SMTL ID : 1nf6.1 (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.6: 4 residues within 4Å: Chain B: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.56, B:E.99, B:E.132, 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.12: 4 residues within 4Å: Chain D: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.56, D:E.99, D:E.132, D:H.135 FE.16: 4 residues within 4Å: Chain E: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain E Metal complexes: 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 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.56, G:E.56, G:E.99, G:E.132, G:H.135 FE.28: 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.32: 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.37: 4 residues within 4Å: Chain J: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.56, J:E.99, J:E.132, J:E.132, J:H.135 FE.39: 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.43: 4 residues within 4Å: Chain L: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:E.56, L:E.99, L:E.132, L:H.135 FE.47: 4 residues within 4Å: Chain M: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:E.56, M:E.99, M:E.132, M:H.135 FE.51: 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.54: 4 residues within 4Å: Chain O: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.56, O:E.56, O:E.99, O:E.132, O:H.135 FE.59: 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.63: 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.68: 4 residues within 4Å: Chain R: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.56, R:E.99, R:E.132, R:E.132, R:H.135 FE.70: 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.74: 4 residues within 4Å: Chain T: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:E.56, T:E.99, T:E.132, T:H.135 FE.78: 4 residues within 4Å: Chain U: E.56, E.99, E.132, H.135 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:E.56, U:E.99, U:E.132, U:H.135 FE.82: 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.85: 4 residues within 4Å: Chain W: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:E.56, W:E.56, W:E.99, W:E.132, W:H.135 FE.90: 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

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

SO4.2: 5 residues within 4Å: Chain A: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: S.144, N.148 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: K.114 Chain I: K.114 Chain Q: K.114 Ligands: SO4.35, SO4.66 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: E.61 Chain B: K.50, S.163, T.164 Ligands: FEC.5 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain C: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain C: S.144, N.148 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain D: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain D: N.4, R.5 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain D: K.114 Chain E: K.114 Chain W: K.114 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain E: K.50, S.163, T.164, G.165 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain E: N.4, R.5 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain F: K.50, 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: SO4.53, SO4.84 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain G: K.50, S.163, T.164, G.165 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain G: N.4, R.5 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain G: S.144, K.147, N.148 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: K.114 Chain C: K.114 Chain H: K.114 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain G: E.61 Chain H: K.50, S.162, S.163, T.164 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain H: N.4, R.5 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain I: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain I: S.144, N.148 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain A: K.114 Chain I: K.114 Chain Q: K.114 Ligands: SO4.4, SO4.66 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain I: E.61 Chain J: K.50, S.163, T.164 Ligands: FEC.36 Ligand excluded by PLIP SO4.40: 5 residues within 4Å: Chain K: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain K: S.144, N.148 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain L: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.45: 2 residues within 4Å: Chain L: N.4, R.5 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain G: K.114 Chain L: K.114 Chain M: K.114 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain M: K.50, S.163, T.164, G.165 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain M: N.4, R.5 Ligand excluded by PLIP SO4.52: 5 residues within 4Å: Chain N: K.50, S.163, T.164, G.165 Ligands: FEC.50 Ligand excluded by PLIP SO4.53: 5 residues within 4Å: Chain F: K.114 Chain N: K.114 Chain V: K.114 Ligands: SO4.22, SO4.84 Ligand excluded by PLIP SO4.55: 4 residues within 4Å: Chain O: K.50, S.163, T.164, G.165 Ligand excluded by PLIP SO4.56: 2 residues within 4Å: Chain O: N.4, R.5 Ligand excluded by PLIP SO4.57: 3 residues within 4Å: Chain O: S.144, K.147, N.148 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain J: K.114 Chain K: K.114 Chain P: K.114 Ligand excluded by PLIP SO4.60: 5 residues within 4Å: Chain O: E.61 Chain P: K.50, S.162, S.163, T.164 Ligand excluded by PLIP SO4.61: 2 residues within 4Å: Chain P: N.4, R.5 Ligand excluded by PLIP SO4.64: 5 residues within 4Å: Chain Q: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.65: 2 residues within 4Å: Chain Q: S.144, N.148 Ligand excluded by PLIP SO4.66: 5 residues within 4Å: Chain A: K.114 Chain I: K.114 Chain Q: K.114 Ligands: SO4.4, SO4.35 Ligand excluded by PLIP SO4.69: 5 residues within 4Å: Chain Q: E.61 Chain R: K.50, S.163, T.164 Ligands: FEC.67 Ligand excluded by PLIP SO4.71: 5 residues within 4Å: Chain S: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.72: 2 residues within 4Å: Chain S: S.144, N.148 Ligand excluded by PLIP SO4.75: 5 residues within 4Å: Chain T: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.76: 2 residues within 4Å: Chain T: N.4, R.5 Ligand excluded by PLIP SO4.77: 3 residues within 4Å: Chain O: K.114 Chain T: K.114 Chain U: K.114 Ligand excluded by PLIP SO4.79: 4 residues within 4Å: Chain U: K.50, S.163, T.164, G.165 Ligand excluded by PLIP SO4.80: 2 residues within 4Å: Chain U: N.4, R.5 Ligand excluded by PLIP SO4.83: 5 residues within 4Å: Chain V: K.50, S.163, T.164, G.165 Ligands: FEC.81 Ligand excluded by PLIP SO4.84: 5 residues within 4Å: Chain F: K.114 Chain N: K.114 Chain V: K.114 Ligands: SO4.22, SO4.53 Ligand excluded by PLIP SO4.86: 4 residues within 4Å: Chain W: K.50, S.163, T.164, G.165 Ligand excluded by PLIP SO4.87: 2 residues within 4Å: Chain W: N.4, R.5 Ligand excluded by PLIP SO4.88: 3 residues within 4Å: Chain W: S.144, K.147, N.148 Ligand excluded by PLIP SO4.89: 3 residues within 4Å: Chain R: K.114 Chain S: K.114 Chain X: K.114 Ligand excluded by PLIP SO4.91: 5 residues within 4Å: Chain W: E.61 Chain X: K.50, S.162, S.163, T.164 Ligand excluded by PLIP SO4.92: 2 residues within 4Å: Chain X: N.4, R.5 Ligand excluded by PLIP

