SMTL ID : 3f2b.1

DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 3 residues within 4Å: Chain A: K.468, D.472, R.571 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.468, A:R.571 PO4.2: 5 residues within 4Å: Chain A: K.342, H.346, N.355, Y.606, H.610 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.606 Salt bridges: A:H.346, A:H.610 PO4.3: 2 residues within 4Å: Chain A: K.222, H.246 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.222, A:H.246

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.505, C.508, C.530, C.533, T.535 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.505, A:C.508, A:C.530, A:C.533

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.559, D.561 Ligands: DGT.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.559, A:D.561, H2O.4 MG.6: 4 residues within 4Å: Chain A: E.179, H.206, C.256 Ligands: MG.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.179, A:H.206, A:C.256, H2O.3 MG.7: 5 residues within 4Å: Chain A: H.120, H.122, E.179, N.329 Ligands: MG.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.120, A:H.122, A:E.179, H2O.3

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

DGT.8: 18 residues within 4Å: Chain A: R.479, G.480, S.481, K.556, P.558, D.559, D.561, H.772, R.799, R.824, Y.855, F.857, P.858, H.861 Chain B: C.17 Chain C: C.5, G.6 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.857 Hydrogen bonds: A:R.479, A:S.481, A:S.481, A:D.559 Water bridges: A:D.559, A:D.559, A:R.824, A:Y.855 Salt bridges: A:K.556, A:R.799, A:R.824, A:R.824

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, R.J. et al., Structure of PolC reveals unique DNA binding and fidelity determinants. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2009-01-20

Peptides

DNA-directed DNA polymerase III alpha chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-directed DNA polymerase III alpha chain

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