SMTL ID : 3n3a.1

Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-oligomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.98, E.158, E.192, H.195 Ligands: MN.2 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.98, A:E.158, A:E.192, A:E.192, A:H.195, H2O.108 MN.2: 6 residues within 4Å: Chain A: D.67, E.98, H.101, E.158, E.192 Ligands: MN.1 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.67, A:E.98, A:H.101, A:E.158, A:E.192, H2O.109 MN.4: 5 residues within 4Å: Chain C: E.98, E.158, E.192, H.195 Ligands: MN.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.98, C:E.158, C:E.192, C:H.195, H2O.227 MN.5: 6 residues within 4Å: Chain C: D.67, E.98, H.101, E.158, E.192 Ligands: MN.4 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.67, C:E.98, C:H.101, C:E.192, H2O.240

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 22 residues within 4Å: Chain A: E.21, R.25, Y.197 Chain B: S.28, S.29, S.31, E.32, N.33, T.34, P.67, S.68, Y.69, G.70, G.71, S.101, G.102, N.103, F.106, A.109, Y.110, G.111, L.131 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.69, B:Y.69, A:R.25, A:Y.197 Hydrogen bonds: B:S.29, B:N.33, B:N.33, B:T.34, B:T.34, B:S.68, B:S.68, B:Y.69, B:G.70, B:N.103, B:A.109, B:G.111, B:L.131, B:L.131 Water bridges: B:S.101 pi-Stacking: B:F.106, B:F.106 FMN.6: 21 residues within 4Å: Chain C: E.21, R.25, Y.197 Chain D: S.28, S.29, S.31, E.32, N.33, T.34, P.67, S.68, Y.69, G.70, S.101, G.102, N.103, F.106, A.109, Y.110, G.111, L.131 21 PLIP interactions: 18 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.69, D:Y.69, C:E.21, C:R.25, C:Y.197 Hydrogen bonds: D:S.29, D:N.33, D:N.33, D:T.34, D:S.68, D:S.68, D:Y.69, D:G.70, D:N.103, D:A.109, D:G.111, D:L.131, D:L.131 Water bridges: D:S.101 pi-Stacking: D:F.106, D:F.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boal, A.K. et al., Structural basis for activation of class Ib ribonucleotide reductase. Science (2010)

Release Date

2010-08-18

Peptides

Ribonucleoside-diphosphate reductase 2 subunit beta: AC
Protein nrdI: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
A

B
C

D
D

Ribonucleoside-diphosphate reductase 2 subunit beta

Protein nrdI

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