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

FEC.5: 26 residues within 4Å: Chain A: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain B: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, T.164, A.167, S.168, K.169 Ligands: SO4.7 20 PLIP interactions: 10 interactions with chain B, 10 interactions with chain A, Hydrophobic interactions: B:I.27, B:I.54, B:E.61, A:I.27, A:I.27, A:M.31, A:I.54, A:M.57, A:E.61 Hydrogen bonds: B:Y.35, B:T.164, B:S.168, B:S.168, B:K.169, A:Y.35, A:Y.35, A:K.169 Salt bridges: B:R.20, B:K.50, A:R.20 FEC.11: 24 residues within 4Å: Chain C: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, R.58, A.60, E.61, A.167, S.168, K.169 Chain D: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168, K.169 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain D, Hydrophobic interactions: C:M.31, C:R.58, C:E.61, D:I.27, D:E.61 Hydrogen bonds: C:Y.35, C:Y.35, C:K.169, D:Y.35, D:S.168, D:K.169 Salt bridges: C:R.20, C:H.28, D:R.20, D:K.50 Water bridges: D:R.20, D:N.32 FEC.19: 23 residues within 4Å: Chain E: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, R.58, E.61, S.168, K.169 Chain F: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, 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:R.58, E:E.61 Hydrogen bonds: F:S.168, F:S.168, F:K.169, E:Y.35, E:Y.35, E:K.169 Water bridges: F:R.20, F:N.32, F:K.50, E:N.32 Salt bridges: F:R.20, F:K.50, E:R.20 FEC.31: 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, S.168 Chain H: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 19 PLIP interactions: 10 interactions with chain H, 9 interactions with chain G, Hydrophobic interactions: H:I.27, H:M.31, H:E.61, G:I.27, G:M.31, G:I.54, G:E.61 Hydrogen bonds: H:Y.35, H:S.168, H:S.168, H:K.169, G:Y.35, G:K.169 Water bridges: H:R.20, G:R.20, G:N.32 Salt bridges: H:R.20, H:K.50, G:R.20 FEC.36: 26 residues within 4Å: Chain I: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain J: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, T.164, A.167, S.168, K.169 Ligands: SO4.38 19 PLIP interactions: 9 interactions with chain J, 10 interactions with chain I, Hydrophobic interactions: J:I.27, J:I.54, J:E.61, I:I.27, I:I.27, I:M.31, I:I.54, I:M.57, I:E.61 Hydrogen bonds: J:T.164, J:S.168, J:S.168, J:K.169, I:Y.35, I:Y.35, I:K.169 Salt bridges: J:R.20, J:K.50, I:R.20 FEC.42: 24 residues within 4Å: Chain K: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, R.58, A.60, E.61, A.167, S.168, K.169 Chain L: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168, K.169 16 PLIP interactions: 7 interactions with chain K, 9 interactions with chain L, Hydrophobic interactions: K:M.31, K:R.58, K:E.61, L:I.27, L:E.61 Hydrogen bonds: K:Y.35, K:K.169, L:S.168, L:K.169 Salt bridges: K:R.20, K:H.28, L:R.20, L:K.50 Water bridges: L:R.20, L:N.32, L:T.164 FEC.50: 23 residues within 4Å: Chain M: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, R.58, E.61, S.168, K.169 Chain N: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.52 