SMTL ID : 2xca.1

TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dGTP - MAGNESIUM FORM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 19 residues within 4Å: Chain A: D.13, F.14, D.15, Y.16, F.17, Y.18, V.38, A.50, T.51, Y.54, R.57, A.63, I.110, D.111, K.165 Chain C: C.4, G.5 Ligands: MG.2, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.18 Hydrogen bonds: A:D.13, A:D.15, A:Y.16, A:F.17, A:Y.18 Water bridges: A:E.112, A:K.165 Salt bridges: A:R.57, A:R.57, A:K.165

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.13, S.109, D.111, E.112 Ligands: DGT.1, MG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.13, A:D.111, A:E.112, H2O.1, H2O.3 MG.3: 6 residues within 4Å: Chain A: D.13, F.14, D.111, K.165 Ligands: DGT.1, MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.13, A:F.14, A:D.111 MG.4: 2 residues within 4Å: Chain A: D.300 Chain B: A.10 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.300, H2O.6, H2O.6, H2O.6, H2O.7 MG.5: 5 residues within 4Å: Chain A: A.187, V.189, P.190, I.192 Chain B: C.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Irimia, A. et al., Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus. Acta Crystallogr.,Sect.F (2010)

Release Date

2010-09-08

Peptides

DNA POLYMERASE IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA POLYMERASE IV

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