SMTL ID : 3cq8.1

Ternary complex of the L415F mutant RB69 exo(-)polymerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain C: D.411, L.412, D.623 Ligands: CA.2, TTP.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.411, C:D.411, C:L.412, C:D.623 CA.2: 4 residues within 4Å: Chain C: D.411, D.623 Ligands: CA.1, TTP.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.411 CA.3: 3 residues within 4Å: Chain C: D.411, E.686, E.716 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.686, H2O.10, H2O.10, H2O.17 CA.4: 3 residues within 4Å: Chain C: C.671, E.672, N.676 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.671, H2O.12 CA.5: 3 residues within 4Å: Chain C: D.114, I.115, E.116 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.116, H2O.13, H2O.14, H2O.15 CA.6: 2 residues within 4Å: Chain C: E.660, D.684 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.660, C:D.684, H2O.10

3 x NA: SODIUM ION(Non-functional Binders)

NA.7: 2 residues within 4Å: Chain C: E.172, E.177 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.177 NA.8: 3 residues within 4Å: Chain C: N.505, N.507, K.531 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.507, C:N.507, C:K.531 NA.9: 4 residues within 4Å: Chain C: N.606, G.610, T.611, E.612 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.611

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.10: 18 residues within 4Å: Chain A: A.3, G.4 Chain B: C.14 Chain C: D.411, L.412, T.413, S.414, F.415, Y.416, P.417, R.482, K.486, K.560, N.564, Y.567, D.623 Ligands: CA.1, CA.2 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.416 Hydrogen bonds: C:L.412, C:S.414, C:F.415, C:Y.416, C:N.564 Salt bridges: C:R.482, C:K.486, C:K.560, C:K.560, C:K.560

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 2 residues within 4Å: Chain C: H.105, N.342 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.342 GOL.12: 7 residues within 4Å: Chain C: Y.139, D.144, F.146, E.181, I.182, K.185, Y.329 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.329, C:Y.329 GOL.13: 6 residues within 4Å: Chain C: Y.53, R.384, H.386, Y.578, D.579, R.581 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.53, C:R.384 Water bridges: C:D.579, C:R.581

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, X. et al., Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity. Nucleic Acids Res. (2008)

Release Date

2008-09-02

Peptides

DNA polymerase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase

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