SMTL ID : 6qo9.1

Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis soaked with manganese ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 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 SO4.2: 3 residues within 4Å: Chain A: M.1, R.2 Ligands: BTB.4 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:K.64, B:K.64, B:K.64, A:M.1, A:M.1 Hydrogen bonds: A:R.2, A:R.2 SO4.3: 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, A:T.106, A:T.106 Salt bridges: A:H.102 SO4.8: 3 residues within 4Å: Chain B: M.1, R.2 Ligands: BTB.7 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.2, B:R.2 Water bridges: B:R.2, B:R.2, A:K.64, A:K.64 SO4.9: 5 residues within 4Å: Chain B: A.32, V.33, S.34, H.102, T.106 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.33, B:S.34, B:T.106 Water bridges: B:S.34, B:H.102, B:T.106 Salt bridges: B:H.102

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.4: 13 residues within 4Å: Chain A: V.75, H.76, L.77, E.78, K.83, P.143, E.144 Chain B: K.64, G.67, E.68, R.138, L.141 Ligands: SO4.2 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:L.77, A:K.83, A:P.143, B:K.64, B:E.68 Water bridges: A:V.75, B:R.138 Salt bridges: A:E.78 BTB.7: 12 residues within 4Å: Chain A: K.64, E.68, R.138, L.141 Chain B: V.75, H.76, L.77, E.78, K.83, P.143, E.144 Ligands: SO4.8 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.75, B:L.77, B:K.83, B:P.143 Water bridges: B:E.144, A:R.138 Salt bridges: B:E.78

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

MN.5: 7 residues within 4Å: Chain A: D.62, E.93, H.96, F.165, I.191, E.195 Ligands: MN.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.62, A:D.62, A:E.93, A:H.96, A:E.195 MN.6: 7 residues within 4Å: Chain A: Q.65, E.93, E.161, F.165, E.195, H.198 Ligands: MN.5 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.10: 7 residues within 4Å: Chain B: D.62, E.93, H.96, F.165, I.191, E.195 Ligands: MN.11 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.62, B:E.93, B:H.96, B:E.195, B:E.195 MN.11: 7 residues within 4Å: Chain B: Q.65, E.93, E.161, F.165, E.195, H.198 Ligands: MN.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.93, B:E.161, B:E.161, B:E.195, B:H.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grave, K. et al., Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access. J.Biol.Inorg.Chem. (2019)

Release Date

2019-08-21

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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