SMTL ID : 1tk8.1

T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain C: D.469, A.470, D.648 Ligands: MG.3, D3T.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.469, C:A.470, C:D.648 MG.3: 5 residues within 4Å: Chain A: A.22 Chain C: D.469, D.648 Ligands: MG.2, D3T.7 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.469, C:D.648, H2O.3, H2O.12 MG.4: 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.5, H2O.8, H2O.18, H2O.18, H2O.18

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

SO4.5: 2 residues within 4Å: Chain C: K.220, R.223 8 PLIP interactions: 8 interactions with chain C Water bridges: C:T.70, C:H.82, C:R.223, C:R.223, C:R.223, C:R.223 Salt bridges: C:K.220, C:R.223 SO4.6: 3 residues within 4Å: Chain C: H.99, E.120, K.178 5 PLIP interactions: 5 interactions with chain C Water bridges: C:E.120, C:E.120, C:K.178 Salt bridges: C:H.99, C:K.178

1 x D3T: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

D3T.7: 18 residues within 4Å: Chain A: A.22 Chain B: A.4 Chain C: R.423, D.469, A.470, S.471, G.472, L.473, E.474, H.500, R.512, K.516, T.517, Y.520, Y.524, D.648 Ligands: MG.2, MG.3 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:E.474, C:Y.520, C:Y.520 Hydrogen bonds: C:R.423, C:A.470, C:G.472, C:L.473, C:Y.520, C:D.648 Water bridges: C:D.469, C:K.516, 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.8: 4 residues within 4Å: Chain C: G.40, 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 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 8 residues within 4Å: Chain C: A.8, A.10, L.11, Y.64, M.107, L.109, K.130, W.154 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.107, 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

2004-08-31

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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