SMTL ID : 8xjr.1

Apo form of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.289, S.291, N.296 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.296 Water bridges: A:R.289, A:S.292, A:S.292 Salt bridges: A:R.289 SO4.2: 4 residues within 4Å: Chain A: L.167, D.168, V.169, A.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.169, A:A.170 SO4.3: 5 residues within 4Å: Chain A: T.285, A.286, T.287, R.289, R.463 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.286, A:T.287, A:T.287 Water bridges: A:R.289, A:R.444 Salt bridges: A:R.289 SO4.4: 2 residues within 4Å: Chain A: R.109, R.135 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.135, A:R.135 Salt bridges: A:R.109, A:R.135 SO4.5: 4 residues within 4Å: Chain A: P.301, V.302, R.303, T.304 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.302, A:R.303, A:T.304 Water bridges: A:I.300 Salt bridges: A:R.303 SO4.6: 5 residues within 4Å: Chain A: R.444, Y.445, V.446, A.460, R.463 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.444 Salt bridges: A:R.444, A:R.463 SO4.7: 2 residues within 4Å: Chain A: K.30, R.279 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.281 Salt bridges: A:K.30, A:R.279 SO4.8: 4 residues within 4Å: Chain A: S.390, A.391, H.392, Y.402 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.391, A:H.392, A:Y.402, A:Y.402 SO4.9: 1 residues within 4Å: Chain A: R.367 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.367 SO4.10: 3 residues within 4Å: Chain A: H.355, R.375, K.379 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.329 Salt bridges: A:R.375, A:K.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wen, C. et al., Structural Basis for C2'-methoxy Recognition by DNA Polymerases and Function Improvement. J.Mol.Biol. (2024)

Release Date

2024-11-27

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable