SMTL ID : 7m4d.1

DNA Polymerase Lambda, dCTP:At Ca2+ Ground State Ternary Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DT-DA-DC.1: 22 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, L.228, R.242, D.244, Y.259, F.260 Chain B: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: NA.5, DCP.6 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: 16 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 Chain B: C.1, G.2, G.3, C.4 Protein-ligand interaction information (PLIP) not available

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.186, D.188 Ligands: NA.4, DCP.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.1

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

NA.4: 5 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: CA.3, DCP.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.188 NA.5: 5 residues within 4Å: Chain A: S.98, I.100, G.102, A.103 Ligands: DC-DA-DG-DT-DA-DC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.102, A:A.103, A:A.103

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.6: 18 residues within 4Å: Chain A: R.145, G.175, S.176, R.179, G.185, D.186, D.188, Y.259, F.260, T.261, G.262, S.263, A.264, N.267 Chain B: A.5 Ligands: DC-DA-DG-DT-DA-DC.1, CA.3, NA.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:S.176, A:R.179, A:G.185, A:D.186, A:N.267 Water bridges: A:Y.177, A:R.179, A:D.188, A:A.264, A:R.271, A:R.271 Salt bridges: A:R.145, A:R.179

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

EDO.7: 3 residues within 4Å: Chain A: N.99, W.101, F.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.99 Water bridges: A:W.101 EDO.8: 5 residues within 4Å: Chain A: F.253, L.257, P.308, T.309, E.310 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.308, A:E.310 Water bridges: A:T.309, A:E.310, A:E.310, A:K.311 EDO.9: 3 residues within 4Å: Chain A: S.124, Q.125, A.126 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain A: R.123, L.128 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamsen, J.A. et al., Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints. Nat Commun (2022)

Release Date

2022-07-06

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

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