SMTL ID : 4dr0.1

Crystal structure of Bacillus subtilis dimanganese(II) NrdF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: E.118, E.185, E.219, H.222 Ligands: MN.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.118, A:E.185, A:E.185, A:E.219, A:H.222 MN.2: 6 residues within 4Å: Chain A: D.87, E.118, H.122, F.189, E.219 Ligands: MN.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.87, A:E.118, A:H.122, A:E.219, A:E.219 MN.4: 5 residues within 4Å: Chain B: E.118, E.185, E.219, H.222 Ligands: MN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.118, B:E.185, B:E.219, B:H.222, H2O.6 MN.5: 5 residues within 4Å: Chain B: D.87, E.118, H.122, E.219 Ligands: MN.4 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.87, B:D.87, B:E.118, B:H.122, B:E.219

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

SO4.3: 3 residues within 4Å: Chain A: H.275, K.278, R.282 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.278, A:K.278 Salt bridges: A:H.275, A:K.278, A:R.282 SO4.6: 4 residues within 4Å: Chain B: G.69, K.70, N.71, E.72 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.70, B:N.71, B:N.71, B:E.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boal, A.K. et al., The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase. Biochemistry (2012)

Release Date

2012-04-11

Peptides

Ribonucleoside-diphosphate reductase subunit beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase subunit beta