SMTL ID : 3lds.1

Crystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 17 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.14 Chain C: G.3, C.4 Ligands: MN.2, MN.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:L.415, A:Y.416, A:N.564 Water bridges: A:K.560, A:K.560, A:S.624 Salt bridges: A:R.482, A:R.482, A:K.486, A:K.560, A:K.560, A:K.560

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.411, D.623 Chain B: G.14 Ligands: DTP.1, MN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.411, A:D.623, H2O.1 MN.3: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: DTP.1, MN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.411, A:L.412, A:D.623 MN.4: 4 residues within 4Å: Chain A: D.114, E.116, N.324, A.327 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.114, A:E.116

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain B: G.3, G.4, C.5 Chain C: G.13 No protein-ligand interaction detected (PLIP) SO4.6: 2 residues within 4Å: Chain B: G.7 Chain C: G.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hogg, M. et al., Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69. Biochemistry (2010)

Release Date

2010-06-02

Peptides

DNA-directed DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-directed DNA polymerase