SMTL ID : 6tqv.1

Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis aerobically soaked with Fe(II) and Mn(II) ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: A.32, V.33, S.34, H.102, T.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.33, A:S.34 Water bridges: A:T.106, A:T.106 Salt bridges: A:H.102 SO4.2: 3 residues within 4Å: Chain A: T.146, K.147, K.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.147 Water bridges: A:V.145, A:K.148 SO4.3: 4 residues within 4Å: Chain A: M.1, R.2 Chain B: K.64, D.121 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.2 Salt bridges: A:R.2 Water bridges: B:K.64 SO4.8: 5 residues within 4Å: Chain B: A.32, V.33, S.34, H.102, T.106 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.33, B:S.34 Water bridges: B:T.106, B:T.106 Salt bridges: B:H.102 SO4.9: 3 residues within 4Å: Chain A: K.64 Chain B: M.1, R.2 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.2 Salt bridges: B:R.2 Water bridges: A:K.64

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

MN.4: 7 residues within 4Å: Chain A: D.62, E.93, H.96, F.165, I.191, E.195 Ligands: MN.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.62, A:E.93, A:H.96, A:E.195, A:E.195 MN.5: 7 residues within 4Å: Chain A: Q.65, E.93, E.161, F.165, E.195, H.198 Ligands: MN.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.93, A:E.161, A:E.161, A:E.195, A:H.198 MN.6: 7 residues within 4Å: Chain B: D.62, E.93, H.96, F.165, I.191, E.195 Ligands: MN.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.62, B:D.62, B:E.93, B:H.96, B:E.195 MN.7: 7 residues within 4Å: Chain B: Q.65, E.93, E.161, F.165, E.195, H.198 Ligands: MN.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.93, B:E.93, B:E.161, B:E.195, B:H.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grave, K. et al., The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron. J.Biol.Inorg.Chem. (2020)

Release Date

2020-04-15

Peptides

Ribonucleoside-diphosphate reductase subunit beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase subunit beta

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