SMTL ID : 4bmo.1

Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex with NrdI (1.8 A resolution)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

hetero-2-2-mer

Ligands

4 x FE2: FE (II) ION(Non-covalent)

FE2.1: 6 residues within 4Å: Chain A: D.62, E.93, H.96, F.165, E.195 Ligands: FE2.2 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 FE2.2: 5 residues within 4Å: Chain A: E.93, E.161, E.195, H.198 Ligands: FE2.1 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 FE2.9: 6 residues within 4Å: Chain C: D.62, E.93, H.96, F.165, E.195 Ligands: FE2.10 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 FE2.10: 5 residues within 4Å: Chain C: E.93, E.161, E.195, H.198 Ligands: FE2.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.93, C:E.161, C:E.161, C:E.195, C:H.198

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: S.196 Chain B: W.74 Ligands: FMN.8 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: T.63, K.64, G.67 Chain C: K.83 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: L.270, E.271 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: G.248, L.249, V.250 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: R.258, F.274, E.275 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: S.196 Chain D: W.74 Ligands: FMN.16 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: K.83 Chain C: T.63, K.64, G.67 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain C: L.270, E.271 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: G.248, L.249, V.250 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: R.258, F.274, E.275 Ligand excluded by PLIP

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.8: 25 residues within 4Å: Chain A: F.17, Q.20, I.197, V.200 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: CL.3 24 PLIP interactions: 20 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.74, A:F.17, A:Q.20, A:I.197, A:V.200 Hydrogen bonds: B:M.8, B:T.9, B:T.9, B:G.10, B:N.11, B:N.11, B:N.11, B:V.12, B:T.42, B:T.42, B:F.45, B:G.46, B:G.70, B:N.71, B:M.77, B:G.79, B:L.99 pi-Stacking: B:W.74, B:W.74 FMN.16: 25 residues within 4Å: Chain C: F.17, Q.20, I.197, V.200 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: CL.11 23 PLIP interactions: 19 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.74, C:F.17, C:Q.20, C:I.197, C:V.200 Hydrogen bonds: D:M.8, D:T.9, D:G.10, D:N.11, D:N.11, D:N.11, D:V.12, D:T.42, D:T.42, D:F.45, D:G.46, D:G.70, D:N.71, D:M.77, D:G.79, D:L.99 pi-Stacking: D:W.74, D:W.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hammerstad, M. et al., Crystal Structure of Bacillus Cereus Class Ib Ribonucleotide Reductase Di-Iron Nrdf in Complex with Nrdi. Acs Chem.Biol. (2014)

Release Date

2014-03-19

Peptides

RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETA: AC
NRDI: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETA

NRDI

Related Entries With Identical Sequence