SMTL ID : 2pfn.1

Na in the active site of DNA Polymerase lambda

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DT- DA- DC: Primer(Non-covalent)

DC-DA-DG-DT-DA-DC.1: 25 residues within 4Å: Chain A: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Chain B: I.101, W.102, G.103, A.104, G.105, T.106, K.107, T.108, D.189, L.234, R.248, D.250, Y.265, F.266 Ligands: NA.3, NA.5, NA.7, DUP.9 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: Downstream Primer(Non-covalent)

DG-DC-DC-DG.2: 19 residues within 4Å: Chain A: C.1, G.2, G.3, C.4 Chain B: Y.27, W.34, R.35, G.38, Y.39, P.63, G.64, I.65, G.66, K.67, R.68, M.69, K.72, K.84 Ligands: NA.8 Protein-ligand interaction information (PLIP) not available

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

NA.3: 3 residues within 4Å: Chain B: W.102 Ligands: DC-DA-DG-DT-DA-DC.1, DC-DA-DG-DT-DA-DC.1 No protein-ligand interaction detected (PLIP) NA.5: 6 residues within 4Å: Chain B: D.187, D.189, D.250 Ligands: DC-DA-DG-DT-DA-DC.1, MG.4, DUP.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.250 Water bridges: B:R.248 NA.6: 2 residues within 4Å: Chain A: T.10 Chain B: S.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.223 Water bridges: B:E.225 NA.7: 6 residues within 4Å: Chain B: S.99, I.101, W.102, G.103, A.104 Ligands: DC-DA-DG-DT-DA-DC.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.103, B:A.104, B:A.104 NA.8: 5 residues within 4Å: Chain B: C.60, S.61, I.62, P.63 Ligands: DG-DC-DC-DG.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.61

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: D.187, D.189 Ligands: NA.5, DUP.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:D.189, H2O.7

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

DUP.9: 19 residues within 4Å: Chain A: A.5 Chain B: R.146, G.176, S.177, R.180, C.185, G.186, D.187, D.189, Y.265, F.266, T.267, G.268, S.269, A.270, N.273 Ligands: DC-DA-DG-DT-DA-DC.1, MG.4, NA.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.270 Hydrogen bonds: B:S.177, B:S.177, B:S.177, B:R.180, B:R.180, B:G.186, B:D.187, B:D.187, B:N.273 Water bridges: B:A.270 Salt bridges: B:R.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Diaz, M. et al., Role of the catalytic metal during polymerization by DNA polymerase lambda. DNA Repair (2007)

Release Date

2007-05-15

Peptides

DNA polymerase lambda: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA polymerase lambda

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