SMTL ID : 1zyq.1

T7 DNA polymerase in complex with 8oG and incoming ddATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain C: D.469, A.470, D.648 Ligands: DAD.4 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.469, C:D.469, C:A.470, C:D.648 MG.2: 6 residues within 4Å: Chain A: G.22 Chain C: D.469, D.648, E.649, H.698 Ligands: DAD.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.469, C:D.648 MG.3: 4 residues within 4Å: Chain C: D.5, I.6, M.129, D.168 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.5

1 x DAD: 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

DAD.4: 17 residues within 4Å: Chain A: G.22 Chain B: G.4, C.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 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:E.474, C:E.474, C:Y.520 Hydrogen bonds: C:R.423, C:D.469, C:A.470, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brieba, L.G. et al., A lysine residue in the fingers subdomain of t7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine. Structure (2005)

Release Date

2005-11-22

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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