SMTL ID : 3rtv.1

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

DCP.1: 18 residues within 4Å: Chain A: R.281, D.318, Y.319, S.320, Q.321, I.322, E.323, H.347, R.367, K.371, T.372, F.375, D.493 Chain B: G.12 Chain C: G.4, C.5 Ligands: MG.2, MG.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:E.323, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:I.322, A:E.323, A:T.372 Water bridges: A:R.367, A:R.367, A:K.371, A:K.371, A:K.371, A:T.372, A:K.539 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 5 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: DCP.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MG.3: 5 residues within 4Å: Chain A: D.318, D.493 Chain B: G.12 Ligands: DCP.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.9, H2O.9 MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.21, W.26, D.259, L.260 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.21, A:R.21, A:D.259 Water bridges: A:E.23, A:E.23 GOL.5: 4 residues within 4Å: Chain A: R.133, W.136, F.432, Y.519 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.133, A:Y.519 GOL.6: 8 residues within 4Å: Chain A: T.252, Y.253, P.256, P.287, N.288, N.291 Chain C: C.9, C.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.288, A:N.291 Water bridges: A:D.286 GOL.7: 5 residues within 4Å: Chain A: D.160, Y.163, R.304, I.307, D.534 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.160, A:D.534 GOL.11: 5 residues within 4Å: Chain A: L.419, E.450, E.453, R.454, F.457 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.453, A:R.454, A:R.454 GOL.13: 4 residues within 4Å: Chain A: A.278, R.436 Chain C: G.6, C.7 No protein-ligand interaction detected (PLIP)

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 3 residues within 4Å: Chain A: V.171, E.174, R.301 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.174 Water bridges: A:R.301 Salt bridges: A:R.301 ACT.9: 4 residues within 4Å: Chain A: W.353, M.354, I.392, E.396 No protein-ligand interaction detected (PLIP) ACT.10: 4 residues within 4Å: Chain A: D.79, W.125, R.139, R.143 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.139, A:R.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Betz, K. et al., KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry. Nat.Chem.Biol. (2012)

Release Date

2012-05-30

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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