SMTL ID : 1bvb.1

HEME-PACKING MOTIFS REVEALED BY THE CRYSTAL STRUCTURE OF CYTOCHROME C554 FROM NITROSOMONAS EUROPAEA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 1 residues within 4Å: Chain A: K.193 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.193, A:K.193 Salt bridges: A:K.193 PO4.2: 4 residues within 4Å: Chain A: V.38, K.39, K.40, E.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.39, A:K.40, A:E.41 PO4.3: 2 residues within 4Å: Chain A: L.184, E.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.185

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.4: 22 residues within 4Å: Chain A: K.10, C.11, C.14, H.15, C.88, H.92, G.95, F.98, R.99, H.102, R.103, G.106, R.118, Q.126, F.128, L.184, E.185, G.186, V.187, H.197, K.211 Ligands: HEM.6 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:K.10, A:H.92, A:F.98, A:R.99, A:H.102, A:R.103, A:L.184, A:V.187, A:K.211 Hydrogen bonds: A:E.185, A:G.186, A:V.187 Salt bridges: A:R.118, A:H.197 pi-Stacking: A:F.98 Metal complexes: A:H.15, A:H.102 HEM.5: 22 residues within 4Å: Chain A: S.33, L.34, K.39, A.42, K.43, L.48, Y.54, D.59, C.60, C.63, H.64, C.137, H.138, N.140, P.152, Y.153, T.154, P.155, F.156, K.163, Y.164 Ligands: HEM.7 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:L.34, A:K.39, A:K.43, A:L.48, A:Y.54, A:Y.54, A:N.140, A:P.152, A:P.155, A:F.156, A:F.156, A:F.156, A:Y.164 Hydrogen bonds: A:Y.164, A:Y.164 Salt bridges: A:K.39, A:H.138, A:K.163 pi-Cation interactions: A:H.64 Metal complexes: A:H.64 HEM.6: 23 residues within 4Å: Chain A: C.11, S.12, H.15, Q.18, A.19, W.22, H.27, V.86, G.87, C.88, C.91, H.92, F.130, M.178, H.179, E.180, H.181, Y.182, L.184, F.194, H.197, F.200 Ligands: HEM.4 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:H.15, A:Q.18, A:Q.18, A:A.19, A:W.22, A:F.130, A:L.184, A:F.194, A:F.200 Hydrogen bonds: A:Q.18, A:Y.182 Water bridges: A:H.181 Salt bridges: A:H.179, A:H.181, A:H.197 pi-Stacking: A:H.92, A:H.92, A:H.92, A:H.179 Metal complexes: A:H.92, A:H.179 HEM.7: 21 residues within 4Å: Chain A: A.26, H.27, A.30, S.33, K.39, C.63, H.64, V.65, V.86, S.90, R.133, C.134, C.137, H.138, F.166, F.168, M.171, V.172, A.177, M.178 Ligands: HEM.5 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:V.86, A:F.166, A:F.168, A:V.172, A:A.177 Hydrogen bonds: A:A.30, A:S.33 Water bridges: A:S.33, A:S.33, A:K.39 Salt bridges: A:K.39, A:H.64 Metal complexes: A:H.27, A:H.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iverson, T.M. et al., Heme packing motifs revealed by the crystal structure of the tetra-heme cytochrome c554 from Nitrosomonas europaea. Nat.Struct.Biol. (1998)

Release Date

1999-05-18

Peptides

CYTOCHROME C-554: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CYTOCHROME C-554

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