SMTL ID : 3pmn.1

ternary crystal structure of polymerase lambda variant with a GT mispair at the primer terminus with Mn2+ in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DT- DA- DG: 5'-D(*CP*AP*GP*TP*AP*G)-3'(Non-covalent)

DC-DA-DG-DT-DA-DG.1: 24 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, D.188, L.228, R.242, D.244, Y.259, F.260 Chain B: C.5, T.6, T.7, A.8, C.9, T.10, G.11 Ligands: 1GC.3, MN.5, NA.6 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: 5'-D(*GP*CP*CP*G)-3'(Non-covalent)

DG-DC-DC-DG.2: 17 residues within 4Å: Chain A: W.33, R.34, G.37, Y.38, I.61, P.62, G.63, I.64, G.65, K.66, R.67, M.68 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.11 Protein-ligand interaction information (PLIP) not available

1 x 1GC: 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine(Non-covalent)

1GC.3: 20 residues within 4Å: Chain A: R.145, G.175, S.176, R.179, C.184, G.185, D.186, D.188, Y.259, F.260, T.261, G.262, S.263, A.264, N.267, R.271 Chain B: C.5 Ligands: DC-DA-DG-DT-DA-DG.1, MG.4, MN.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:R.179, A:R.179, A:G.185, A:D.186, A:D.188, A:N.267, A:R.271 Water bridges: A:D.186, A:D.186, A:A.264, A:R.268 Salt bridges: A:R.145

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.186, D.188 Ligands: 1GC.3, MN.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.4

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

MN.5: 6 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: DC-DA-DG-DT-DA-DG.1, 1GC.3, MG.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, A:D.244, H2O.4 MN.7: 3 residues within 4Å: Chain A: D.141, H.240 Ligands: CL.9 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.141, A:H.240, H2O.4, H2O.4, H2O.4 MN.8: 3 residues within 4Å: Chain A: H.284 Chain B: T.7, A.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.284, H2O.1, H2O.5

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

NA.6: 6 residues within 4Å: Chain A: S.98, I.100, W.101, G.102, A.103 Ligands: DC-DA-DG-DT-DA-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.98, A:G.102, A:A.103 NA.11: 4 residues within 4Å: Chain A: C.59, I.61, I.64 Ligands: DG-DC-DC-DG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.61

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 2 residues within 4Å: Chain A: H.240 Ligands: MN.7 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: R.268 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bebenek, K. et al., Replication infidelity via a mismatch with Watson-Crick geometry. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-02-02

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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