SMTL ID : 4elt.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x 0R5: 2'-deoxy-5-[(4-ethynylphenyl)ethynyl]uridine 5'-(tetrahydrogen triphosphate)(Non-covalent)

0R5.1: 22 residues within 4Å: Chain A: R.281, 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.12 Chain C: A.4, G.5 Ligands: MG.2, MG.3, GOL.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:R.295, 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:D.318, A:R.367, A:R.367, A:K.371, A:K.539 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 pi-Cation interactions: A:R.295, A:K.371

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: 0R5.1, 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: C.12 Ligands: 0R5.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:D.493, H2O.1, H2O.1 MG.17: 2 residues within 4Å: Chain C: G.13, G.14 No protein-ligand interaction detected (PLIP)

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: R.368, K.371, K.539 Chain B: C.12 Ligands: 0R5.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.368, A:K.371, A:K.539 Water bridges: A:R.303, A:R.367, A:K.371, A:K.371 GOL.6: 6 residues within 4Å: Chain A: G.380, E.450, E.453, R.454, F.457 Chain C: A.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.380, A:E.453, A:R.454 GOL.7: 9 residues within 4Å: Chain A: T.252, Y.253, P.256, P.287, N.288, N.291 Chain C: C.9, C.10 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.288, A:N.291 Water bridges: A:N.291 GOL.9: 7 residues within 4Å: Chain A: L.60, K.62, D.63, R.271, F.272, N.273, Q.274 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.62, A:D.63, A:D.63, A:R.271, A:Q.274 Water bridges: A:T.275, A:T.275 GOL.10: 6 residues within 4Å: Chain A: L.260, D.286, P.287 Chain C: C.9, C.10 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.286, A:D.286 Water bridges: A:E.23, A:E.23 GOL.11: 6 residues within 4Å: Chain A: R.423, L.441, E.442, A.443, R.444, R.449 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.442, A:R.444 GOL.13: 6 residues within 4Å: Chain A: S.91, R.436, Y.437, V.438, M.455 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.436, A:Y.437 Water bridges: A:S.91, A:Y.437 GOL.15: 6 residues within 4Å: Chain B: C.6, G.7, G.8, C.9 Chain C: G.8, C.9 No protein-ligand interaction detected (PLIP) GOL.16: 4 residues within 4Å: Chain A: R.436 Chain C: G.6, C.7 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.278

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

ACT.5: 5 residues within 4Å: Chain A: D.160, Y.163, R.304, I.307, D.534 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.304 Hydrogen bonds: A:R.304 ACT.8: 4 residues within 4Å: Chain A: R.21, W.26, D.259, L.260 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.26 Hydrogen bonds: A:W.26 Water bridges: A:R.21 Salt bridges: A:R.21 ACT.12: 3 residues within 4Å: Chain A: S.168, A.172, K.250 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.250

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.14: 4 residues within 4Å: Chain A: E.55, R.57, G.78, D.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Obeid, S. et al., Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site. Chem.Commun.(Camb.) (2012)

Release Date

2013-03-27

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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