SMTL ID : 3uq0.1

Crystal structure of the post-catalytic product complex of polymerase lambda with an rAMP at the primer terminus.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC-A.1: 26 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, D.188, K.226, D.244, Y.259, F.260, T.261, G.262, S.263, A.264, N.267 Chain B: T.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: NA.3 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, P.62, 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 NA: SODIUM ION(Non-functional Binders)

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

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

SO4.4: 4 residues within 4Å: Chain A: R.145, S.176, G.185, D.186 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:G.185, A:D.186 Water bridges: A:S.176, A:S.176, A:S.176 Salt bridges: A:R.145 SO4.5: 4 residues within 4Å: Chain A: G.201, I.202, F.203, S.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.201, A:S.204 Water bridges: A:I.202, A:I.202 SO4.6: 3 residues within 4Å: Chain A: H.199, R.200, P.249 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.199, A:R.200 Salt bridges: A:H.199, A:R.200

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

CL.7: 1 residues within 4Å: Chain A: R.178 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.34 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 1 residues within 4Å: Chain A: R.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.232, A:R.232 EDO.10: 2 residues within 4Å: Chain A: R.123, S.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.123, A:R.123

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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