HEADER TRANSFERASE/DNA 11-APR-11 3RH4 TITLE DNA POLYMERASE BETA WITH A DIDEOXY-TERMINATED PRIMER WITH AN INCOMING TITLE 2 RIBONUCLEOTIDE (RCTP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'; COMPND 3 CHAIN: T; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DDG))-3'; COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(P*GP*TP*CP*GP*G)-3'; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA POLYMERASE BETA; COMPND 15 CHAIN: A; COMPND 16 EC: 2.7.7.7, 4.2.99.-; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: POLB; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: TAP56; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PWL11 KEYWDS DNA POLYMERASE, RIBONUCLEOTIDE INSERTION, RCTP, TRANSFERASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.A.CAVANAUGH,W.A.BEARD,V.K.BATRA,L.PERERA,L.G.PEDERSEN,S.H.WILSON REVDAT 3 21-SEP-11 3RH4 1 JRNL REVDAT 2 20-JUL-11 3RH4 1 JRNL REVDAT 1 06-JUL-11 3RH4 0 JRNL AUTH N.A.CAVANAUGH,W.A.BEARD,V.K.BATRA,L.PERERA,L.G.PEDERSEN, JRNL AUTH 2 S.H.WILSON JRNL TITL MOLECULAR INSIGHTS INTO DNA POLYMERASE DETERRENTS FOR JRNL TITL 2 RIBONUCLEOTIDE INSERTION. JRNL REF J.BIOL.CHEM. V. 286 31650 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21733843 JRNL DOI 10.1074/JBC.M111.253401 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 27776 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 22.5954 - 4.1243 0.97 2867 334 0.1439 0.1764 REMARK 3 2 4.1243 - 3.2768 0.99 2868 339 0.1421 0.2025 REMARK 3 3 3.2768 - 2.8635 0.90 2619 278 0.1906 0.2623 REMARK 3 4 2.8635 - 2.6021 0.85 2438 293 0.1860 0.2584 REMARK 3 5 2.6021 - 2.4159 0.87 2507 282 0.1862 0.2787 REMARK 3 6 2.4159 - 2.2736 0.87 2563 266 0.1902 0.2885 REMARK 3 7 2.2736 - 2.1598 0.91 2619 294 0.1847 0.2825 REMARK 3 8 2.1598 - 2.0658 0.94 2708 291 0.1727 0.2554 REMARK 3 9 2.0658 - 1.9864 0.78 2265 250 0.1783 0.2878 REMARK 3 10 1.9864 - 1.9179 0.53 1543 152 0.2129 0.3253 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 61.86 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.18810 REMARK 3 B22 (A**2) : -1.67910 REMARK 3 B33 (A**2) : -2.50890 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.73030 REMARK 3 B23 (A**2) : -0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3537 REMARK 3 ANGLE : 1.150 4917 REMARK 3 CHIRALITY : 0.061 531 REMARK 3 PLANARITY : 0.004 525 REMARK 3 DIHEDRAL : 20.740 1400 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RH4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-11. REMARK 100 THE RCSB ID CODE IS RCSB064924. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VIRAMAX REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27776 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.918 REMARK 200 RESOLUTION RANGE LOW (A) : 22.594 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.42100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.070 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 2FMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG3350, 350 MM SODIUM ACETATE, 50 REMARK 280 MM IMIDAZOLE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.89500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -148.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, T, P REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG D 1 P DG D 1 OP3 -0.130 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC T 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC T 5 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG T 6 O4' - C1' - N9 ANGL. DEV. = -7.2 DEGREES REMARK 500 DC T 7 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DA T 11 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC P 8 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG D 1 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT D 2 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 29 -60.84 -101.04 REMARK 500 LYS A 120 9.19 -150.61 REMARK 500 ASP A 170 117.24 -162.04 REMARK 500 CYS A 178 -135.86 -116.02 REMARK 500 SER A 275 -178.87 -67.48 REMARK 500 ASN A 294 -168.45 -126.