SMTL ID : 4khq.1

Ternary complex of RB69 mutant L415F wit DUMPNPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: DUP.4, NA.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.411, A:L.412, A:D.623 CA.2: 2 residues within 4Å: Chain A: D.192, E.196 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:E.196, A:E.196, H2O.14, H2O.14 CA.3: 4 residues within 4Å: Chain A: N.505, N.507, K.531, K.532 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.505, A:K.531, H2O.15, H2O.15, H2O.18

1 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.4: 19 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, F.415, Y.416, P.417, R.482, K.486, K.560, N.564, Y.567, T.622, D.623 Chain B: A.3, G.4 Chain C: C.14 Ligands: CA.1, NA.9 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:D.411, A:S.414, A:F.415, A:Y.416, A:K.560, A:N.564, A:N.564 Water bridges: A:R.482, A:R.482, A:K.486, A:K.486, A:Q.556, A:K.560 Salt bridges: A:R.482, A:K.486, A:K.560

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

NA.5: 3 residues within 4Å: Chain A: D.114, I.115, E.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.114 NA.6: 2 residues within 4Å: Chain A: E.172, E.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.177 NA.7: 1 residues within 4Å: Chain A: N.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.232, A:N.232 NA.8: 2 residues within 4Å: Chain A: G.610, T.611 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.610 NA.9: 6 residues within 4Å: Chain A: D.411, D.623, S.624 Chain C: C.14 Ligands: CA.1, DUP.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.411, A:D.623 NA.10: 2 residues within 4Å: Chain A: E.686, E.716 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.716 NA.11: 3 residues within 4Å: Chain A: D.411, E.686, E.716 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.411, A:K.486 NA.12: 2 residues within 4Å: Chain A: E.660, D.684 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.684

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clausen, A.R. et al., Structure-function analysis of ribonucleotide bypass by B family DNA replicases. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-10-09

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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