SMTL ID : 1nf6.2 (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-24-mer

Ligands

24 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 FE.8: 4 residues within 4Å: Chain C: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.56, C:E.56, C:E.99, C:E.132, C:H.135 FE.10: 4 residues within 4Å: Chain D: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.56, D:E.56, D:E.99, D:E.132, D:H.135 FE.15: 4 residues within 4Å: Chain E: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.56, E:E.56, E:E.99, E:E.132, E:H.135 FE.20: 4 residues within 4Å: Chain F: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.56, F:E.56, F:E.99, F:E.132, F:H.135 FE.23: 4 residues within 4Å: Chain G: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.56, G:E.99, G:E.132, G:H.135 FE.26: 4 residues within 4Å: Chain H: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.56, H:E.99, H:E.132, H:H.135 FE.29: 4 residues within 4Å: Chain I: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.56, I:E.56, I:E.99, I:E.132, I:H.135 FE.33: 4 residues within 4Å: Chain J: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.56, J:E.99, J:E.132, J:H.135 FE.36: 4 residues within 4Å: Chain K: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.56, K:E.56, K:E.99, K:E.132, K:H.135 FE.38: 4 residues within 4Å: Chain L: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.56, L:E.56, L:E.99, L:E.132, L:H.135 FE.43: 4 residues within 4Å: Chain M: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.56, M:E.56, M:E.99, M:E.132, M:H.135 FE.48: 4 residues within 4Å: Chain N: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.56, N:E.56, N:E.99, N:E.132, N:H.135 FE.51: 4 residues within 4Å: Chain O: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:E.56, O:E.99, O:E.132, O:H.135 FE.54: 4 residues within 4Å: Chain P: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:E.56, P:E.99, P:E.132, P:H.135 FE.57: 4 residues within 4Å: Chain Q: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:E.56, Q:E.56, Q:E.99, Q:E.132, Q:H.135 FE.61: 4 residues within 4Å: Chain R: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:E.56, R:E.99, R:E.132, R:H.135 FE.64: 4 residues within 4Å: Chain S: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.56, S:E.56, S:E.99, S:E.132, S:H.135 FE.66: 4 residues within 4Å: Chain T: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.56, T:E.56, T:E.99, T:E.132, T:H.135 FE.71: 4 residues within 4Å: Chain U: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:E.56, U:E.56, U:E.99, U:E.132, U:H.135 FE.76: 4 residues within 4Å: Chain V: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.56, V:E.56, V:E.99, V:E.132, V:H.135 FE.79: 4 residues within 4Å: Chain W: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:E.56, W:E.99, W:E.132, W:H.135 FE.82: 4 residues within 4Å: Chain X: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:E.56, X:E.99, X:E.132, X:H.135

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

SO4.2: 2 residues within 4Å: Chain A: N.4, R.5 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: K.114 Chain I: K.114 Chain Q: K.114 Ligands: SO4.31, SO4.59 Ligand excluded by PLIP SO4.6: 6 residues within 4Å: Chain B: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.4 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain C: K.114 Chain W: K.114 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain C: K.50, S.163, T.164 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain D: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.13 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain D: S.144, N.148 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain D: K.114 Chain E: K.114 Chain H: K.114 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain E: K.50, T.164, G.165 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain E: N.4, R.5 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain E: S.144, N.148 Ligand excluded by PLIP SO4.21: 6 residues within 4Å: Chain F: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.19 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain F: K.114 Chain N: K.114 Chain V: K.114 Ligands: SO4.50, SO4.78 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain G: K.50, S.163, T.164, G.165 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain H: K.50, S.163, T.164, G.165 Ligands: FEC.25 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain I: N.4, R.5 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain A: K.114 Chain I: K.114 Chain Q: K.114 Ligands: SO4.3, SO4.59 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain J: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.32 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain G: K.114 Chain K: K.114 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain K: K.50, S.163, T.164 Ligand excluded by PLIP SO4.39: 6 residues within 4Å: Chain L: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.41 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain L: S.144, N.148 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain L: K.114 Chain M: K.114 Chain P: K.114 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain M: K.50, T.164, G.165 Ligand excluded by PLIP SO4.45: 2 residues within 4Å: Chain M: N.4, R.5 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain M: S.144, N.148 Ligand excluded by PLIP SO4.49: 6 residues within 4Å: Chain N: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.47 Ligand excluded by PLIP SO4.50: 5 residues within 4Å: Chain F: K.114 Chain N: K.114 Chain V: K.114 Ligands: SO4.22, SO4.78 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain O: K.50, S.163, T.164, G.165 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain P: K.50, S.163, T.164, G.165 Ligands: FEC.53 Ligand excluded by PLIP SO4.58: 2 residues within 4Å: Chain Q: N.4, R.5 Ligand excluded by PLIP SO4.59: 5 residues within 4Å: Chain A: K.114 Chain I: K.114 Chain Q: K.114 Ligands: SO4.3, SO4.31 Ligand excluded by PLIP SO4.62: 6 residues within 4Å: Chain R: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.60 Ligand excluded by PLIP SO4.63: 2 residues within 4Å: Chain O: K.114 Chain S: K.114 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain S: K.50, S.163, T.164 Ligand excluded by PLIP SO4.67: 6 residues within 4Å: Chain T: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.69 Ligand excluded by PLIP SO4.68: 2 residues within 4Å: Chain T: S.144, N.148 Ligand excluded by PLIP SO4.70: 3 residues within 4Å: Chain T: K.114 Chain U: K.114 Chain X: K.114 Ligand excluded by PLIP SO4.72: 3 residues within 4Å: Chain U: K.50, T.164, G.165 Ligand excluded by PLIP SO4.73: 2 residues within 4Å: Chain U: N.4, R.5 Ligand excluded by PLIP SO4.74: 2 residues within 4Å: Chain U: S.144, N.148 Ligand excluded by PLIP SO4.77: 6 residues within 4Å: Chain V: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.75 Ligand excluded by PLIP SO4.78: 5 residues within 4Å: Chain F: K.114 Chain N: K.114 Chain V: K.114 Ligands: SO4.22, SO4.50 Ligand excluded by PLIP SO4.80: 4 residues within 4Å: Chain W: K.50, S.163, T.164, G.165 Ligand excluded by PLIP SO4.83: 5 residues within 4Å: Chain X: K.50, S.163, T.164, G.165 Ligands: FEC.81 Ligand excluded by PLIP

