SMTL ID : 1t8e.1

T7 DNA Polymerase Ternary Complex with dCTP at the Insertion Site.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

hetero-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain C: D.469, A.470, D.648 Ligands: MG.2, DCT.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.469, C:A.470, C:D.648 MG.2: 6 residues within 4Å: Chain A: T.22 Chain C: D.469, D.648, H.698 Ligands: MG.1, DCT.5 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.469, C:D.648, H2O.2, H2O.2 MG.3: 1 residues within 4Å: Chain C: D.5 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.5, H2O.2, H2O.2, H2O.2, H2O.2

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain C: K.220, R.223 4 PLIP interactions: 4 interactions with chain C Water bridges: C:T.70, C:R.223 Salt bridges: C:K.220, C:R.223

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.5: 17 residues within 4Å: Chain A: T.22 Chain B: G.4, A.5 Chain C: R.423, D.469, A.470, S.471, G.472, L.473, E.474, H.500, R.512, K.516, Y.520, D.648 Ligands: MG.1, MG.2 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:E.474, C:Y.520 Hydrogen bonds: C:R.423, C:G.472, C:L.473, C:Y.520 Water bridges: C:N.605 Salt bridges: C:H.500, C:H.500, C:R.512, C:K.516, C:K.516, C:K.516 pi-Stacking: C:Y.520

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 3 residues within 4Å: Chain C: L.77, N.78, R.79 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.79 Salt bridges: C:R.79

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 6 residues within 4Å: Chain C: A.8, A.10, L.11, Y.64, K.130, W.154 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.130 Water bridges: C:K.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brieba, L.G. et al., Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. Embo J. (2004)

Release Date

2004-10-12

Peptides

DNA polymerase: C
thioredoxin 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

DNA polymerase

thioredoxin 1

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