SMTL ID : 4elv.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: D.318, E.494 Ligands: 0R7.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.318, A:E.494, H2O.1, H2O.5, H2O.8 MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain C: G.13, G.14 No protein-ligand interaction detected (PLIP)

1 x 0R7: [[(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

0R7.2: 20 residues within 4Å: Chain A: R.281, D.318, Y.319, S.320, Q.321, I.322, E.323, L.324, H.347, R.367, R.368, K.371, T.372, F.375, D.493 Chain B: X.12 Chain C: G.4, G.5 Ligands: MG.1, CA.8 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:E.323, A:R.368, A:K.371, A:T.372, A:F.375, A:F.375, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:I.322 Water bridges: A:E.323, A:R.368, A:R.368, A:R.368, A:K.371, A:E.494 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Cation interactions: A:K.371

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: T.252, Y.253, P.256, P.287, N.288, N.291 Chain C: C.9, C.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.288, A:N.288, A:N.291 Water bridges: A:Y.253, A:D.286 GOL.5: 5 residues within 4Å: Chain A: R.133, W.136, L.431, F.432, Y.519 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.133, A:Y.519, A:Y.519 GOL.6: 4 residues within 4Å: Chain A: D.160, Y.163, R.304, I.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.304 Water bridges: A:D.160 GOL.10: 3 residues within 4Å: Chain C: G.5, G.6 Ligands: EDO.12 No protein-ligand interaction detected (PLIP)

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

PGE.4: 4 residues within 4Å: Chain A: D.79, W.125, R.139, R.143 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.79, A:R.139, A:R.139, A:R.143, A:R.143

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

EDO.7: 4 residues within 4Å: Chain A: V.18, L.19, E.108, R.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.17, A:L.19, A:R.113 Water bridges: A:R.113 EDO.12: 5 residues within 4Å: Chain A: A.278, R.436 Chain C: G.6, C.7 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.278

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: 0R7.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Obeid, S. et al., Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines. To be Published

Release Date

2013-04-24

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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