SMTL ID : 3n3b.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

hetero-oligomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.67, E.98, H.101, E.158, E.192 Ligands: MN.2 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.53 MN.2: 5 residues within 4Å: Chain A: E.98, E.158, E.192, H.195 Ligands: MN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.98, A:E.158, A:E.192, A:H.195, H2O.55 MN.5: 6 residues within 4Å: Chain C: D.67, E.98, H.101, E.158, E.192 Ligands: MN.6 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.67, C:E.98, C:H.101, C:E.158, C:E.192, H2O.140 MN.6: 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.115

2 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.3: 6 residues within 4Å: Chain A: S.159, A.193, K.260, N.264 Chain B: N.103, N.105 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.260, A:K.260, B:N.103, B:N.105 Water bridges: A:S.159, A:Y.163, A:N.264 PEO.7: 6 residues within 4Å: Chain C: S.159, A.193, K.260, N.264 Chain D: N.103, N.105 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.260, C:K.260, C:N.264, D:N.103, D:N.105 Water bridges: C:Y.163, C:Y.163, C:N.264, C:N.264

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 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 23 PLIP interactions: 20 interactions with chain B, 3 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:S.101, B:N.103, B:A.109, B:G.111, B:L.131, A:R.25 Water bridges: B:N.33, B:S.101 pi-Stacking: B:F.106, B:F.106 FMN.8: 20 residues within 4Å: Chain C: 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 20 PLIP interactions: 17 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.69, 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:Y.69, D:G.70, D:S.101, D:N.103, D:A.109, D:G.111, D:L.131, C:R.25 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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