SMTL ID : 3ghq.1

Crystal Structure of E. coli W35F BFR mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-24-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: R.117 Chain J: R.117, I.121 Chain P: R.117, I.121 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.57, M.119 Chain J: R.125 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain B: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain B: R.117, I.121 Chain C: R.117, I.121 Chain H: R.117, I.121 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain C: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain C: R.57, M.119 Chain H: R.125 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain D: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain E: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain F: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain F: R.117 Chain I: R.117, I.121 Chain K: R.117, I.121 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain F: R.57, M.119 Chain I: R.125 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain G: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain G: R.117 Chain L: R.117 Chain Q: R.117 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain G: R.57, M.119 Chain Q: R.125 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain H: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain I: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain J: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain K: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain F: R.125 Chain K: R.57, M.119 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain L: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain M: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.43: 5 residues within 4Å: Chain D: R.117, I.121 Chain M: R.117 Chain V: R.117, I.121 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain M: R.57, M.119 Chain V: R.125 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain N: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.47: 6 residues within 4Å: Chain N: R.117, I.121 Chain O: R.117, I.121 Chain T: R.117, I.121 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain O: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain O: R.57, M.119 Chain T: R.125 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain P: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain Q: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.57: 3 residues within 4Å: Chain R: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.59: 5 residues within 4Å: Chain R: R.117 Chain U: R.117, I.121 Chain W: R.117, I.121 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain R: R.57, M.119 Chain U: R.125 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain S: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.64: 3 residues within 4Å: Chain E: R.117 Chain S: R.117 Chain X: R.117 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain E: R.125 Chain S: R.57, M.119 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain T: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.68: 3 residues within 4Å: Chain U: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.71: 3 residues within 4Å: Chain V: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.73: 3 residues within 4Å: Chain W: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.75: 3 residues within 4Å: Chain R: R.125 Chain W: R.57, M.119 Ligand excluded by PLIP SO4.77: 3 residues within 4Å: Chain X: G.145, L.146, Q.147 Ligand excluded by PLIP

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

FE.2: 4 residues within 4Å: Chain A: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.18, A:E.18, A:E.51, A:E.51, A:E.127 FE.7: 4 residues within 4Å: Chain B: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.18, B:E.18, B:E.51, B:E.51, B:E.127 FE.10: 4 residues within 4Å: Chain C: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.18, C:E.51, C:E.51, C:H.54, C:E.127 FE.14: 4 residues within 4Å: Chain D: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.18, D:E.18, D:E.51, D:E.51, D:E.127 FE.16: 4 residues within 4Å: Chain E: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.18, E:E.18, E:E.51, E:E.51, E:E.127 FE.19: 4 residues within 4Å: Chain F: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.18, F:E.18, F:E.51, F:E.51, F:E.127 FE.23: 4 residues within 4Å: Chain G: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.18, G:E.18, G:E.51, G:E.51, G:E.127 FE.28: 4 residues within 4Å: Chain H: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.18, H:E.18, H:E.51, H:E.51, H:E.127 FE.30: 4 residues within 4Å: Chain I: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.18, I:E.18, I:E.51, I:E.51, I:E.127 FE.33: 4 residues within 4Å: Chain J: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.18, J:E.18, J:E.51, J:E.51, J:E.127 FE.35: 4 residues within 4Å: Chain K: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.18, K:E.18, K:E.51, K:E.51, K:E.127 FE.39: 4 residues within 4Å: Chain L: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.18, L:E.51, L:E.51, L:H.54, L:E.127 FE.41: 4 residues within 4Å: Chain M: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.18, M:E.18, M:E.51, M:E.51, M:E.127 FE.46: 4 residues within 4Å: Chain N: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.18, N:E.18, N:E.51, N:E.51, N:E.127 FE.49: 4 residues within 4Å: Chain O: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.18, O:E.51, O:E.51, O:H.54, O:E.127 FE.53: 4 residues within 4Å: Chain P: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.18, P:E.18, P:E.51, P:E.51, P:E.127 FE.55: 4 residues within 4Å: Chain Q: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:E.18, Q:E.18, Q:E.51, Q:E.51, Q:E.127 FE.58: 4 residues within 4Å: Chain R: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.18, R:E.18, R:E.51, R:E.51, R:E.127 FE.62: 4 residues within 4Å: Chain S: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.18, S:E.18, S:E.51, S:E.51, S:E.127 FE.67: 4 residues within 4Å: Chain T: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.18, T:E.18, T:E.51, T:E.51, T:E.127 FE.69: 4 residues within 4Å: Chain U: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:E.18, U:E.18, U:E.51, U:E.51, U:E.127 FE.72: 4 residues within 4Å: Chain V: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.18, V:E.18, V:E.51, V:E.51, V:E.127 FE.74: 4 residues within 4Å: Chain W: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:E.18, W:E.18, W:E.51, W:E.51, W:E.127 FE.78: 4 residues within 4Å: Chain X: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.18, X:E.51, X:E.51, X:H.54, X:E.127

