SMTL ID : 1nf6.5 (9 other biounits)

X-ray structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different catalytic states ("cycled" structure: reduced in solution and allowed to reoxidise before crystallisation)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.56, A:E.56, A:E.99, A:E.132, A:H.135 FE.5: 4 residues within 4Å: Chain B: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.56, B:E.99, B:E.132, B:H.135

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

SO4.2: 2 residues within 4Å: Chain A: N.4, R.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.5 SO4.3: 1 residues within 4Å: Chain A: K.114 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.114 SO4.6: 6 residues within 4Å: Chain B: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.162, B:T.164 Water bridges: B:T.164, B:T.164 Salt bridges: B:K.50

1 x FEC: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX(Non-covalent)

FEC.4: 22 residues within 4Å: Chain A: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, R.58, A.60, E.61, S.168, K.169 Chain B: R.20, Y.35, K.50, I.54, M.57, E.61, A.167, S.168 Ligands: SO4.6 20 PLIP interactions: 11 interactions with chain A, 9 interactions with chain B, Hydrophobic interactions: A:L.24, A:I.27, A:I.27, A:M.31, A:R.58, A:E.61, B:I.54, B:M.57, B:E.61 Hydrogen bonds: A:Y.35, A:K.169, B:S.168, B:S.168 Water bridges: A:R.20, A:N.32, B:T.164, B:T.164 Salt bridges: A:R.20, B:R.20, B:K.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Macedo, S. et al., The nature of the di-iron site in the bacterioferritin fromDesulfovibrio desulfuricans. NAT.STRUCT.BIOL. (2003)

Release Date

2003-04-01

Peptides

bacterioferritin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

bacterioferritin

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