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 377 DISTANCE = 5.13 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 339 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CTP A 338 O2B REMARK 620 2 ASP A 190 OD1 173.3 REMARK 620 3 ASP A 192 OD2 89.2 96.4 REMARK 620 4 CTP A 338 O1G 86.1 88.0 174.0 REMARK 620 5 CTP A 338 O1A 92.4 91.1 92.6 91.3 REMARK 620 6 HOH A 403 O 88.6 88.2 84.8 91.4 177.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 340 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 192 OD1 REMARK 620 2 ASP A 190 OD2 115.2 REMARK 620 3 ASP A 256 OD2 94.6 96.8 REMARK 620 4 CTP A 338 O1A 95.4 101.1 153.4 REMARK 620 5 HOH P 11 O 153.1 91.6 83.9 76.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 341 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 145 OD2 REMARK 620 2 HIS A 252 ND1 88.4 REMARK 620 3 HOH A 555 O 101.5 101.3 REMARK 620 4 HOH A 552 O 86.7 91.6 164.8 REMARK 620 5 HOH A 553 O 90.1 173.6 85.0 82.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 343 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CTP A 350 O3G REMARK 620 2 CTP A 350 O1B 64.7 REMARK 620 3 CTP A 350 O1A 103.3 67.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 346 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CTP A 338 O2G REMARK 620 2 HOH A 644 O 85.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN P 345 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 N7 REMARK 620 2 HOH P 213 O 97.8 REMARK 620 3 HOH P 128 O 92.0 76.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 342 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 285 ND1 REMARK 620 2 HOH A 413 O 99.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 351 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 THR A 101 O 162.9 REMARK 620 3 VAL A 103 O 100.1 93.5 REMARK 620 4 ILE A 106 O 101.1 89.8 86.5 REMARK 620 5 HOH P 130 O 92.0 74.2 167.7 92.9 REMARK 620 6 HOH A 572 O 90.2 80.5 85.9 167.3 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 352 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 VAL A 65 O 90.8 REMARK 620 3 LEU A 62 O 91.3 94.3 REMARK 620 4 DC D 3 OP1 176.6 92.4 89.3 REMARK 620 5 HOH A 585 O 94.3 172.7 80.5 82.5 REMARK 620 6 HOH D 93 O 95.8 88.2 172.5 83.5 96.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN P 345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN D 344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 346 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 351 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 352 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 353 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 354 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 355 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 356 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 357 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 358 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CTP A 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CTP A 350 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RH5 RELATED DB: PDB REMARK 900 RELATED ID: 3RH6 RELATED DB: PDB DBREF 3RH4 A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 3RH4 T 1 16 PDB 3RH4 3RH4 1 16 DBREF 3RH4 P 1 10 PDB 3RH4 3RH4 1 10 DBREF 3RH4 D 1 5 PDB 3RH4 3RH4 1 5 SEQRES 1 T 16 DC DC DG DA DC DG DC DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DDG SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU MODRES 3RH4 DDG P 10 DG HET DDG P 10 21 HET MN P 345 1 HET MN D 344 1 HET MN A 339 1 HET MN A 340 1 HET MN A 341 1 HET MN A 342 1 HET MN A 343 1 HET MN A 346 1 HET NA A 351 1 HET NA A 352 1 HET CL A 353 1 HET CL A 354 1 HET CL A 355 1 HET CL A 356 1 HET CL A 357 1 HET CL A 358 1 HET CTP A 338 29 HET CTP A 350 29 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM CTP CYTIDINE-5'-TRIPHOSPHATE FORMUL 2 DDG C10 H14 N5 O6 P FORMUL 5 MN 8(MN 2+) FORMUL 13 NA 2(NA 1+) FORMUL 15 CL 6(CL 1-) FORMUL 21 CTP 2(C9 H16 N3 O14 P3) FORMUL 23 HOH *450(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 TYR A 49 