SMTL ID : 4jo0.1

Crystal Structure of CmlA, a diiron beta-hydroxylase from Streptomyces venezuelae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: H.307, H.309, E.379, D.405 Ligands: FE.2, O.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.307, A:H.309, A:E.379, A:D.405, O.3 FE.2: 7 residues within 4Å: Chain A: H.260, D.311, H.312, D.405 Ligands: FE.1, O.3, ACT.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:D.311, A:H.312, A:D.405, O.3, ACT.4 FE.9: 6 residues within 4Å: Chain B: H.307, H.309, E.379, D.405 Ligands: FE.10, O.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.307, B:H.309, B:E.379, B:D.405, O.11 FE.10: 7 residues within 4Å: Chain B: H.260, D.311, H.312, D.405 Ligands: FE.9, O.11, ACT.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:D.311, B:H.312, B:D.405, O.11, ACT.12

2 x O: OXYGEN ATOM(Non-covalent)

O.3: 9 residues within 4Å: Chain A: H.307, H.309, D.311, H.312, E.379, D.405 Ligands: FE.1, FE.2, ACT.4 No protein-ligand interaction detected (PLIP) O.11: 9 residues within 4Å: Chain B: H.307, H.309, D.311, H.312, E.379, D.405 Ligands: FE.9, FE.10, ACT.12 No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 10 residues within 4Å: Chain A: H.260, D.311, H.312, E.379, D.405, E.432, A.484, M.495 Ligands: FE.2, O.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.432 Salt bridges: A:H.260, A:H.312 ACT.12: 10 residues within 4Å: Chain B: H.260, D.311, H.312, E.379, D.405, E.432, A.484, M.495 Ligands: FE.10, O.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.432 Salt bridges: B:H.260, B:H.312

4 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: Y.151, A.152, S.153, Y.156 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.151, A:S.153, A:Y.156, H2O.5 K.6: 3 residues within 4Å: Chain A: S.368, R.394, G.396 No protein-ligand interaction detected (PLIP) K.13: 4 residues within 4Å: Chain B: Y.151, A.152, S.153, Y.156 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.151, B:S.153, B:Y.156, H2O.11 K.14: 3 residues within 4Å: Chain B: S.368, R.394, G.396 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: D.201, R.322, H.323, V.325, G.326, G.351, F.352, T.353 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.201, A:G.326, A:T.353 Water bridges: A:D.354 GOL.8: 12 residues within 4Å: Chain A: Y.257, H.260, V.482, Y.483, A.484, M.485, G.486, L.487, E.488, R.525, L.526, H.527 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.257, A:Y.257, A:M.485, A:L.487, A:E.488 GOL.15: 8 residues within 4Å: Chain B: D.201, R.322, H.323, V.325, G.326, G.351, F.352, T.353 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.201, B:G.326, B:T.353 Water bridges: B:D.354 GOL.16: 12 residues within 4Å: Chain B: Y.257, H.260, V.482, Y.483, A.484, M.485, G.486, L.487, E.488, R.525, L.526, H.527 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.257, B:Y.257, B:M.485, B:L.487, B:E.488

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makris, T.M. et al., Structure of a Dinuclear Iron Cluster-Containing beta-Hydroxylase Active in Antibiotic Biosynthesis. Biochemistry (2013)

Release Date

2013-09-11

Peptides

CmlA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CmlA