SMTL ID : 5dmp.1

Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: D.154, T.161, M.162, D.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.153, A:D.154, A:M.162, A:D.163 EDO.2: 5 residues within 4Å: Chain A: K.114, D.154, S.155, V.156, G.159 No protein-ligand interaction detected (PLIP) EDO.3: 5 residues within 4Å: Chain A: F.109, K.116, G.117, E.139 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.139 EDO.4: 4 residues within 4Å: Chain A: K.116, K.136, E.139 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.116 EDO.5: 4 residues within 4Å: Chain A: N.84, E.87, T.96, I.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.84, A:E.87, A:I.97 Water bridges: A:N.84 EDO.6: 4 residues within 4Å: Chain A: V.27, D.52, H.53, P.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.53 EDO.7: 2 residues within 4Å: Chain A: E.146, D.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.147

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 5 residues within 4Å: Chain A: H.11, H.17, D.19, G.70 Ligands: VN4.9 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.11, H2O.1

1 x VN4: oxido(dioxo)vanadium(Non-covalent)

VN4.9: 7 residues within 4Å: Chain A: H.11, D.19, R.21, H.53, Y.57, V.74 Ligands: MG.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.21, A:R.21, A:Y.57, A:Y.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bartlett, E.J. et al., Molecular basis for DNA strand displacement by NHEJ repair polymerases. Nucleic Acids Res. (2016)

Release Date

2015-10-07

Peptides

Uncharacterized protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uncharacterized protein