12 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 FEC.13: 22 residues within 4Å: Chain C: R.20, H.28, M.31, Y.35, K.50, I.54, M.57, R.58, E.61 Chain D: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.11 16 PLIP interactions: 9 interactions with chain D, 7 interactions with chain C, Hydrophobic interactions: D:I.27, D:M.31, D:E.61, C:M.31, C:I.54, C:M.57, C:R.58 Hydrogen bonds: D:S.168, D:S.168, D:K.169, C:Y.35 Water bridges: D:T.164, C:N.32 Salt bridges: D:R.20, D:K.50, C:R.20 FEC.19: 22 residues within 4Å: Chain E: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168, K.169 Chain F: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168, K.169 Ligands: SO4.21 21 PLIP interactions: 11 interactions with chain F, 10 interactions with chain E, Hydrophobic interactions: F:I.27, F:M.31, F:E.61, E:I.27, E:M.31, E:M.57, E:E.61 Hydrogen bonds: F:Y.35, F:T.164, F:S.168, F:S.168, F:K.169, E:Y.35, E:K.169 Water bridges: F:R.20, E:R.20, E:N.32 Salt bridges: F:R.20, F:K.50, E:R.20, E:H.28 FEC.25: 23 residues within 4Å: Chain G: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, R.58, E.61, A.167, S.168, K.169 Chain H: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168 Ligands: SO4.27 16 PLIP interactions: 8 interactions with chain H, 8 interactions with chain G, Hydrophobic interactions: H:I.27, H:E.61, G:I.27, G:M.31, G:I.54, G:R.58, G:E.61 Hydrogen bonds: H:S.168, H:S.168, G:Y.35, G:K.169 Water bridges: H:N.32, H:T.164 Salt bridges: H:R.20, H:K.50, G:R.20 FEC.32: 22 residues within 4Å: Chain I: 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 J: R.20, Y.35, K.50, I.54, M.57, E.61, A.167, S.168 Ligands: SO4.34 20 PLIP interactions: 9 interactions with chain J, 11 interactions with chain I, Hydrophobic interactions: J:I.54, J:M.57, J:E.61, I:L.24, I:I.27, I:I.27, I:M.31, I:R.58, I:E.61 Hydrogen bonds: J:S.168, J:S.168, I:Y.35, I:K.169 Water bridges: J:T.164, J:T.164, I:R.20, I:N.32 Salt bridges: J:R.20, J:K.50, I:R.20 FEC.41: 22 residues within 4Å: Chain K: R.20, H.28, M.31, Y.35, K.50, I.54, M.57, R.58, E.61 Chain L: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.39 16 PLIP interactions: 7 interactions with chain K, 9 interactions with chain L, Hydrophobic interactions: K:M.31, K:I.54, K:M.57, K:R.58, L:I.27, L:M.31, L:E.61 Hydrogen bonds: K:Y.35, L:Y.35, L:S.168, L:S.168, L:K.169 Water bridges: K:N.32 Salt bridges: K:R.20, L:R.20, L:K.50 FEC.47: 22 residues within 4Å: Chain M: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168, K.169 Chain N: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168, K.169 Ligands: SO4.49 22 PLIP interactions: 11 interactions with chain N, 11 interactions with chain M, Hydrophobic interactions: N:I.27, N:M.31, N:E.61, M:I.27, M:M.31, M:M.57, M:E.61 Hydrogen bonds: N:Y.35, N:T.164, N:S.168, N:S.168, N:K.169, M:Y.35, M:Y.35, M:K.169 Water bridges: N:R.20, M:R.20, M:N.32 Salt bridges: N:R.20, N:K.50, M:R.20, M:H.28 FEC.53: 23 residues within 4Å: Chain O: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, R.58, E.61, A.167, S.168, K.169 Chain P: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168 