SMTL ID : 8xk9.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 1 residues within 4Å: Chain A: G.8 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain C: D.317, Y.318, D.492 Ligands: MG.3, 01.4 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.317, C:Y.318, C:D.492 MG.3: 5 residues within 4Å: Chain A: C.12 Chain C: D.317, D.492 Ligands: MG.2, 01.4 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.317, C:D.492, H2O.7, H2O.9 MG.7: 1 residues within 4Å: Chain D: G.8 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain F: D.317, Y.318, D.492 Ligands: MG.9, 01.10 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.317, F:Y.318, F:D.492 MG.9: 5 residues within 4Å: Chain D: C.12 Chain F: D.317, D.492 Ligands: MG.8, 01.10 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.317, F:D.317, F:D.492, H2O.11, H2O.13

2 x 01: [[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

01.4: 19 residues within 4Å: Chain A: C.12 Chain B: C.3, G.4 Chain C: R.280, D.317, Y.318, S.319, Q.320, E.321, G.322, H.346, R.366, R.367, K.370, F.374, Y.378, D.492 Ligands: MG.2, MG.3 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:R.280, C:Q.320, C:E.321, C:E.321, C:E.321, C:G.322, C:R.367, C:R.367, C:D.492 Water bridges: C:K.370, C:K.370, C:N.457 Salt bridges: C:H.346, C:R.366, C:K.370, C:K.370, C:K.370 01.10: 19 residues within 4Å: Chain D: C.12 Chain E: C.3, G.4 Chain F: R.280, D.317, Y.318, S.319, Q.320, E.321, G.322, H.346, R.366, R.367, K.370, F.374, Y.378, D.492 Ligands: MG.8, MG.9 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:R.280, F:Q.320, F:E.321, F:G.322, F:R.367, F:R.367, F:D.492, F:D.492 Water bridges: F:K.370, F:K.370, F:Y.378, F:N.457 Salt bridges: F:H.346, F:R.366, F:K.370, F:K.370, F:K.370

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

PEG.5: 7 residues within 4Å: Chain C: H.328, L.430, Y.518 Chain F: H.328, L.430, Y.518 Ligands: PEG.11 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: F:L.430, F:Y.518 Hydrogen bonds: F:Y.518, C:H.328 PEG.11: 4 residues within 4Å: Chain F: H.328, L.329, W.413 Ligands: PEG.5 No protein-ligand interaction detected (PLIP)

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

PO4.6: 3 residues within 4Å: Chain C: W.124, R.138, R.142 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.142, C:R.142 Salt bridges: C:R.142 PO4.12: 3 residues within 4Å: Chain F: W.124, R.138, R.142 3 PLIP interactions: 3 interactions with chain F Water bridges: F:R.142, F:R.142 Salt bridges: F:R.142

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: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

F
D

DNA polymerase I, thermostable