SMTL ID : 3upq.1

Crystal structure of the pre-catalytic ternary complex of polymerase lambda with an rATP analog opposite a templating T.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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.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: T.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: ZAN.3, MN.5, NA.7 Protein-ligand interaction information (PLIP) not available

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

DG-DC-DC-DG.2: 18 residues within 4Å: Chain A: Y.26, W.33, R.34, G.37, Y.38, I.61, G.63, I.64, G.65, K.66, R.67, M.68, K.71, K.83 Chain B: C.1, G.2, G.3, C.4 Protein-ligand interaction information (PLIP) not available

1 x ZAN: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

ZAN.3: 19 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 Chain B: T.5, G.6 Ligands: DC-DA-DG-DT-DA-DC.1, MN.4, MN.5 11 PLIP interactions: 11 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:T.261, A:N.267 Water bridges: A:D.186, A:A.264 Salt bridges: A:R.145

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

MN.4: 4 residues within 4Å: Chain A: D.186, D.188 Ligands: ZAN.3, MN.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.6 MN.5: 6 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: DC-DA-DG-DT-DA-DC.1, ZAN.3, MN.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.6 MN.6: 2 residues within 4Å: Chain A: D.141, H.240 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.141, A:H.240, H2O.6, H2O.6, H2O.6, H2O.6

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

NA.7: 6 residues within 4Å: Chain A: S.98, I.100, W.101, G.102, A.103 Ligands: DC-DA-DG-DT-DA-DC.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.102, A:A.103 Water bridges: A:S.98, A:W.101, A:A.103

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 6 residues within 4Å: Chain A: R.200, G.201, I.202, F.203, S.204, E.224 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.201, A:I.202, A:F.203, A:S.204, A:E.224 SO4.9: 3 residues within 4Å: Chain A: H.199, R.200, P.249 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.199, A:R.200 SO4.10: 2 residues within 4Å: Chain A: K.32, W.33 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.32 SO4.11: 2 residues within 4Å: Chain A: R.178, P.324 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gosavi, R.A. et al., The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda. Nucleic Acids Res. (2012)

Release Date

2012-05-23

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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