Ligands: SO4.55 17 PLIP interactions: 8 interactions with chain P, 9 interactions with chain O, Hydrophobic interactions: P:I.27, P:E.61, O:I.27, O:M.31, O:I.54, O:R.58, O:E.61 Hydrogen bonds: P:Y.35, P:S.168, P:S.168, O:Y.35, O:Y.35, O:K.169 Water bridges: P:N.32 Salt bridges: P:R.20, P:K.50, O:R.20 FEC.60: 22 residues within 4Å: Chain Q: 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 R: R.20, Y.35, K.50, I.54, M.57, E.61, A.167, S.168 Ligands: SO4.62 19 PLIP interactions: 8 interactions with chain R, 11 interactions with chain Q, Hydrophobic interactions: R:I.54, R:M.57, R:E.61, Q:L.24, Q:I.27, Q:I.27, Q:M.31, Q:R.58, Q:E.61 Hydrogen bonds: R:Y.35, R:S.168, R:S.168, Q:Y.35, Q:K.169 Salt bridges: R:R.20, R:K.50, Q:R.20 Water bridges: Q:R.20, Q:N.32 FEC.69: 22 residues within 4Å: Chain S: R.20, H.28, M.31, Y.35, K.50, I.54, M.57, R.58, E.61 Chain T: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.67 17 PLIP interactions: 8 interactions with chain S, 9 interactions with chain T, Hydrophobic interactions: S:M.31, S:I.54, S:M.57, S:R.58, T:I.27, T:M.31, T:E.61 Hydrogen bonds: S:Y.35, S:Y.35, T:Y.35, T:S.168, T:S.168, T:K.169 Water bridges: S:N.32 Salt bridges: S:R.20, T:R.20, T:K.50 FEC.75: 22 residues within 4Å: Chain U: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168, K.169 Chain V: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168, K.169 Ligands: SO4.77 22 PLIP interactions: 11 interactions with chain U, 11 interactions with chain V, Hydrophobic interactions: U:I.27, U:M.31, U:M.57, U:E.61, V:I.27, V:M.31, V:E.61 Hydrogen bonds: U:Y.35, U:Y.35, U:K.169, V:Y.35, V:T.164, V:S.168, V:S.168, V:K.169 Water bridges: U:R.20, U:N.32, V:R.20 Salt bridges: U:R.20, U:H.28, V:R.20, V:K.50 FEC.81: 23 residues within 4Å: Chain W: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, R.58, E.61, A.167, S.168, K.169 Chain X: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168 Ligands: SO4.83 16 PLIP interactions: 8 interactions with chain W, 8 interactions with chain X, Hydrophobic interactions: W:I.27, W:M.31, W:I.54, W:R.58, W:E.61, X:I.27, X:E.61 Hydrogen bonds: W:Y.35, W:K.169, X:Y.35, X:S.168, X:S.168 Salt bridges: W:R.20, X:R.20, X:K.50 Water bridges: X:N.32

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.28: 7 residues within 4Å: Chain E: E.104 Chain H: R.5, R.8, K.9, V.12, G.117, D.118 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:R.5, H:R.5, H:D.118, H:D.118 GOL.56: 7 residues within 4Å: Chain M: E.104 Chain P: R.5, R.8, K.9, V.12, G.117, D.118 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:R.5, P:R.5, P:D.118 GOL.84: 7 residues within 4Å: Chain U: E.104 Chain X: R.5, R.8, K.9, V.12, G.117, D.118 4 PLIP interactions: 4 interactions with chain X Hydrogen bonds: X:R.5, X:R.5, X:D.118, X:D.118

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: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

E
K

F
L

G
O

H
P

I
C

J
D

K
E

L
F

M
K

N
L

O
O

P
P

Q
C

R
D

S
E

T
F

U
K

V
L

W
O

X
P

bacterioferritin

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