SMTL ID : 6us5.2 (1 other biounit)

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, 3'-amino primer, dGpNHpp analog, and Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x DG- DC- DG- DA- DT- DC- DA- DG- C42: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3')(Non-covalent)

DG-DC-DG-DA-DT-DC-DA-DG-C42.1: 32 residues within 4Å: Chain A: T.253, K.254, S.258, T.259, S.260, A.261, R.281, Q.282, K.285, Y.290, R.318, Q.327, N.328, I.329, P.330, I.331, R.332, R.340, V.531, H.532, D.533, E.534 Chain B: G.4, C.5, T.6, G.7, A.8, T.9, C.10, G.11, C.12 Ligands: XG4.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:R.318, A:R.318, A:D.533, A:E.534, A:N.230, A:S.233, A:K.285, A:K.285, A:S.288, A:L.313, A:Q.315, A:R.318, A:R.318, A:S.320, A:E.323, A:N.328, A:G.423, A:N.485, A:R.492, A:Q.500 Salt bridges: A:R.332, A:R.340, A:R.474, A:R.492 Water bridges: A:E.292, A:Q.315, A:M.493, A:N.496, A:N.496 pi-Stacking: A:Y.422

1 x XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.2: 19 residues within 4Å: Chain A: R.318, D.356, Y.357, S.358, Q.359, I.360, E.361, H.385, R.405, K.409, A.410, Y.413, Y.417, D.533, E.534 Chain B: C.3, G.4 Ligands: DG-DC-DG-DA-DT-DC-DA-DG-C42.1, MN.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:E.361, A:Y.413 Hydrogen bonds: A:R.318, A:D.356, A:Q.359, A:I.360, A:E.361, A:K.409, A:K.409, A:Y.413, A:N.496, A:E.534 Water bridges: A:E.361, A:N.496 Salt bridges: A:E.361, A:H.385, A:R.405, A:K.409

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

MN.3: 4 residues within 4Å: Chain A: D.356, Y.357, D.533 Ligands: XG4.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Y.357, A:D.533

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

SO4.4: 4 residues within 4Å: Chain A: R.9, V.10, T.11, E.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.12 Salt bridges: A:R.9 SO4.5: 5 residues within 4Å: Chain A: E.24, V.25, R.78, D.128, K.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.24 Water bridges: A:D.75, A:K.153 Salt bridges: A:R.78, A:K.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lelyveld, V.S. et al., Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-03-18

Peptides

DNA polymerase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

DNA polymerase I

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