SMTL ID : 3mgi.1

Ternary complex of a DNA polymerase lambda loop mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DT- DA- DT: DNA (5'-D(*CP*AP*GP*TP*AP*T)-3')(Non-covalent)

DC-DA-DG-DT-DA-DT.1: 22 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, K.226, L.228, R.242, D.244, Y.259 Chain B: A.5, A.6, T.7, A.8, C.9, T.10, G.11 Ligands: D3T.3, NA.5 Protein-ligand interaction information (PLIP) not available

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

DG-DC-DC-DG.2: 17 residues within 4Å: Chain A: Y.26, W.33, R.34, G.37, Y.38, P.62, G.63, I.64, G.65, K.66, R.67, M.68, K.71 Chain B: C.1, G.2, G.3, C.4 Protein-ligand interaction information (PLIP) not available

1 x D3T: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

D3T.3: 16 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, G.262, A.264, N.267 Chain B: A.5 Ligands: DC-DA-DG-DT-DA-DT.1, MG.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.264 Hydrogen bonds: A:S.176, A:S.176, A:G.185, A:D.186, A:N.267 Water bridges: A:D.188, A:R.242, A:R.242, A:R.242, A:D.244 Salt bridges: A:R.145, A:R.179

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: S.176, D.186, D.188 Ligands: D3T.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.186, A:D.188, H2O.3

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

NA.5: 4 residues within 4Å: Chain A: S.98, I.100, A.103 Ligands: DC-DA-DG-DT-DA-DT.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bebenek, K. et al., Loop 1 modulates the fidelity of DNA polymerase lambda. Nucleic Acids Res. (2010)

Release Date

2010-05-19

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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