SMTL ID : 6nk8.1

C-terminal region of the Burkholderia pseudomallei OLD protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.28, D.83, T.134 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.28, A:D.83, H2O.1, H2O.1, H2O.1 MG.2: 2 residues within 4Å: Chain A: E.136, K.190 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: E.41, D.48 Chain B: E.41, D.48 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.41, B:E.41, H2O.2, H2O.2, H2O.3 MG.4: 4 residues within 4Å: Chain A: D.44, H.46 Chain B: D.44, H.46 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.44, A:D.44, H2O.1, H2O.2, H2O.3 MG.5: 1 residues within 4Å: Chain B: D.204 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.204, H2O.2, H2O.3 MG.6: 2 residues within 4Å: Chain B: E.28, D.83 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.28, B:D.83, H2O.2, H2O.2, H2O.3 MG.7: 3 residues within 4Å: Chain C: E.28, D.83, T.134 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.28, C:D.83, H2O.4, H2O.4, H2O.4 MG.8: 2 residues within 4Å: Chain C: E.136, K.190 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain C: E.41, D.48 Chain D: E.41, D.48 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:E.41, D:E.41, H2O.5, H2O.5, H2O.6 MG.10: 4 residues within 4Å: Chain C: D.44, H.46 Chain D: D.44, H.46 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: D:D.44, C:D.44, H2O.4, H2O.5, H2O.6 MG.11: 1 residues within 4Å: Chain D: D.204 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.204, H2O.5, H2O.6 MG.12: 2 residues within 4Å: Chain D: E.28, D.83 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.28, D:D.83, H2O.5, H2O.5, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiltz, C.J. et al., Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage. Nucleic Acids Res. (2019)

Release Date

2019-08-07

Peptides

Class 2 OLD family nuclease: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Class 2 OLD family nuclease