SMTL ID : 2pfq.1

Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC-DC.1: 34 residues within 4Å: Chain A: G.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, G.176, R.180, D.187, D.189, R.248, D.250, Y.265, F.266, T.267, G.268, A.270, N.273 Ligands: MG.3, NA.4, MN.5, MN.6, NA.7, DCP.8, PPV.9 Protein-ligand interaction information (PLIP) not available

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

DG-DC-DC-DG.2: 17 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 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 8 residues within 4Å: Chain B: D.187, D.189 Ligands: DC-DA-DG-DT-DA-DC-DC.1, NA.4, MN.5, MN.6, DCP.8, PPV.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:D.189, H2O.9

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

NA.4: 9 residues within 4Å: Chain B: D.187, D.189, D.250 Ligands: DC-DA-DG-DT-DA-DC-DC.1, DC-DA-DG-DT-DA-DC-DC.1, MG.3, MN.5, MN.6, DCP.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.250 NA.7: 5 residues within 4Å: Chain B: S.99, I.101, W.102, A.104 Ligands: DC-DA-DG-DT-DA-DC-DC.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.101, B:G.103, B:A.104

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

MN.5: 8 residues within 4Å: Chain B: D.187, D.189 Ligands: DC-DA-DG-DT-DA-DC-DC.1, MG.3, NA.4, MN.6, DCP.8, PPV.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:D.189, H2O.9 MN.6: 9 residues within 4Å: Chain B: D.187, D.189, D.250 Ligands: DC-DA-DG-DT-DA-DC-DC.1, DC-DA-DG-DT-DA-DC-DC.1, MG.3, NA.4, MN.5, DCP.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:D.189, B:D.250, H2O.3

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.8: 21 residues within 4Å: Chain A: G.5 Chain B: R.146, G.176, S.177, R.180, G.186, D.187, D.189, Y.265, F.266, T.267, G.268, A.270, N.273 Ligands: DC-DA-DG-DT-DA-DC-DC.1, DC-DA-DG-DT-DA-DC-DC.1, MG.3, NA.4, MN.5, MN.6, PPV.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.177, B:S.177, B:R.180, B:G.186, B:D.187, B:N.273 Water bridges: B:A.270 Salt bridges: B:R.146, B:R.180

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.9: 12 residues within 4Å: Chain B: R.146, G.176, S.177, R.180, C.185, G.186, D.187, D.189 Ligands: DC-DA-DG-DT-DA-DC-DC.1, MG.3, MN.5, DCP.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.177, B:S.177, B:S.177, B:G.186, B:D.187 Salt bridges: B:R.146, B:R.180

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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