SMTL ID : 1tk0.1

T7 DNA polymerase ternary complex with 8 oxo guanosine and ddCTP at the insertion site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.469, C:A.470, C:D.648 MG.2: 5 residues within 4Å: Chain A: G.22 Chain C: D.469, D.648 Ligands: MG.1, DCT.6 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.469, C:D.648, H2O.12, H2O.19 MG.3: 1 residues within 4Å: Chain C: D.5 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.5, H2O.4, H2O.6, H2O.19, H2O.19, H2O.19

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

SO4.4: 2 residues within 4Å: Chain C: K.220, R.223 10 PLIP interactions: 10 interactions with chain C Water bridges: C:K.220, C:R.223, C:R.223, C:R.223, C:R.223, C:R.223, C:R.223, C:H.634 Salt bridges: C:K.220, C:R.223 SO4.5: 2 residues within 4Å: Chain C: H.99, K.178 3 PLIP interactions: 3 interactions with chain C Water bridges: C:A.121 Salt bridges: C:H.99, C:K.178

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

DCT.6: 16 residues within 4Å: Chain A: G.22 Chain B: G.4 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 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:E.474, C:Y.520 Hydrogen bonds: C:R.423, C:D.469, C:A.470, C:G.472, C:L.473 Water bridges: C:D.469, C:K.516 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 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.7: 8 residues within 4Å: Chain C: A.8, A.10, L.11, Y.64, M.107, L.109, K.130, W.154 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.130

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

MES.8: 3 residues within 4Å: Chain C: L.77, N.78, R.79 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.79, C:R.79 Salt bridges: C:R.79

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

2004-08-31

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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