SMTL ID : 6sa0.1 (1 other biounit)

Ternary complex of Prim-PolC from Mycobacterium smegmatis with 2nt gapped DNA and UpNHpp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

monomer

Ligands

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

DG-DC-DG-DA-DG-DC-DG.1: 20 residues within 4Å: Chain A: R.17, T.19, N.20, K.23, Y.25, K.35, R.63, P.65, K.81, Q.115, M.116, G.117 Chain B: C.1, G.2, C.3, T.4, C.5, G.6, C.7, A.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.73 Hydrogen bonds: A:R.63, A:E.71, A:K.76, A:K.76, A:R.77, A:R.77 Salt bridges: A:R.77 pi-Stacking: A:Y.74

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

DC-DG-DT-DG-DC-DG.2: 17 residues within 4Å: Chain A: D.142, W.219, W.220, K.221, R.224, D.231, Q.234, R.239, P.320 Chain B: A.9, C.10, C.12, A.13, C.14, G.15 Ligands: 2KH.3, MN.4 Protein-ligand interaction information (PLIP) not available

1 x 2KH: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine(Non-covalent)

2KH.3: 20 residues within 4Å: Chain A: Y.74, H.122, D.140, D.142, S.176, G.178, R.179, G.180, H.182, Q.234, T.240, F.241, A.242, R.248 Chain B: A.9 Ligands: DC-DG-DT-DG-DC-DG.2, MN.4, MN.5, CAC.6, EDO.7 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:H.122, A:S.176, A:R.179, A:G.180, A:G.180, A:Q.234, A:T.240, A:A.242, A:R.248, A:R.248 Water bridges: A:V.181, A:T.240, A:T.240

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

MN.4: 6 residues within 4Å: Chain A: D.140, D.142, D.231 Ligands: DC-DG-DT-DG-DC-DG.2, 2KH.3, MN.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.140, A:D.142, A:D.231 MN.5: 4 residues within 4Å: Chain A: D.140, D.142 Ligands: 2KH.3, MN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.140, A:D.142, H2O.3

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.6: 7 residues within 4Å: Chain A: Q.62, E.72, Y.74, R.248, K.249 Ligands: 2KH.3, EDO.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.249

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

EDO.7: 7 residues within 4Å: Chain A: G.177, G.178, R.248, K.249, T.250 Ligands: 2KH.3, CAC.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.62, A:R.248 EDO.8: 4 residues within 4Å: Chain A: K.161, S.260, W.261, D.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.261, A:D.262 Water bridges: A:S.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brissett, N.C. et al., Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C. Nat Commun (2020)

Release Date

2020-11-18

Peptides

DNA polymerase LigD, polymerase domain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase LigD, polymerase domain

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