SMTL ID : 6ur9.2 (1 other biounit)

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, dideoxy primer, 3'-amino-ddGTP (nGTP), and Ca2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

DG-DC-DG-DA-DT-DC-DA-DG-DOC.1: 30 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, 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.417 Hydrogen bonds: A:N.230, A:K.285, A:K.285, A:S.288, A:Q.315, A:R.318, A:R.318, A:S.320, A:E.323, A:N.325, A:N.328, A:G.423, A:N.427, A:N.485, A:R.492, A:Q.500, A:R.318, A:R.318 Water bridges: A:S.233, A:Q.236, A:L.313, A:Q.315, A:E.323, A:E.361, A:R.474, A:N.496, A:Y.417, A:Y.417, A:Y.417 Salt bridges: A:K.235, A:E.361, A:R.474, A:R.492 pi-Stacking: A:Y.417, A:Y.417, A:Y.422, A:Y.422

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

SO4.2: 3 residues within 4Å: Chain A: R.9, T.11, E.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.12 Salt bridges: A:R.9

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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