLU 131 A OE2 GLU 131 1 Y 1 A CG LYS 135 A CG LYS 135 1 Y 1 A CD LYS 135 A CD LYS 135 1 Y 1 A CE LYS 135 A CE LYS 135 1 Y 1 A NZ LYS 135 A NZ LYS 135 1 Y 1 A CG GLN 137 A CG GLN 137 1 Y 1 A CD GLN 137 A CD GLN 137 1 Y 1 A OE1 GLN 137 A OE1 GLN 137 1 Y 1 A NE2 GLN 137 A NE2 GLN 137 1 Y 1 A LYS 1 A LYS 1 1 Y 1 A ARG 2 A ARG 2 1 Y 1 A VAL 3 A VAL 3 1 Y 1 A GLU 4 A GLU 4 1 Y 1 A GLY 5 A GLY 5 1 Y 1 A PRO 6 A PRO 6 1 Y 1 A ALA 7 A ALA 7 1 Y 1 A PRO 8 A PRO 8 1 Y 1 A GLY 9 A GLY 9 1 Y 1 A PRO 10 A PRO 10 1 Y 1 A GLU 11 A GLU 11 1 Y 1 A THR 12 A THR 12 1 Y 1 A SER 13 A SER 13 1 Y 1 A LEU 14 A LEU 14 1 Y 1 A TRP 15 A TRP 15 1 Y 1 A GLY 16 A GLY 16 1 Y 1 A SER 17 A SER 17 1 Y 1 A GLN 18 A GLN 18 1 Y 1 A LEU 19 A LEU 19 1 Y 1 A CYS 20 A CYS 20 1 Y 1 A SER 21 A SER 21 1 Y 1 A SER 22 A SER 22 1 Y 1 A GLN 23 A GLN 23 1 Y 1 A GLN 24 A GLN 24 1 Y 1 A GLN 138 A GLN 138 1 Y 1 A PRO 139 A PRO 139 1 Y 1 A TYR 140 A TYR 140 1 Y 1 A ARG 141 A ARG 141 1 Y 1 A GLY 142 A GLY 142 1 Y 1 A GLN 143 A GLN 143 1 Y 1 A GLY 144 A GLY 144 1 Y 1 A SER 145 A SER 145 1 Y 1 A PHE 146 A PHE 146 1 Y 1 A GLY 147 A GLY 147 1 Y 1 A SER 148 A SER 148 1 Y 1 A SER 149 A SER 149 1 Y 1 A ASP 150 A ASP 150 1 Y 1 A ILE 151 A ILE 151 1 Y 1 A TYR 152 A TYR 152 1 Y 1 A A N O LYS HOH 25 239 2.08 1 A A OG O SER HOH 45 163 2.08 B 1 A A O O HOH HOH 234 250 2.08 1 A ASN 110 -140.14 -5.42 1 A VAL 136 -102.12 65.08 52.670 25.398 13.380 0.6700 0.3300 0.0000 0.6700 0.0000 -1.0000 0.9700 0.9610 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.1688 0.1538 0.1546 1.8500 20 614 11477 10863 5.3000 99.8400 1.000 0.300 5.2080 0.0700 RANDOM 1 TLS and isotropic individual THROUGHOUT 0.000 rigid body refinement 0.0970 0.8000 0.8000 1.2000 PDB entry 2D4L MAXIMUM LIKELIHOOD BABINET MODEL WITH MASK 1.8500 20 99 973 49 0 825 0.019 0.022 919 1.812 2.070 1270 6.456 5.000 121 37.671 25.600 25 12.472 15.000 151 29.618 15.000 3 0.129 0.200 158 0.008 0.020 646 0.212 0.200 378 0.313 0.200 641 0.203 0.200 82 0.059 0.200 1 0.227 0.200 60 0.168 0.200 18 1.115 1.500 593 1.751 2.000 952 2.715 3.000 360 3.958 4.500 314 0.2500 0.2130 1.8980 36 819 855 20 99.6500 1.85 52.4900 3TQ3 11478 11478 -3.0 0.078 1 20.2 11.2 99.8 1.85 1.96 5.0 1821 0.539 1 11.2 99.7 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.2.0005 data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 data collection MAR345 data reduction XDS data scaling XSCALE phasing REFMAC 5.2.0005 Crystal structure of M-PMV dUTPase with a mixed population of substrate (dUPNPP) and post-inversion product (dUMP) in the active sites 1 N N 2 N N 3 N N 4 N N 5 N N A SER 29 A SER 29 HELX_P A LEU 31 A LEU 31 5 1 3 A