SMTL ID : 1nf4.1 (2 other biounits)

X-Ray Structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different states (reduced structure)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-16-mer

Ligands

32 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: E.23, E.56, H.59, E.132 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.23, A:E.56, A:H.59, A:E.132, H2O.4 FE2.2: 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.99, A:E.99, A:E.132, A:H.135 FE2.8: 4 residues within 4Å: Chain B: E.23, E.56, H.59, E.132 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.23, B:E.56, B:H.59, B:E.132, H2O.8 FE2.9: 4 residues within 4Å: Chain B: E.56, E.99, E.132, H.135 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.56, B:E.99, B:E.132, B:H.135, H2O.9 FE2.14: 5 residues within 4Å: Chain C: E.23, E.56, H.59, E.132 Ligands: FE2.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.23, C:E.23, C:H.59, C:E.132, H2O.12 FE2.15: 5 residues within 4Å: Chain C: E.56, E.99, E.132, H.135 Ligands: FE2.14 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.56, C:E.99, C:E.99, C:E.132, C:H.135 FE2.21: 4 residues within 4Å: Chain D: E.23, E.56, H.59, E.132 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.23, D:E.56, D:H.59, D:E.132, H2O.15 FE2.22: 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.99, D:E.99, D:E.132, D:H.135 FE2.27: 5 residues within 4Å: Chain E: E.23, E.56, H.59, E.132 Ligands: FE2.28 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.23, E:E.56, E:H.59, E:E.132, H2O.20 FE2.28: 5 residues within 4Å: Chain E: E.56, E.99, E.132, H.135 Ligands: FE2.27 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.56, E:E.99, E:E.132, E:H.135, H2O.21 FE2.32: 4 residues within 4Å: Chain F: E.23, E.56, H.59, E.132 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.23, F:E.56, F:H.59, F:E.132, H2O.23 FE2.33: 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.99, F:E.99, F:E.132, F:H.135 FE2.37: 4 residues within 4Å: Chain G: E.23, E.56, H.59, E.132 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.23, G:E.56, G:H.59, G:E.132, H2O.27 FE2.38: 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.99, G:E.99, G:E.132, G:H.135 FE2.43: 4 residues within 4Å: Chain H: E.23, E.56, H.59, E.132 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.23, H:E.56, H:H.59, H:E.132, H2O.31 FE2.44: 4 residues within 4Å: Chain H: E.56, E.99, E.132, H.135 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.56, H:E.99, H:E.99, H:E.132, H:H.135 FE2.50: 5 residues within 4Å: Chain I: E.23, E.56, H.59, E.132 Ligands: FE2.51 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.23, I:E.23, I:H.59, I:E.132, H2O.35 FE2.51: 5 residues within 4Å: Chain I: E.56, E.99, E.132, H.135 Ligands: FE2.50 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.56, I:E.99, I:E.99, I:E.132, I:H.135 FE2.57: 5 residues within 4Å: Chain J: E.23, E.56, H.59, E.132 Ligands: FE2.58 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.23, J:E.56, J:H.59, J:E.132, H2O.39 FE2.58: 5 residues within 4Å: Chain J: E.56, E.99, E.132, H.135 Ligands: FE2.57 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.56, J:E.99, J:E.99, J:E.132, J:H.135 FE2.62: 5 residues within 4Å: Chain K: E.23, E.56, H.59, E.132 Ligands: FE2.63 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.23, K:E.56, K:H.59, K:E.132, H2O.43 FE2.63: 5 residues within 4Å: Chain K: E.56, E.99, E.132, H.135 Ligands: FE2.62 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.56, K:E.99, K:E.99, K:E.132, K:H.135 FE2.67: 4 residues within 4Å: Chain L: E.23, E.56, H.59, E.132 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.23, L:E.56, L:H.59, L:E.132, H2O.47 FE2.68: 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.99, L:E.99, L:E.132, L:H.135 FE2.74: 5 residues within 4Å: Chain M: E.23, E.56, H.59, E.132 Ligands: FE2.75 5 PLIP interactions: 4 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.23, M:E.56, M:H.59, M:E.132, H2O.49 FE2.75: 5 residues within 4Å: Chain M: E.56, E.99, E.132, H.135 Ligands: FE2.74 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.56, M:E.99, M:E.99, M:E.132, M:H.135 FE2.81: 4 residues within 4Å: Chain N: E.23, E.56, H.59, E.132 5 PLIP interactions: 4 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.23, N:E.56, N:H.59, N:E.132, H2O.54 FE2.82: 4 residues within 4Å: Chain N: E.56, E.99, E.132, H.135 5 PLIP interactions: 4 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.56, N:E.99, N:E.132, N:H.135, H2O.58 FE2.86: 5 residues within 4Å: Chain O: E.23, E.56, H.59, E.132 Ligands: FE2.87 5 PLIP interactions: 4 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.23, O:E.56, O:H.59, O:E.132, H2O.58 FE2.87: 5 residues within 4Å: Chain O: E.56, E.99, E.132, H.135 Ligands: FE2.86 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.56, O:E.99, O:E.99, O:E.132, O:H.135 FE2.91: 5 residues within 4Å: Chain P: E.23, E.56, H.59, E.132 Ligands: FE2.92 5 PLIP interactions: 4 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.23, P:E.56, P:H.59, P:E.132, H2O.61 FE2.92: 5 residues within 4Å: Chain P: E.56, E.99, E.132, H.135 Ligands: FE2.91 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.56, P:E.99, P:E.99, P:E.132, P:H.135

