SMTL ID : 3pml.1 (1 other biounit)

crystal structure of a polymerase lambda variant with a dGTP analog opposite a templating T

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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

DG-DC-DC-DG.1: 17 residues within 4Å: Chain A: Y.26, W.33, R.34, G.37, Y.38, I.61, P.62, G.63, I.64, G.65, R.67, M.68, K.71 Chain B: C.1, G.2, G.3, C.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.33 Hydrogen bonds: A:K.222, A:K.222, A:E.224, A:K.226, A:R.271 Water bridges: A:T.130, A:K.275, A:K.275, A:K.275 Salt bridges: A:K.226, A:R.268, A:K.275, A:K.275, A:E.283, A:H.284 pi-Stacking: A:W.33

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

DC-DA-DG-DT-DA-DC.2: 23 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 Chain B: T.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: 1GC.3, MG.5, NA.6 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, A.264, N.267, R.271 Chain B: T.5, G.6 Ligands: DC-DA-DG-DT-DA-DC.2, MG.4, MG.5 10 PLIP interactions: 10 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:N.267, A:R.271 Water bridges: A:R.145 Salt bridges: A:R.145

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.186, D.188 Ligands: 1GC.3, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.1 MG.5: 6 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: DC-DA-DG-DT-DA-DC.2, 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

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

NA.6: 4 residues within 4Å: Chain A: S.98, I.100, A.103 Ligands: DC-DA-DG-DT-DA-DC.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.103

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

2011-01-26

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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