20 PLIP interactions: 9 interactions with chain M, 11 interactions with chain N, Hydrophobic interactions: M:I.27, M:M.31, M:M.57, M:R.58, M:E.61, N:I.27, N:M.31, N:E.61 Hydrogen bonds: M:Y.35, M:K.169, N:S.168, N:S.168, N:K.169 Water bridges: M:N.32, N:R.20, N:N.32, N:K.50 Salt bridges: M:R.20, N:R.20, N:K.50 FEC.62: 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, S.168 Chain P: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 18 PLIP interactions: 9 interactions with chain O, 9 interactions with chain P, Hydrophobic interactions: O:I.27, O:M.31, O:I.54, O:E.61, P:I.27, P:M.31, P:E.61 Hydrogen bonds: O:Y.35, O:K.169, P:S.168, P:S.168, P:K.169 Water bridges: O:R.20, O:N.32, P:R.20 Salt bridges: O:R.20, P:R.20, P:K.50 FEC.67: 26 residues within 4Å: Chain Q: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169 Chain R: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, T.164, A.167, S.168, K.169 Ligands: SO4.69 20 PLIP interactions: 10 interactions with chain Q, 10 interactions with chain R, Hydrophobic interactions: Q:I.27, Q:I.27, Q:M.31, Q:I.54, Q:M.57, Q:E.61, R:I.27, R:I.54, R:E.61 Hydrogen bonds: Q:Y.35, Q:Y.35, Q:K.169, R:Y.35, R:T.164, R:S.168, R:S.168, R:K.169 Salt bridges: Q:R.20, R:R.20, R:K.50 FEC.73: 24 residues within 4Å: Chain S: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, R.58, A.60, E.61, A.167, S.168, K.169 Chain T: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168, K.169 17 PLIP interactions: 9 interactions with chain T, 8 interactions with chain S, Hydrophobic interactions: T:I.27, T:E.61, S:M.31, S:R.58, S:E.61 Hydrogen bonds: T:S.168, T:K.169, S:Y.35, S:Y.35, S:K.169 Water bridges: T:R.20, T:N.32, T:T.164 Salt bridges: T:R.20, T:K.50, S:R.20, S:H.28 FEC.81: 23 residues within 4Å: Chain U: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, R.58, E.61, S.168, K.169 Chain V: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.83 20 PLIP interactions: 9 interactions with chain U, 11 interactions with chain V, Hydrophobic interactions: U:I.27, U:M.31, U:M.57, U:R.58, U:E.61, V:I.27, V:M.31, V:E.61 Hydrogen bonds: U:Y.35, U:K.169, V:S.168, V:S.168, V:K.169 Water bridges: U:N.32, V:R.20, V:N.32, V:K.50 Salt bridges: U:R.20, V:R.20, V:K.50 FEC.93: 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, S.168 Chain X: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 20 PLIP interactions: 10 interactions with chain X, 10 interactions with chain W, Hydrophobic interactions: X:I.27, X:M.31, X:E.61, W:I.27, W:M.31, W:I.54, W:E.61 Hydrogen bonds: X:Y.35, X:S.168, X:S.168, X:K.169, W:Y.35, W:Y.35, W:K.169 Water bridges: X:R.20, W:R.20, W:N.32 Salt bridges: X:R.20, X:K.50, W:R.20

Links

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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
A

B
B

C
G

D
H

E
I

F
J

G
M

H
N

I
A

J
B

K
G

L
H

M
I

N
J

O
M

P
N

Q
A

R
B

S
G

T
H

U
I

V
J

W
M

X
N

bacterioferritin

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