1 18 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 ASP A 91 THR A 101 1 11 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 LYS A 127 1 7 HELIX 9 9 ASN A 128 LEU A 132 5 5 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 GLU A 147 1 6 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 CYS A 178 ARG A 183 1 6 HELIX 14 14 LYS A 209 VAL A 221 1 13 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 GLY A 274 1 11 HELIX 17 17 SER A 275 LYS A 289 1 15 HELIX 18 18 SER A 315 ILE A 323 1 9 HELIX 19 19 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 VAL A 177 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ASP A 256 N VAL A 193 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DG P 9 P DDG P 10 1555 1555 1.60 LINK MN MN A 339 O2B CTP A 338 1555 1555 2.09 LINK OD1 ASP A 190 MN MN A 339 1555 1555 2.13 LINK OD2 ASP A 192 MN MN A 339 1555 1555 2.14 LINK MN MN A 339 O1G CTP A 338 1555 1555 2.17 LINK OD1 ASP A 192 MN MN A 340 1555 1555 2.17 LINK OD2 ASP A 190 MN MN A 340 1555 1555 2.18 LINK OD2 ASP A 256 MN MN A 340 1555 1555 2.21 LINK OD2 ASP A 145 MN MN A 341 1555 1555 2.26 LINK MN MN A 340 O1A CTP A 338 1555 1555 2.27 LINK MN MN A 339 O1A CTP A 338 1555 1555 2.29 LINK MN MN A 343 O3G CTP A 350 1555 1555 2.31 LINK MN MN A 346 O2G CTP A 338 1555 1555 2.37 LINK N7 DG P 9 MN MN P 345 1555 1555 2.37 LINK MN MN A 343 O1B CTP A 350 1555 1555 2.40 LINK MN MN A 343 O1A CTP A 350 1555 1555 2.42 LINK ND1 HIS A 252 MN MN A 341 1555 1555 2.45 LINK ND1 HIS A 285 MN MN A 342 1555 1555 2.49 LINK OP1 DG P 9 NA NA A 351 1555 1555 2.49 LINK O LYS A 60 NA NA A 352 1555 1555 2.50 LINK O THR A 101 NA NA A 351 1555 1555 2.52 LINK O VAL A 65 NA NA A 352 1555 1555 2.54 LINK N7 DG D 4 MN MN D 344 1555 1555 2.58 LINK O LEU A 62 NA NA A 352 1555 1555 2.60 LINK O VAL A 103 NA NA A 351 1555 1555 2.63 LINK O ILE A 106 NA NA A 351 1555 1555 2.63 LINK OP1 DC D 3 NA NA A 352 1555 1555 2.71 LINK MN MN A 346 O HOH A 644 1555 1555 2.25 LINK MN MN A 339 O HOH A 403 1555 1555 2.27 LINK MN MN A 341 O HOH A 555 1555 1555 2.31 LINK MN MN A 340 O HOH P 11 1555 1555 2.37 LINK MN MN A 341 O HOH A 552 1555 1555 2.43 LINK MN MN A 342 O HOH A 413 1555 1555 2.44 LINK MN MN P 345 O HOH P 213 1555 1555 2.47 LINK MN MN A 341 O HOH A 553 1555 1555 2.61 LINK MN MN P 345 O HOH P 128 1555 1555 2.65 LINK NA NA A 351 O HOH P 130 1555 1555 2.72 LINK NA NA A 352 O HOH A 585 1555 1555 2.87 LINK NA NA A 352 O HOH D 93 1555 1555 2.88 LINK NA NA A 351 O HOH A 572 1555 1555 2.90 CISPEP 1 GLY A 274 SER A 275 0 6.16 SITE 1 AC1 4 HOH A 602 DG P 9 HOH P 128 HOH P 213 SITE 1 AC2 2 DG D 4 DG D 5 SITE 1 AC3 5 ASP A 190 ASP A 192 CTP A 338 MN A 340 SITE 2 AC3 5 HOH A 403 SITE 1 AC4 6 ASP A 190 ASP A 192 ASP A 256 CTP A 338 SITE 2 AC4 6 MN A 339 HOH P 11 SITE 1 AC5 6 ASP A 145 HIS A 252 HOH A 552 HOH A 553 SITE 2 AC5 6 HOH A 555 HOH D 155 SITE 1 AC6 3 HIS A 285 GLU A 288 HOH A 413 SITE 1 AC7 1 CTP A 350 SITE 1 AC8 3 CTP A 338 HOH A 442 HOH A 644 SITE 1 AC9 6 THR A 101 VAL A 103 ILE A 106 HOH A 572 SITE 2 AC9 6 DG P 9 HOH P 130 SITE 1 BC1 6 LYS A 60 LEU A 62 VAL A 65 HOH A 585 SITE 2 BC1 6 DC D 3 HOH D 93 SITE 1 BC2 2 ASN A 294 THR A 297 SITE 1 BC3 4 ALA A 32 ILE A 33 HIS A 34 LYS A 35 SITE 1 BC4 3 LEU A 82 GLU A 86 ARG A 89 SITE 1 BC5 2 PRO A 330 LYS A 331 SITE 1 BC6 2 GLN A 159 VAL A 177 SITE 1 BC7 2 LYS A 84 HOH A 633 SITE 1 BC8 24 GLY A 179 SER A 180 ARG A 183 GLY A 189 SITE 2 BC8 24 ASP A 190 ASP A 192 TYR A 271 PHE A 272 SITE 3 BC8 24 THR A 273 GLY A 274 ASP A 276 ASN A 279 SITE 4 BC8 24 MN A 339 MN A 340 MN A 346 HOH A 379 SITE 5 BC8 24 HOH A 383 HOH A 403 HOH A 442 HOH A 644 SITE 6 BC8 24 DDG P 10 HOH P 11 HOH P 66 DG T 6 SITE 1 BC9 11 ILE A 174 THR A 176 THR A 196 LYS A 262 SITE 2 BC9 11 TYR A 265 TYR A 266 MN A 343 HOH A 409 SITE 3 BC9 11 HOH A 423 HOH A 581 HOH A 591 CRYST1 51.170 79.790 55.000 90.00 107.95 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019543 0.000000 0.006331 0.00000 SCALE2 0.000000 0.012533 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019112 0.00000