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

SO4.3: 5 residues within 4Å: Chain A: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: S.144, N.148 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: P.161, S.162, S.163 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain A: T.76, Q.77 Chain B: K.78, G.80, K.81, V.82 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: K.50, S.163, T.164 Ligands: FEC.6 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: S.144, N.148 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: K.114 Chain G: K.114 Chain N: K.114 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: P.161, S.162, S.163 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain C: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain C: S.144, N.148 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Chain C: K.114 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: P.161, S.162, S.163 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain D: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.20 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain D: S.144, K.147, N.148 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain D: P.161, S.162, S.163 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain E: K.114 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain E: S.144, K.147, N.148 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain E: P.161, S.162, S.163 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain F: K.50, S.163, T.164, G.165 Ligands: FEC.31 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain F: N.4, R.5 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain F: P.161, S.162, S.163 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain G: K.50, S.162, S.163, T.164 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain G: S.144, N.148 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain G: P.161, S.162, S.163 Ligand excluded by PLIP SO4.45: 6 residues within 4Å: Chain H: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.42 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain H: N.4, R.5 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain H: S.144, N.148 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain H: P.161, S.162, S.163 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain H: K.114 Chain I: K.114 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain I: K.50, T.164, G.165 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain I: N.4, R.5 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain I: S.144, K.147, N.148 Ligand excluded by PLIP SO4.55: 3 residues within 4Å: Chain I: P.161, S.162, S.163 Ligand excluded by PLIP SO4.59: 5 residues within 4Å: Chain J: K.50, S.163, T.164, G.165 Ligands: FEC.56 Ligand excluded by PLIP SO4.60: 1 residues within 4Å: Chain J: K.114 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain J: P.161, S.162, S.163 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain K: K.50, S.163, T.164, G.165 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain K: S.144, K.147, N.148 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain K: P.161, S.162, S.163 Ligand excluded by PLIP SO4.69: 6 residues within 4Å: Chain L: K.50, S.162, S.163, T.164, G.165 Ligands: FEC.73 Ligand excluded by PLIP SO4.70: 2 residues within 4Å: Chain L: N.4, R.5 Ligand excluded by PLIP SO4.71: 1 residues within 4Å: Chain L: K.114 Ligand excluded by PLIP SO4.72: 3 residues within 4Å: Chain L: P.161, S.162, S.163 Ligand excluded by PLIP SO4.76: 5 residues within 4Å: Chain M: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.77: 3 residues within 4Å: Chain M: N.4, R.5, E.6 Ligand excluded by PLIP SO4.78: 3 residues within 4Å: Chain M: S.144, K.147, N.148 Ligand excluded by PLIP SO4.79: 3 residues within 4Å: Chain M: P.161, S.162, S.163 Ligand excluded by PLIP SO4.83: 5 residues within 4Å: Chain N: K.50, S.162, S.163, T.164, G.165 Ligand excluded by PLIP SO4.84: 2 residues within 4Å: Chain N: S.144, N.148 Ligand excluded by PLIP SO4.85: 3 residues within 4Å: Chain N: P.161, S.162, S.163 Ligand excluded by PLIP SO4.88: 2 residues within 4Å: Chain O: S.144, N.148 Ligand excluded by PLIP SO4.89: 3 residues within 4Å: Chain O: P.161, S.162, S.163 Ligand excluded by PLIP SO4.90: 3 residues within 4Å: Chain F: K.114 Chain K: K.114 Chain P: K.114 Ligand excluded by PLIP SO4.93: 5 residues within 4Å: Chain P: K.50, S.163, T.164, G.165 Ligands: FEC.96 Ligand excluded by PLIP SO4.94: 3 residues within 4Å: Chain P: S.144, K.147, N.148 Ligand excluded by PLIP SO4.95: 3 residues within 4Å: Chain P: P.161, S.162, S.163 Ligand excluded by PLIP

