SMTL ID : 3ndk.1

RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.1: 18 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, L.415, Y.416, R.482, K.486, K.560, N.564, T.622, D.623 Chain B: G.4, G.5 Chain C: C.13 Ligands: CA.2, CA.3, CA.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:L.415, A:Y.416, A:N.564, A:N.564, A:D.623 Water bridges: A:R.482, A:R.482, A:R.482, A:K.560 Salt bridges: A:R.482, A:K.486, A:K.560, A:K.560, A:K.560

7 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: DCP.1, CA.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.411, A:D.411, A:L.412, A:D.623 CA.3: 6 residues within 4Å: Chain A: D.411, D.623, S.624 Chain C: C.13 Ligands: DCP.1, CA.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.411, A:D.623, H2O.15, H2O.15 CA.4: 3 residues within 4Å: Chain A: N.505, N.507, K.531 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.505, A:K.531, H2O.4, H2O.14, H2O.22 CA.5: 5 residues within 4Å: Chain A: D.411, K.486, E.686, E.716 Ligands: DCP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.411, A:E.686, H2O.10, H2O.15, H2O.15 CA.6: 1 residues within 4Å: Chain A: E.116 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.116, A:E.116, H2O.7, H2O.13, H2O.15 CA.7: 1 residues within 4Å: Chain A: D.792 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.792, H2O.18, H2O.18, H2O.18, H2O.18 CA.8: 2 residues within 4Å: Chain A: D.144, K.185 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures. J.Mol.Biol. (2011)

Release Date

2011-01-26

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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