SMTL ID : 7m4k.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 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: 25 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: A.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: NA.4, NA.5, EDO.11, YQS.14 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: 19 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, K.66, R.67, M.68, K.71 Chain B: C.1, G.2, G.3, C.4 Ligands: NA.6 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, YQS.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.3

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

NA.4: 6 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: DC-DA-DG-DT-DA-DC.1, CA.3, YQS.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.188 NA.5: 6 residues within 4Å: Chain A: S.98, I.100, W.101, 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 NA.6: 4 residues within 4Å: Chain A: C.59, I.61, I.64 Ligands: DG-DC-DC-DG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.59, A:I.64 NA.7: 1 residues within 4Å: Chain A: Q.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.125, A:Q.125

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

EDO.8: 4 residues within 4Å: Chain A: N.99, W.101, F.142, L.143 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.99, A:N.99, A:W.101 EDO.9: 4 residues within 4Å: Chain A: R.123, L.128, A.133, L.136 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain A: F.253, L.257, T.309, E.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.310, A:E.310, A:E.310 EDO.11: 3 residues within 4Å: Chain A: T.107, M.110 Ligands: DC-DA-DG-DT-DA-DC.1 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: R.211, L.216, T.217, D.218, D.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.216 EDO.13: 2 residues within 4Å: Chain A: Y.112, R.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.117

1 x YQS: [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

YQS.14: 18 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: A.5 Ligands: DC-DA-DG-DT-DA-DC.1, CA.3, NA.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.264 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:R.145, A:R.145, A:Y.177, A:Y.177, A:G.185, A:A.264 Salt bridges: A:R.145, A:R.179

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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