12 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 17 residues within 4Å: Chain A: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain B: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A, Hydrophobic interactions: B:L.19, B:I.22, B:I.22, B:F.26, B:F.26, B:F.26, B:I.49, B:I.49, B:A.55, A:L.19, A:I.22, A:F.26, A:F.26, A:F.26, A:I.49, A:I.49, A:M.52, A:A.55 Salt bridges: A:K.53 HEM.12: 17 residues within 4Å: Chain C: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain D: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55 19 PLIP interactions: 10 interactions with chain C, 9 interactions with chain D, Hydrophobic interactions: C:L.19, C:I.22, C:F.26, C:F.26, C:F.26, C:I.49, C:I.49, C:M.52, C:A.55, D:L.19, D:I.22, D:I.22, D:F.26, D:F.26, D:I.49, D:I.49, D:M.52, D:A.55 Salt bridges: C:K.53 HEM.17: 15 residues within 4Å: Chain E: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain F: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 19 PLIP interactions: 9 interactions with chain E, 10 interactions with chain F, Hydrophobic interactions: E:F.26, E:F.26, E:F.26, E:I.49, E:I.49, E:M.52, E:A.55, E:D.56, F:L.19, F:I.22, F:I.22, F:F.26, F:F.26, F:F.26, F:Y.45, F:I.49, F:I.49, F:M.52 Salt bridges: E:K.53 HEM.24: 16 residues within 4Å: Chain G: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain H: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 16 PLIP interactions: 7 interactions with chain H, 9 interactions with chain G, Hydrophobic interactions: H:L.19, H:I.22, H:F.26, H:F.26, H:I.49, H:I.49, H:M.52, G:L.19, G:I.22, G:F.26, G:F.26, G:F.26, G:I.49, G:I.49, G:A.55 Salt bridges: G:K.53 HEM.31: 16 residues within 4Å: Chain I: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain J: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 15 PLIP interactions: 7 interactions with chain J, 8 interactions with chain I, Hydrophobic interactions: J:L.19, J:F.26, J:F.26, J:F.26, J:F.26, J:I.49, J:M.52, I:L.19, I:I.22, I:I.22, I:F.26, I:I.49, I:M.52, I:A.55 Salt bridges: I:K.53 HEM.37: 17 residues within 4Å: Chain K: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain L: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55 17 PLIP interactions: 8 interactions with chain L, 9 interactions with chain K, Hydrophobic interactions: L:L.19, L:I.22, L:F.26, L:F.26, L:F.26, L:I.49, L:M.52, L:A.55, K:L.19, K:I.22, K:I.22, K:F.26, K:F.26, K:M.52, K:A.55 Water bridges: K:Y.45 Salt bridges: K:K.53 HEM.42: 17 residues within 4Å: Chain M: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain N: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55 19 PLIP interactions: 10 interactions with chain M, 9 interactions with chain N, Hydrophobic interactions: M:L.19, M:I.22, M:F.26, M:F.26, M:F.26, M:I.49, M:I.49, M:M.52, M:A.55, N:L.19, N:I.22, N:I.22, N:F.26, N:F.26, N:F.26, N:I.49, N:I.49, N:A.55 Salt bridges: M:K.53 HEM.51: 17 residues within 4Å: Chain O: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain P: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55 19 PLIP interactions: 9 interactions with chain P, 10 interactions with chain O, Hydrophobic interactions: P:L.19, P:I.22, P:I.22, P:F.26, P:F.26, P:I.49, P:I.49, P:M.52, P:A.55, O:L.19, O:I.22, O:F.26, O:F.26, O:F.26, O:I.49, O:I.49, O:M.52, O:A.55 Salt bridges: O:K.53 HEM.56: 15 residues within 4Å: Chain Q: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain R: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 19 PLIP interactions: 9 interactions with chain Q, 10 interactions with chain R, Hydrophobic interactions: Q:F.26, Q:F.26, Q:F.26, Q:I.49, Q:I.49, Q:M.52, Q:A.55, Q:D.56, R:L.19, R:I.22, R:I.22, R:F.26, R:F.26, R:F.26, R:Y.45, R:I.49, R:I.49, R:M.52 Salt bridges: Q:K.53 HEM.63: 16 residues within 4Å: Chain S: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain T: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 16 PLIP interactions: 9 interactions with chain S, 7 interactions with chain T, Hydrophobic interactions: S:L.19, S:I.22, S:F.26, S:F.26, S:F.26, S:I.49, S:I.49, S:A.55, T:L.19, T:I.22, T:F.26, T:F.26, T:I.49, T:I.49, T:M.52 Salt bridges: S:K.53 HEM.70: 16 residues within 4Å: Chain U: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain V: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 15 PLIP interactions: 7 interactions with chain V, 8 interactions with chain U, Hydrophobic interactions: V:L.19, V:F.26, V:F.26, V:F.26, V:F.26, V:I.49, V:M.52, U:L.19, U:I.22, U:I.22, U:F.26, U:I.49, U:M.52, U:A.55 Salt bridges: U:K.53 HEM.76: 17 residues within 4Å: Chain W: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56 Chain X: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55 16 PLIP interactions: 8 interactions with chain W, 8 interactions with chain X, Hydrophobic interactions: W:L.19, W:I.22, W:I.22, W:F.26, W:F.26, W:M.52, W:A.55, X:L.19, X:I.22, X:F.26, X:F.26, X:F.26, X:I.49, X:M.52, X:A.55 Salt bridges: W:K.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lawson, T.L. et al., Monitoring the iron status of the ferroxidase center of Escherichia coli bacterioferritin using fluorescence spectroscopy. Biochemistry (2009)

Release Date

2009-10-06

Peptides

Bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX

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
A

N
B

O
C

P
D

Q
E

R
F

S
G

T
H

U
I

V
J

W
K

X
L

Bacterioferritin