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Figure 4.
Figure 4. The PDZ domain. a, Schematic diagram of the
secondary structures of the B domain of D1P (upper) and the
third PDZ domain of human D1gA (PDB accession code 1PDR,
residues 463 -544)24, the third PDZ domain of the synaptic
protein PSD-95 (1KWA, residues 487 -570)25 and the PDZ domain of
neuronal nitric oxide synthase (1QAU, residues 14 -101)26. The
location of the conserved Arg/Lys (Arg 247 in D1P, Arg 471 in
1PDR, Lys 495 in 1KWA and Arg 23 in 1QAU) is marked by a red
circle. The location of the GLGF repeat of the carboxylate
binding loop in 1PDR and 1QAU (GVGL in D1P and PMGL in 1KWA) is
labeled by a yellow circle. Their three-dimensional structures
are also very similar. The r.m.s.d. for C  atoms
between D1P and 1PDR is 1.5 Å using 76 matching residues for the
alignment. The r.m.s.d. is 1.79 Å for 81 matching pairs of C
atoms
between D1P and 1QAU. For D1P and 1KWA, the r.m.s.d. is 1.9 Å
for 71 matching pairs. b, The conserved Arg 247 in the B domain
of D1P. The side chain of Arg 247 is partially buried with a
solvent accessible area of 23 Å2.
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