SMTL ID : 3e1q.1

Crystal structure of W133F variant E. coli Bacterioferritn with iron.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-24-mer

Ligands

32 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 SO4.6: 3 residues within 4Å: Chain B: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.9: 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 SO4.10: 3 residues within 4Å: Chain C: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain D: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain E: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain F: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain F: R.117, I.121 Chain I: R.117, I.121 Chain K: R.117, I.121 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain G: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain G: R.117, I.121 Chain L: R.117, I.121 Chain Q: R.117, I.121 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain H: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain I: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain J: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain K: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain L: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain M: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.50: 5 residues within 4Å: Chain D: R.117, I.121 Chain M: R.117 Chain V: R.117, I.121 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain N: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.55: 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 SO4.56: 3 residues within 4Å: Chain O: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.59: 3 residues within 4Å: Chain P: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain Q: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain R: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.69: 6 residues within 4Å: Chain R: R.117, I.121 Chain U: R.117, I.121 Chain W: R.117, I.121 Ligand excluded by PLIP SO4.71: 3 residues within 4Å: Chain S: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.74: 6 residues within 4Å: Chain E: R.117, I.121 Chain S: R.117, I.121 Chain X: R.117, I.121 Ligand excluded by PLIP SO4.76: 3 residues within 4Å: Chain T: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.79: 3 residues within 4Å: Chain U: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.83: 3 residues within 4Å: Chain V: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.86: 3 residues within 4Å: Chain W: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.89: 3 residues within 4Å: Chain X: G.145, L.146, Q.147 Ligand excluded by PLIP

