SMTL ID : 8xk7.1

binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: D.317, Y.318, S.319, Q.320, E.321, D.492 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.319, A:Q.320, A:E.321, A:D.492, A:D.492 Water bridges: A:D.317, A:D.317, A:D.492, A:E.493 PO4.2: 4 residues within 4Å: Chain A: Q.320, H.346, R.366, K.370 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.320 Water bridges: A:H.346, A:K.370 Salt bridges: A:R.366, A:K.370

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

SO4.3: 3 residues within 4Å: Chain A: W.124, R.138, R.142 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.138, A:R.142 SO4.4: 5 residues within 4Å: Chain A: S.381, A.382, H.383, Y.393, K.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.382, A:H.383, A:Y.393 Salt bridges: A:K.445 SO4.5: 4 residues within 4Å: Chain A: L.158, D.159, V.160, A.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.160, A:A.161

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: R.20, E.22, W.25, L.259, D.285 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.20, A:R.20 Water bridges: A:D.285, A:D.285

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