THR 52 A THR 52 HELX_P A GLY 56 A GLY 56 5 2 5 A ARG 79 A ARG 79 HELX_P A LYS 85 A LYS 85 1 3 7 metalc 1.931 B A DUP 153 C O1A DUP 1_555 A MG 154 D MG MG 1_555 metalc 2.012 B A DUP 153 C O2G DUP 1_555 A MG 154 D MG MG 1_555 metalc 2.124 B A DUP 153 C O1B DUP 1_555 A MG 154 D MG MG 1_555 metalc 2.171 A MG 154 D MG MG 1_555 A HOH 226 E O HOH 1_555 metalc 2.150 A MG 154 D MG MG 1_555 A HOH 230 E O HOH 1_555 metalc 2.524 A A MG 154 D MG MG 1_555 A UMP 777 B OP1 UMP 1_555 HYDROLASE jelly roll, hydrolase A GLY 66 A GLY 66 1 A PRO 67 A PRO 67 9.34 O92810_MPMV UNP 1 608 O92810 NRVEGPAPGPETSLWGSQLCSSQQKQPISKLTRATPGSAGLDLCSTSHTVLTPEMGPQALSTGIYGPLPPNTFGLILGRS SITMKGLQVYPGVIDNDYTGEIKIMAKAVNNIVTVSQGNRIAQLILLPLIETDNKVQQPYRGQGSFGSSDIY 608 759 3TQ3 1 152 O92810 A 1 1 152 1 ASN engineered mutation LYS 1 3TQ3 A O92810 UNP 608 1 2 4 2 3 parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A GLN 26 A GLN 26 A PRO 27 A PRO 27 A ILE 64 A ILE 64 A TYR 65 A TYR 65 A LEU 41 A LEU 41 A CYS 44 A CYS 44 A ARG 120 A ARG 120 A PRO 128 A PRO 128 A THR 72 A THR 72 A LEU 77 A LEU 77 A GLY 92 A GLY 92 A ILE 94 A ILE 94 A THR 49 A THR 49 A LEU 51 A LEU 51 A VAL 113 A VAL 113 A VAL 115 A VAL 115 A GLN 58 A GLN 58 A LEU 60 A LEU 60 A ILE 104 A ILE 104 A ALA 108 A ALA 108 A LEU 87 A LEU 87 A VAL 89 A VAL 89 BINDING SITE FOR RESIDUE UMP A 777 A UMP 777 Software 16 BINDING SITE FOR RESIDUE DUP A 153 A DUP 153 Software 23 BINDING SITE FOR RESIDUE MG A 154 A MG 154 Software 5 A ILE 76 A ILE 76 16 1_555 A ARG 79 A ARG 79 16 3_575 A SER 80 A SER 80 16 3_575 A GLY 92 A GLY 92 16 1_555 A VAL 93 A VAL 93 16 1_555 A ILE 94 A ILE 94 16 1_555 A ASP 95 A ASP 95 16 1_555 A TYR 98 A TYR 98 16 1_555 A GLU 101 A GLU 101 16 1_555 A ILE 102 A ILE 102 16 1_555 A LYS 103 A LYS 103 16 1_555 A MET 105 A MET 105 16 1_555 A GLN 123 A GLN 123 16 3_575 A MG 154 D MG 16 1_555 A HOH 155 E HOH 16 1_555 A HOH 158 E HOH 16 1_555 A ILE 76 A ILE 76 23 1_555 A ARG 79 A ARG 79 23 3_575 A SER 80 A SER 80 23 3_575 A SER 81 A SER 81 23 3_575 A GLY 92 A GLY 92 23 1_555 A VAL 93 A VAL 93 23 1_555 A ILE 94 A ILE 94 23 1_555 A ASP 95 A ASP 95 23 1_555 A TYR 98 A TYR 98 23 1_555 A GLU 101 A GLU 101 23 1_555 A ILE 102 A ILE 102 23 1_555 A LYS 103 A LYS 103 23 1_555 A MET 105 A MET 105 23 1_555 A GLN 123 A GLN 123 23 3_575 A MG 154 D MG 23 1_555 A HOH 155 E HOH 23 1_555 A HOH 158 E HOH 23 1_555 A HOH 226 E HOH 23 1_555 A HOH 230 E HOH 23 1_555 A HOH 235 E HOH 23 3_575 A HOH 245 E HOH 23 1_555 A HOH 246 E HOH 23 3_575 A HOH 247 E HOH 23 1_555 A DUP 153 C DUP 5 1_555 A HOH 226 E HOH 5 1_555 A HOH 230 E HOH 5 1_555 A HOH 235 E HOH 5 3_575 A UMP 777 B UMP 5 1_555 173 P 63