SMTL ID : 4jyd.1

X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 9 residues within 4Å: Chain A: C.63, K.65, C.67, Y.69, C.70, R.73, G.109, E.110 Ligands: SAH.2 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.110 Metal complexes: A:C.63, A:C.67, A:C.70

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 18 residues within 4Å: Chain A: Y.69, C.70, Q.107, S.108, S.136, G.138, L.158, R.159, E.161, R.180, M.199, P.229, F.230, I.231, Y.303, L.305, Y.306 Ligands: SF4.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.107 Hydrogen bonds: A:R.159, A:E.161, A:I.231, A:I.231 Water bridges: A:Y.69, A:E.139, A:E.161, A:E.161, A:R.180, A:R.180 Salt bridges: A:R.180

1 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.3: 6 residues within 4Å: Chain A: V.97, Q.98, F.99, G.100, M.324 Ligands: 1N7.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.98, A:F.99 Hydrogen bonds: A:Q.98

4 x 1N7: CHAPSO(Non-covalent)

1N7.4: 8 residues within 4Å: Chain A: E.33, F.36, K.37, D.40, R.284, C.285 Ligands: 1N7.5, 1N7.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.33, A:F.36, A:R.284 Hydrogen bonds: A:D.40 Water bridges: A:E.33 1N7.5: 10 residues within 4Å: Chain A: R.29, E.33, F.36, F.246, T.247, L.250, V.275, I.281 Ligands: 1N7.4, 1N7.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.36, A:F.246, A:L.250, A:V.275 Hydrogen bonds: A:E.33, A:E.33, A:T.247 1N7.6: 3 residues within 4Å: Chain A: R.29 Ligands: 1N7.4, 1N7.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29, A:R.29 1N7.7: 5 residues within 4Å: Chain A: P.321, M.324, K.325, E.328 Ligands: CPS.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.324, A:K.325, A:E.328

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

FE.8: 4 residues within 4Å: Chain A: C.311, C.319 Ligands: H2S.9, H2S.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.311, A:C.319

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.9: 7 residues within 4Å: Chain A: R.279, C.311, C.319, C.322, V.323 Ligands: FE.8, H2S.10 No protein-ligand interaction detected (PLIP) H2S.10: 6 residues within 4Å: Chain A: C.311, E.314, C.319, C.322 Ligands: FE.8, H2S.9 No protein-ligand interaction detected (PLIP)

4 x BR: BROMIDE ION(Non-covalent)

BR.11: 3 residues within 4Å: Chain A: R.64, W.140, P.141 Ligand excluded by PLIP BR.12: 4 residues within 4Å: Chain A: R.54, T.103, T.134, R.155 Ligand excluded by PLIP BR.13: 5 residues within 4Å: Chain A: R.159, G.226, P.266, T.268, M.291 Ligand excluded by PLIP BR.14: 5 residues within 4Å: Chain A: R.159, T.268, T.269, A.270, Y.306 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicolet, Y. et al., X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-05-01

Peptides

FEFE-HYDROGENASE MATURASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

FEFE-HYDROGENASE MATURASE

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