SMTL ID : 3oju.1

Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing c5 modified thymidies

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x SSJ: 2'-deoxy-5-[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)ethynyl]uridine 5'-(tetrahydrogen triphosphate)(Non-covalent)

SSJ.1: 23 residues within 4Å: Chain A: R.281, V.294, R.295, D.318, Y.319, S.320, Q.321, I.322, E.323, H.347, R.367, R.368, K.371, T.372, F.375, Y.379, D.493 Chain B: C.11, C.12 Chain C: A.4, G.5 Ligands: MG.2, MG.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:E.323, A:R.368, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:I.322, A:E.323 Water bridges: A:R.281, A:R.367, A:K.371, A:K.371, A:K.371, A:K.371 Salt bridges: A:H.347, A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.318, Y.319, S.320, Q.321, D.493 Ligands: SSJ.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MG.3: 7 residues within 4Å: Chain A: D.318, D.493, E.494, K.539 Chain B: C.12 Ligands: SSJ.1, MG.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.318, H2O.1

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: L.60, K.62, D.63, R.271, F.272, N.273, Q.274, T.275 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.62, A:D.63, A:D.63, A:N.273, A:Q.274 Water bridges: A:R.271, A:Q.274, A:T.275, A:T.275 GOL.5: 13 residues within 4Å: Chain A: T.252, Y.253, P.256, L.257, L.260, D.286, P.287, N.288, L.289, N.291, I.292 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.6: 9 residues within 4Å: Chain A: L.192, N.193, R.195, R.244 Chain B: G.7, G.8 Chain C: G.11, T.12 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.244 Water bridges: A:L.192, A:L.192, A:S.194 GOL.9: 9 residues within 4Å: Chain A: N.193, S.194, R.195, D.196 Chain B: C.6 Chain C: G.11, T.12, G.13 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.193, A:R.195, A:D.196, A:D.196 GOL.15: 6 residues within 4Å: Chain A: E.132, R.133, W.136, L.137, F.432, Y.519 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.133, A:R.133, A:R.133, A:Y.519 GOL.19: 6 residues within 4Å: Chain A: A.278, R.436, M.455 Chain C: G.6, C.7 Ligands: PGE.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.436

11 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 6 residues within 4Å: Chain A: E.55, R.57, G.78, D.79, R.143 Ligands: PGE.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.57, A:D.79 Water bridges: A:R.143 PGE.8: 6 residues within 4Å: Chain A: G.380, L.419, E.450, E.453, R.454, F.457 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.454 PGE.10: 3 residues within 4Å: Chain A: K.475, R.479, V.514 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.475, A:R.479 Water bridges: A:G.517 PGE.11: 8 residues within 4Å: Chain A: R.57, D.79, F.121, W.125, Y.138, R.139, R.143 Ligands: PGE.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.57, A:R.143, A:R.143 PGE.12: 6 residues within 4Å: Chain A: R.21, E.23, W.26, D.259, L.260, D.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.21, A:R.21 Water bridges: A:W.26 PGE.13: 7 residues within 4Å: Chain A: G.104, E.105, T.107, E.112, A.115, L.116, R.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.105, A:R.119, A:R.119 PGE.14: 5 residues within 4Å: Chain A: S.168, L.169, A.172, K.250, D.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.168, A:K.250 PGE.16: 5 residues within 4Å: Chain A: T.155, T.265, R.267, E.309, R.486 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.486, A:R.486 PGE.17: 4 residues within 4Å: Chain A: R.184, L.185, A.186, G.187 No protein-ligand interaction detected (PLIP) PGE.18: 6 residues within 4Å: Chain A: R.423, L.441, E.442, A.443, R.444, R.449 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.441, A:A.443 Water bridges: A:R.449 PGE.20: 4 residues within 4Å: Chain C: G.5, G.6, C.7 Ligands: GOL.19 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Obeid, S. et al., Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-12-15

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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