SMTL ID : 7mmr.3 (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 Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

3 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: 2 residues within 4Å: Chain A: H.256, A.265 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.256 CU1.5: 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: 8 residues within 4Å: Chain A: Y.6, S.11, R.25, S.100, L.101, T.102, E.103, Q.106 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.11, A:S.11, A:R.25, A:R.25, A:S.100, A:Q.106 Water bridges: A:S.11

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 6 residues within 4Å: Chain A: W.63, N.64, Q.71, L.130, T.132, Q.135 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.64, A:Q.71, A:Q.135, A:Q.135

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 1 residues within 4Å: Chain A: E.299 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.299 CA.7: 3 residues within 4Å: Chain A: G.263, D.266, E.267 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:G.263, A:D.266, A:D.266, A:E.267 CA.8: 2 residues within 4Å: Chain A: E.52, R.121 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.52, A:E.52 CA.10: 6 residues within 4Å: Chain A: V.211, F.215, N.282 Chain B: N.92, L.120 Ligands: FMN.9 No protein-ligand interaction detected (PLIP)

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.9: 22 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: CA.10 24 PLIP interactions: 22 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.15, B:T.49, B:T.49, B:Y.50, B:S.51, B:G.52, B:G.53, B:N.92, B:S.98, B:A.100, B:L.120 Water bridges: B:S.90 pi-Stacking: B:F.95, B:F.95

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
C

B
G

Ribonucleoside-diphosphate reductase

Protein NrdI

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