SMTL ID : 7z3e.1

XFEL structure of Class Ib ribonucleotide reductase dimanganese(II) NrdF in complex with hydroquinone NrdI from Bacillus cereus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.62, E.93, H.96, F.165, E.195 Ligands: MN.2 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.2: 5 residues within 4Å: Chain A: E.93, E.161, E.195, H.198 Ligands: MN.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.93, A:E.93, A:E.161, A:E.195, A:H.198 MN.5: 6 residues within 4Å: Chain C: D.62, E.93, H.96, F.165, E.195 Ligands: MN.6 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.62, C:E.93, C:H.96, C:E.195, C:E.195 MN.6: 5 residues within 4Å: Chain C: E.93, E.161, E.195, H.198 Ligands: MN.5 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.93, C:E.93, C:E.161, C:E.195, C:H.198

2 x FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)

FNR.3: 23 residues within 4Å: Chain A: F.17, Q.20 Chain B: S.7, M.8, T.9, G.10, N.11, V.12, Y.41, T.42, T.43, G.44, F.45, G.46, S.69, G.70, N.71, W.74, M.77, F.78, G.79, L.99 Ligands: UNX.4 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.74, A:F.17, A:Q.20 Hydrogen bonds: B:M.8, B:T.9, B:T.9, B:T.9, B:N.11, B:N.11, B:V.12, B:T.42, B:T.42, B:G.44, B:G.46, B:N.71, B:M.77, B:G.79, B:L.99, B:L.99 pi-Stacking: B:W.74, B:W.74 FNR.7: 23 residues within 4Å: Chain C: F.17, Q.20 Chain D: S.7, M.8, T.9, G.10, N.11, V.12, Y.41, T.42, T.43, G.44, F.45, G.46, S.69, G.70, N.71, W.74, M.77, F.78, G.79, L.99 Ligands: UNX.8 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.74, C:F.17, C:Q.20 Hydrogen bonds: D:M.8, D:T.9, D:T.9, D:N.11, D:N.11, D:V.12, D:T.42, D:T.42, D:G.44, D:G.46, D:N.71, D:M.77, D:G.79, D:L.99, D:L.99 pi-Stacking: D:W.74, D:W.74

2 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 3 residues within 4Å: Chain A: V.200 Chain B: N.71 Ligands: FNR.3 No protein-ligand interaction detected (PLIP) UNX.8: 3 residues within 4Å: Chain C: V.200 Chain D: N.71 Ligands: FNR.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

John, J. et al., Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b-NrdI complex monitored by serial femtosecond crystallography. Elife (2022)

Release Date

2022-09-21

Peptides

Ribonucleoside-diphosphate reductase subunit beta: AC
Protein NrdI: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Ribonucleoside-diphosphate reductase subunit beta

Protein NrdI

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