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

FEC.6: 20 residues within 4Å: Chain A: R.20, L.24, H.28, M.31, Y.35, K.50, M.57, E.61, S.168 Chain B: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168 Ligands: SO4.10 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain B, Hydrophobic interactions: A:L.24, A:E.61, B:I.27, B:M.31, B:E.61 Hydrogen bonds: A:Y.35, A:Y.35, B:Y.35, B:S.168, B:S.168 Water bridges: A:R.20, B:R.20, B:K.169 Salt bridges: A:R.20, A:H.28, B:R.20, B:K.50 FEC.20: 22 residues within 4Å: Chain C: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, R.58, E.61 Chain D: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.23 17 PLIP interactions: 7 interactions with chain D, 10 interactions with chain C, Hydrophobic interactions: D:I.27, D:M.31, D:E.61, C:L.24, C:I.27, C:M.31, C:R.58, C:E.61 Hydrogen bonds: D:S.168, D:K.169, C:Y.35, C:R.58 Salt bridges: D:R.20, D:K.50, C:R.20, C:H.28 Water bridges: C:R.20 FEC.31: 23 residues within 4Å: Chain E: R.20, L.24, H.28, M.31, Y.35, K.50, I.54, M.57, 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: SO4.34 17 PLIP interactions: 8 interactions with chain E, 9 interactions with chain F, Hydrophobic interactions: E:L.24, E:M.31, E:I.54, E:E.61, F:I.27, F:E.61 Hydrogen bonds: E:Y.35, E:K.169, F:S.168, F:S.168, F:K.169 Salt bridges: E:R.20, E:H.28, F:R.20, F:H.28, F:K.50 Water bridges: F:T.164 FEC.42: 21 residues within 4Å: Chain G: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61 Chain H: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.45 17 PLIP interactions: 9 interactions with chain G, 8 interactions with chain H, Hydrophobic interactions: G:L.24, G:I.27, G:M.31, G:M.57, G:E.61, H:E.61 Hydrogen bonds: G:Y.35, G:Y.35, H:Y.35, H:S.168, H:S.168, H:K.169 Salt bridges: G:R.20, G:H.28, H:R.20, H:K.50 Water bridges: H:R.20 FEC.56: 20 residues within 4Å: Chain I: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, E.61 Chain J: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168 Ligands: SO4.59 15 PLIP interactions: 6 interactions with chain J, 9 interactions with chain I, Hydrophobic interactions: J:I.27, J:E.61, I:L.24, I:I.27, I:I.27, I:M.31, I:E.61 Hydrogen bonds: J:S.168, J:S.168, I:Y.35, I:Y.35 Salt bridges: J:R.20, J:K.50, I:R.20, I:H.28 FEC.73: 20 residues within 4Å: Chain K: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61 Chain L: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, S.168, K.169 Ligands: SO4.69 18 PLIP interactions: 8 interactions with chain K, 10 interactions with chain L, Hydrophobic interactions: K:I.27, K:I.27, K:I.54, K:E.61, 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:R.20, L:R.20 Salt bridges: K:R.20, K:H.28, L:R.20, L:K.50 FEC.80: 20 residues within 4Å: Chain M: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, R.58, E.61 Chain N: R.20, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 15 PLIP interactions: 8 interactions with chain M, 7 interactions with chain N, Hydrophobic interactions: M:L.24, M:I.27, M:M.31, M:R.58, M:E.61, N:E.61 Hydrogen bonds: M:Y.35, N:Y.35, N:S.168, N:S.168, N:K.169 Water bridges: M:R.20 Salt bridges: M:R.20, N:R.20, N:K.50 FEC.96: 23 residues within 4Å: Chain O: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168 Chain P: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169 Ligands: SO4.93 19 PLIP interactions: 10 interactions with chain P, 9 interactions with chain O, Hydrophobic interactions: P:I.27, P:M.31, P:E.61, O:L.24, O:I.27, O:M.31, O:I.54, O:M.57, O:E.61 Hydrogen bonds: P:S.168, P:S.168, P:K.169, O:Y.35 Water bridges: P:T.164, P:T.164 Salt bridges: P:R.20, P:K.50, O:R.20, O:H.28

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: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

bacterioferritin

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