SMTL ID : 7mmr.1 (3 other biounits)

Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-NrdI complex from Aerococcus urinae in Oxidized Form with Cu(I) bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

2 x CU1: COPPER (I) ION(Non-covalent)

CU1.1: 3 residues within 4Å: Chain A: V.116, P.176, H.213 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.213, H2O.3, H2O.4 CU1.2: 4 residues within 4Å: Chain A: W.63, T.75, C.131, Q.135 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.75, A:C.131

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: E.39, N.42, R.43 Chain B: Y.50, S.51, G.52 Ligands: FMN.4 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.51, A:E.39, A:R.43, A:R.43

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 23 residues within 4Å: Chain A: R.43, F.215 Chain B: S.9, T.10, S.12, N.13, N.14, T.15, P.48, T.49, Y.50, S.51, G.52, G.53, G.91, N.92, F.95, S.98, F.99, A.100, L.120 Ligands: GOL.3, CA.5 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.50, B:Y.50, A:R.43, A:F.215 Hydrogen bonds: B:T.10, B:S.12, B:N.14, B:N.14, B:T.15, B:T.15, B:T.49, B:T.49, B:S.51, B:G.52, B:G.53, B:N.92, B:S.98, B:A.100, B:L.120, B:L.120 Water bridges: B:S.90 pi-Stacking: B:F.95, B:F.95

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: F.215, N.282 Chain B: N.92, L.120 Ligands: FMN.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palowitch, G.M. et al., Ribonucleotide Reductase. To be published

Release Date

2022-05-04

Peptides

Ribonucleoside-diphosphate reductase: A
Protein NrdI: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Ribonucleoside-diphosphate reductase

Protein NrdI

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