SMTL ID : 4jxc.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 1.50 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: SAM.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.110 Metal complexes: A:C.63, A:C.67, A:C.70, SAM.2

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 17 residues within 4Å: Chain A: Y.69, C.70, Q.107, S.108, S.136, G.138, R.159, E.161, R.180, M.199, P.229, F.230, I.231, Y.303, L.305, Y.306 Ligands: SF4.1 13 PLIP interactions: 13 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:S.136, A:G.138, A:E.139, A:E.161, A:E.161, A:R.180, A:R.180 Salt bridges: A:R.180

5 x 1N7: CHAPSO(Non-covalent)

1N7.3: 7 residues within 4Å: Chain A: V.97, Q.98, F.99, G.100, M.324 Ligands: 1N7.7, IPA.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.98, A:F.99 Hydrogen bonds: A:Q.98 1N7.4: 7 residues within 4Å: Chain A: E.33, F.36, K.37, D.40, R.284 Ligands: 1N7.5, 1N7.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.36, A:R.284 Hydrogen bonds: A:D.40 Water bridges: A:E.33, A:K.37, A:R.284 1N7.5: 9 residues within 4Å: Chain A: R.29, E.33, F.246, T.247, L.250, V.275, I.281 Ligands: 1N7.4, 1N7.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.246, A:L.250, A:V.275, A:I.281, A:I.281 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: 3 residues within 4Å: Chain A: P.321, E.328 Ligands: 1N7.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.321, A:E.328

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: V.47, H.52, D.262, N.264, G.339, G.340, R.341, K.342 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.52, A:D.262, A:K.342, A:K.342 Water bridges: A:Y.46, A:V.47

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.9: 8 residues within 4Å: Chain A: R.279, P.292, C.311, C.319, C.322, V.323 Ligands: H2S.10, H2S.11 1 PLIP interactions: 1 interactions with chain A, Metal complexes: A:C.311

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.10: 4 residues within 4Å: Chain A: C.311, E.314, C.319 Ligands: FES.9 No protein-ligand interaction detected (PLIP) H2S.11: 5 residues within 4Å: Chain A: R.279, C.322, V.323, M.326 Ligands: FES.9 No protein-ligand interaction detected (PLIP)

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.12: 3 residues within 4Å: Chain A: G.100, K.102 Ligands: 1N7.3 No protein-ligand interaction detected (PLIP)

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

CL.13: 4 residues within 4Å: Chain A: R.54, T.103, T.134, R.155 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: R.159, T.268, T.269, A.270, Y.306 Ligand excluded by PLIP

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

SO4.15: 5 residues within 4Å: Chain A: D.337, W.338, G.339, G.340, K.342 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.337, A:W.338, A:G.339, A:G.340 Salt bridges: A:K.342

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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