SMTL ID : 5ci1.1

Ribonucleotide reductase Y122 2,3-F2Y variant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x FEO: MU-OXO-DIIRON(Covalent)

FEO.1: 9 residues within 4Å: Chain A: D.84, Q.87, W.111, E.115, H.118, E.204, I.234, E.238, H.241 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.84, A:E.115, A:E.115, A:H.118, A:E.204, A:E.238, A:H.241, H2O.2, H2O.4 FEO.8: 9 residues within 4Å: Chain B: D.84, Q.87, W.111, E.115, H.118, E.204, I.234, E.238, H.241 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.84, B:E.115, B:E.115, B:H.118, B:E.204, B:E.238, B:H.241, H2O.10, H2O.12

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: G.294, S.295, N.300 Chain B: P.66, E.67, H.68 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.295, A:S.295, B:E.67 Water bridges: A:N.300, B:H.68 SO4.3: 6 residues within 4Å: Chain A: R.221, L.223, I.297 Chain B: R.221, I.297 Ligands: SO4.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.221, A:R.221 SO4.4: 4 residues within 4Å: Chain A: Q.145, K.148, R.149, D.285 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.148, A:K.148, A:D.285 Salt bridges: A:K.148, A:R.149 SO4.5: 4 residues within 4Å: Chain A: R.236, S.341, D.342, N.343 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.341, A:D.342, A:N.343 Salt bridges: A:R.236 SO4.9: 6 residues within 4Å: Chain A: P.66, E.67, H.68 Chain B: G.294, S.295, N.300 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.67, B:S.295, B:S.295 Water bridges: A:H.68, B:N.300 SO4.10: 6 residues within 4Å: Chain A: R.221, I.297 Chain B: R.221, L.223, I.297 Ligands: SO4.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.221, A:R.221 SO4.11: 4 residues within 4Å: Chain B: Q.145, K.148, R.149, D.285 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.148, B:K.148, B:D.285 Salt bridges: B:K.148, B:R.149 SO4.12: 4 residues within 4Å: Chain B: R.236, S.341, D.342, N.343 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.341, B:D.342, B:D.342, B:N.343 Salt bridges: B:R.236

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

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.253, G.320 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: R.253, G.320 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oyala, P.H. et al., Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example. J.Am.Chem.Soc. (2016)

Release Date

2016-06-22

Peptides

Ribonucleoside-diphosphate reductase 1, beta subunit, ferritin-like protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribonucleoside-diphosphate reductase 1, beta subunit, ferritin-like protein

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