SMTL ID : 3hcr.1

Human Ferrochelatase with deuteroporphyrin and Ni Bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

FES.1: 6 residues within 4Å: Chain A: C.132, R.208, S.338, C.339, C.342, C.347 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.132, A:C.339, A:C.342, A:C.347 FES.9: 6 residues within 4Å: Chain B: C.132, R.208, S.338, C.339, C.342, C.347 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.132, B:C.339, B:C.342, B:C.347

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 6 residues within 4Å: Chain A: H.199, S.200, Q.238, S.239, W.246 Ligands: FDE.7 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.199 IMD.10: 5 residues within 4Å: Chain B: H.199, S.200, S.239, W.246 Ligands: FDE.15 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:H.199

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.3: 11 residues within 4Å: Chain A: L.37, R.50, R.51, P.202, S.204, G.242, P.243, M.244 Ligands: CHD.4, FDE.7, SO4.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.37, A:P.202, A:M.244 Hydrogen bonds: A:S.204, A:S.204 Water bridges: A:M.244 Salt bridges: A:R.50, A:R.51 CHD.4: 4 residues within 4Å: Chain A: L.37, P.38, L.43 Ligands: CHD.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.37, A:L.43 CHD.11: 10 residues within 4Å: Chain B: L.37, R.50, R.51, P.202, S.204, V.241, G.242, M.244 Ligands: CHD.12, FDE.15 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.37, B:P.202 Hydrogen bonds: B:S.204, B:S.204 Water bridges: B:M.244 Salt bridges: B:R.50, B:R.51 CHD.12: 2 residues within 4Å: Chain B: L.37 Ligands: CHD.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.37

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.5: 3 residues within 4Å: Chain A: Y.101, S.133 Ligands: FDE.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.101, A:S.133 OXY.14: 4 residues within 4Å: Chain B: M.12, Y.101, S.133 Ligands: FDE.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.101, B:Y.101

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

CL.6: 4 residues within 4Å: Chain A: R.263 Chain B: T.336, S.338, K.351 Ligand excluded by PLIP

2 x FDE: FE(III) DEUTEROPORPHYRIN IX(Non-covalent)

FDE.7: 22 residues within 4Å: Chain A: M.12, L.25, L.28, F.29, L.34, R.51, I.55, Y.59, S.133, T.134, H.199, L.201, P.202, Y.212, V.241, W.246, F.273, H.277, I.278 Ligands: IMD.2, CHD.3, OXY.5 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:L.25, A:L.28, A:F.29, A:L.34, A:I.55, A:T.134, A:H.199, A:P.202, A:Y.212, A:W.246, A:F.273 Hydrogen bonds: A:Y.59, A:I.278 Water bridges: A:S.239 Salt bridges: A:R.51, A:H.199 FDE.15: 22 residues within 4Å: Chain B: M.12, L.25, L.28, F.29, L.34, R.51, I.55, Y.59, S.133, T.134, H.199, L.201, P.202, Y.212, V.241, W.246, F.273, H.277, I.278 Ligands: IMD.10, CHD.11, OXY.14 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:L.25, B:L.28, B:F.29, B:L.34, B:I.55, B:T.134, B:H.199, B:L.201, B:P.202, B:Y.212, B:F.273 Hydrogen bonds: B:Y.59, B:I.278 Water bridges: B:S.239, B:S.239, B:H.277 Salt bridges: B:R.51, B:H.199 pi-Stacking: B:W.246

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

SO4.8: 5 residues within 4Å: Chain A: R.51, K.54, V.241, G.242 Ligands: CHD.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.242 Salt bridges: A:R.51, A:K.54 SO4.16: 3 residues within 4Å: Chain B: R.51, K.54, G.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.242 Salt bridges: B:R.51, B:K.54

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain A: P.213, S.217, W.237, L.247 Chain B: P.213, S.217, W.237 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.217, B:S.217, B:S.217 Water bridges: A:W.237, A:W.237, B:Q.214, B:W.237, B:W.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medlock, A.E. et al., Product release rather than chelation determines metal specificity for ferrochelatase. J.Mol.Biol. (2009)

Release Date

2009-11-10

Peptides

Ferrochelatase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ferrochelatase, mitochondrial

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