SMTL ID : 3sv3.1

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dNaM-d5SICSTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x 5SI: 2-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-6-methylisoquinoline-1(2H)-thione(Non-covalent)

5SI.1: 6 residues within 4Å: Chain A: R.509, K.512, E.513, E.516 Ligands: MG.3, MG.14 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.509, A:E.513 Hydrogen bonds: A:R.509, A:E.516 Water bridges: A:R.509, A:R.509, A:K.512 Salt bridges: A:R.509, A:K.512, A:K.512 pi-Cation interactions: A:R.509 5SI.2: 19 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, Y.379, D.493 Chain B: C.12 Chain C: X.4, G.5 Ligands: MG.8, MG.9 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.375 Hydrogen bonds: A:R.281, A:S.320, A:S.320, A:Q.321, A:I.322, A:E.323 Water bridges: A:R.281, A:D.318, A:R.367, A:K.371 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371

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

MG.3: 3 residues within 4Å: Chain A: R.509, K.512 Ligands: 5SI.1 No protein-ligand interaction detected (PLIP) MG.8: 7 residues within 4Å: Chain A: D.318, Y.319, S.320, Q.321, D.493 Ligands: 5SI.2, MG.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MG.9: 7 residues within 4Å: Chain A: D.318, D.493, E.494, K.539 Chain B: C.12 Ligands: 5SI.2, MG.8 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.318, A:D.493, H2O.5, H2O.6 MG.14: 3 residues within 4Å: Chain A: K.512, E.528 Ligands: 5SI.1 No protein-ligand interaction detected (PLIP) MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: T.252, Y.253, P.256, L.257, L.260, 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.5: 4 residues within 4Å: Chain A: R.21, W.26, D.259, L.260 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.21, A:R.21 Water bridges: A:E.23, A:E.23 GOL.21: 3 residues within 4Å: Chain C: G.5, G.6, C.7 No protein-ligand interaction detected (PLIP) GOL.26: 5 residues within 4Å: Chain B: C.4, A.5 Chain C: C.10, G.11, T.12 No protein-ligand interaction detected (PLIP)

16 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 6 residues within 4Å: Chain A: W.7, A.43, P.44, E.45, K.48, A.49 Ligand excluded by PLIP FMT.7: 4 residues within 4Å: Chain A: L.69, H.151, A.154, T.155 Ligand excluded by PLIP FMT.10: 4 residues within 4Å: Chain A: I.531, G.532, E.533, S.537 Ligand excluded by PLIP FMT.11: 4 residues within 4Å: Chain A: P.500, K.501, E.502, R.503 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain A: R.133, W.136, F.432 Ligand excluded by PLIP FMT.13: 4 residues within 4Å: Chain A: V.18, L.19, E.108, R.113 Ligand excluded by PLIP FMT.15: 6 residues within 4Å: Chain A: R.195, D.196, K.219 Chain B: C.6 Chain C: T.12 Ligands: FMT.25 Ligand excluded by PLIP FMT.16: 4 residues within 4Å: Chain A: E.416, L.419, E.420, R.423 Ligand excluded by PLIP FMT.17: 5 residues within 4Å: Chain A: N.193, R.195, R.244 Chain B: G.7, G.8 Ligand excluded by PLIP FMT.18: 5 residues within 4Å: Chain A: G.380, E.450, E.453, R.454, F.457 Ligand excluded by PLIP FMT.19: 5 residues within 4Å: Chain A: D.160, Y.163, R.304, I.307, D.534 Ligand excluded by PLIP FMT.22: 3 residues within 4Å: Chain A: R.436 Chain C: G.6, C.7 Ligand excluded by PLIP FMT.23: 2 residues within 4Å: Chain C: C.7, G.8 Ligand excluded by PLIP FMT.24: 3 residues within 4Å: Chain B: C.3 Chain C: G.13, G.14 Ligand excluded by PLIP FMT.25: 6 residues within 4Å: Chain A: N.193, S.194, R.195 Chain C: G.11, T.12 Ligands: FMT.15 Ligand excluded by PLIP FMT.27: 4 residues within 4Å: Chain B: C.3 Chain C: G.14, T.15, C.16 Ligand excluded by PLIP

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

2012-06-06

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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