SMTL ID : 4elu.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 0R6: 2'-deoxy-5-[(4-ethynylphenyl)ethynyl]cytidine 5'-(tetrahydrogen triphosphate)(Non-covalent)

0R6.1: 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, D.493 Chain B: G.12 Chain C: G.4, C.5 Ligands: MG.2, MG.3, GOL.4, GOL.17 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:R.295, A:E.323, A:R.368, A:K.371, A:T.372, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:I.322, A:E.323 Water bridges: A:D.318, A:K.539, 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 pi-Cation interactions: A:R.295

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: 0R6.1, 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: 0R6.1, 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.15: 1 residues within 4Å: Chain B: G.8 No protein-ligand interaction detected (PLIP)

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: V.294, R.303, R.368, K.371, K.539 Chain B: G.12 Ligands: 0R6.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.303, A:R.368, A:K.371, A:K.539 Water bridges: A:R.303, A:R.367, A:R.367, A:K.371, A:E.494 GOL.5: 8 residues within 4Å: Chain A: T.252, Y.253, P.256, P.287, N.288, N.291 Chain C: C.9, C.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.288, 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.534 GOL.9: 3 residues within 4Å: Chain A: P.209, A.229, A.233 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.233 GOL.11: 4 residues within 4Å: Chain A: R.21, W.26, D.259, L.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.21, A:R.21, A:D.259 GOL.12: 5 residues within 4Å: Chain A: W.353, M.354, F.355, G.356, I.392 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.396 GOL.16: 6 residues within 4Å: Chain A: R.244, K.248 Chain B: G.7, G.8, C.9 Chain C: C.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.248, A:K.248 Water bridges: A:N.193, A:N.193 GOL.17: 7 residues within 4Å: Chain A: R.295, T.372, R.385 Chain B: C.11, G.12 Chain C: G.4 Ligands: 0R6.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.295, A:R.295, A:R.385 GOL.19: 5 residues within 4Å: Chain A: A.278, R.436 Chain C: G.6, C.7 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.436 GOL.20: 5 residues within 4Å: Chain B: C.3 Chain C: T.12, G.13, G.14, T.15 No protein-ligand interaction detected (PLIP) GOL.21: 3 residues within 4Å: Chain C: C.5, G.6 Ligands: GOL.19 No protein-ligand interaction detected (PLIP)

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

PGE.6: 3 residues within 4Å: Chain A: T.155, R.267, R.486 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.155 Water bridges: A:E.309, A:R.486 PGE.14: 1 residues within 4Å: Chain B: G.1 No protein-ligand interaction detected (PLIP)

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

ACT.8: 3 residues within 4Å: Chain A: D.79, W.125, R.143 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.125 Hydrogen bonds: A:R.139, A:R.139 Salt bridges: A:R.143 ACT.10: 5 residues within 4Å: Chain A: H.188, Q.197, R.200, V.201, E.205 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.200 ACT.13: 4 residues within 4Å: Chain A: R.133, W.136, F.432, Y.519 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.432 Hydrogen bonds: A:Y.519, A:Y.519 ACT.18: 2 residues within 4Å: Chain C: C.7, G.8 No protein-ligand interaction detected (PLIP)

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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