SMTL ID : 5dmu.1

Structure of the NHEJ polymerase from Methanocella paludicola

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: Q.63, H.123, R.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.63, A:H.123, A:R.247 Water bridges: A:A.248 EDO.2: 7 residues within 4Å: Chain A: R.5, S.7, P.25, D.26, T.36, G.38, E.39 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.5, A:S.7, A:P.25 Water bridges: A:G.38

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: R.58, V.124, F.125, L.126, R.137, I.139, G.240, P.243, W.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.124, A:G.240 Water bridges: A:L.54, A:R.58

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

SO4.4: 3 residues within 4Å: Chain A: D.187, R.188, R.295 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.295, A:R.295 Salt bridges: A:R.188, A:R.295 SO4.5: 3 residues within 4Å: Chain A: T.23, K.37, Q.117 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.23, A:S.116, A:Q.117 Water bridges: A:T.23, A:K.37, A:K.37 Salt bridges: A:K.37

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 6 residues within 4Å: Chain A: L.126, P.135, R.137, F.192, V.195, N.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.234

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

NHEJ Polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NHEJ Polymerase