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

FE2.2: 5 residues within 4Å: Chain A: E.18, E.51, H.54, E.127 Ligands: FE2.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.18, A:E.18, A:E.51, A:H.54, A:E.127 FE2.3: 5 residues within 4Å: Chain A: E.51, E.94, E.127, H.130 Ligands: FE2.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.51, A:E.94, A:E.94, A:E.127, A:H.130 FE2.7: 5 residues within 4Å: Chain B: E.18, E.51, H.54, E.127 Ligands: FE2.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.18, B:E.18, B:E.51, B:H.54, B:E.127 FE2.8: 5 residues within 4Å: Chain B: E.51, E.94, E.127, H.130 Ligands: FE2.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.51, B:E.94, B:E.94, B:E.127, B:H.130 FE2.11: 5 residues within 4Å: Chain C: E.18, E.51, H.54, E.127 Ligands: FE2.12 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.18, C:E.18, C:E.51, C:H.54, C:E.127 FE2.12: 5 residues within 4Å: Chain C: E.51, E.94, E.127, H.130 Ligands: FE2.11 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.51, C:E.94, C:E.94, C:E.127, C:H.130 FE2.14: 5 residues within 4Å: Chain D: E.18, E.51, H.54, E.127 Ligands: FE2.15 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.18, D:E.18, D:E.51, D:H.54, D:E.127 FE2.15: 5 residues within 4Å: Chain D: E.51, E.94, E.127, H.130 Ligands: FE2.14 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.51, D:E.94, D:E.94, D:E.127, D:H.130 FE2.18: 5 residues within 4Å: Chain E: E.18, E.51, H.54, E.127 Ligands: FE2.19 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.18, E:E.18, E:E.51, E:H.54, E:E.127 FE2.19: 5 residues within 4Å: Chain E: E.51, E.94, E.127, H.130 Ligands: FE2.18 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.51, E:E.94, E:E.94, E:E.127, E:H.130 FE2.21: 5 residues within 4Å: Chain F: E.18, E.51, H.54, E.127 Ligands: FE2.22 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.18, F:E.18, F:E.51, F:H.54, F:E.127 FE2.22: 5 residues within 4Å: Chain F: E.51, E.94, E.127, H.130 Ligands: FE2.21 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.51, F:E.94, F:E.94, F:E.127, F:H.130 FE2.26: 5 residues within 4Å: Chain G: E.18, E.51, H.54, E.127 Ligands: FE2.27 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.18, G:E.18, G:E.51, G:H.54, G:E.127 FE2.27: 5 residues within 4Å: Chain G: E.51, E.94, E.127, H.130 Ligands: FE2.26 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.51, G:E.94, G:E.94, G:E.127, G:H.130 FE2.31: 5 residues within 4Å: Chain H: E.18, E.51, H.54, E.127 Ligands: FE2.32 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.18, H:E.18, H:E.51, H:H.54, H:E.127 FE2.32: 5 residues within 4Å: Chain H: E.51, E.94, E.127, H.130 Ligands: FE2.31 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.51, H:E.94, H:E.94, H:E.127, H:H.130 FE2.34: 5 residues within 4Å: Chain I: E.18, E.51, H.54, E.127 Ligands: FE2.35 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.18, I:E.18, I:E.51, I:H.54, I:E.127 FE2.35: 5 residues within 4Å: Chain I: E.51, E.94, E.127, H.130 Ligands: FE2.34 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.51, I:E.94, I:E.94, I:E.127, I:H.130 FE2.38: 5 residues within 4Å: Chain J: E.18, E.51, H.54, E.127 Ligands: FE2.39 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.18, J:E.18, J:E.51, J:H.54, J:E.127 FE2.39: 5 residues within 4Å: Chain J: E.51, E.94, E.127, H.130 Ligands: FE2.38 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.51, J:E.94, J:E.94, J:E.127, J:H.130 FE2.41: 5 residues within 4Å: Chain K: E.18, E.51, H.54, E.127 Ligands: FE2.42 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.18, K:E.18, K:E.51, K:H.54, K:E.127 FE2.42: 5 residues within 4Å: Chain K: E.51, E.94, E.127, H.130 Ligands: FE2.41 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.51, K:E.94, K:E.94, K:E.127, K:H.130 FE2.44: 5 residues within 4Å: Chain L: E.18, E.51, H.54, E.127 Ligands: FE2.45 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.18, L:E.18, L:E.51, L:H.54, L:E.127 FE2.45: 5 residues within 4Å: Chain L: E.51, E.94, E.127, H.130 Ligands: FE2.44 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.51, L:E.94, L:E.94, L:E.127, L:H.130 FE2.48: 5 residues within 4Å: Chain M: E.18, E.51, H.54, E.127 Ligands: FE2.49 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.18, M:E.18, M:E.51, M:H.54, M:E.127 FE2.49: 5 residues within 4Å: Chain M: E.51, E.94, E.127, H.130 Ligands: FE2.48 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.51, M:E.94, M:E.94, M:E.127, M:H.130 FE2.53: 5 residues within 4Å: Chain N: E.18, E.51, H.54, E.127 Ligands: FE2.54 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.18, N:E.18, N:E.51, N:H.54, N:E.127 FE2.54: 5 residues within 4Å: Chain N: E.51, E.94, E.127, H.130 Ligands: FE2.53 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.51, N:E.94, N:E.94, N:E.127, N:H.130 FE2.57: 5 residues within 4Å: Chain O: E.18, E.51, H.54, E.127 Ligands: FE2.58 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.18, O:E.18, O:E.51, O:H.54, O:E.127 FE2.58: 5 residues within 4Å: Chain O: E.51, E.94, E.127, H.130 Ligands: FE2.57 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.51, O:E.94, O:E.94, O:E.127, O:H.130 FE2.60: 5 residues within 4Å: Chain P: E.18, E.51, H.54, E.127 Ligands: FE2.61 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.18, P:E.18, P:E.51, P:H.54, P:E.127 FE2.61: 5 residues within 4Å: Chain P: E.51, E.94, E.127, H.130 Ligands: FE2.60 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.51, P:E.94, P:E.94, P:E.127, P:H.130 FE2.64: 5 residues within 4Å: Chain Q: E.18, E.51, H.54, E.127 Ligands: FE2.65 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:E.18, Q:E.18, Q:E.51, Q:H.54, Q:E.127 FE2.65: 5 residues within 4Å: Chain Q: E.51, E.94, E.127, H.130 Ligands: FE2.64 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:E.51, Q:E.94, Q:E.94, Q:E.127, Q:H.130 FE2.67: 5 residues within 4Å: Chain R: E.18, E.51, H.54, E.127 Ligands: FE2.68 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.18, R:E.18, R:E.51, R:H.54, R:E.127 FE2.68: 5 residues within 4Å: Chain R: E.51, E.94, E.127, H.130 Ligands: FE2.67 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.51, R:E.94, R:E.94, R:E.127, R:H.130 FE2.72: 5 residues within 4Å: Chain S: E.18, E.51, H.54, E.127 Ligands: FE2.73 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.18, S:E.18, S:E.51, S:H.54, S:E.127 FE2.73: 5 residues within 4Å: Chain S: E.51, E.94, E.127, H.130 Ligands: FE2.72 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.51, S:E.94, S:E.94, S:E.127, S:H.130 FE2.77: 5 residues within 4Å: Chain T: E.18, E.51, H.54, E.127 Ligands: FE2.78 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.18, T:E.18, T:E.51, T:H.54, T:E.127 FE2.78: 5 residues within 4Å: Chain T: E.51, E.94, E.127, H.130 Ligands: FE2.77 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.51, T:E.94, T:E.94, T:E.127, T:H.130 FE2.80: 5 residues within 4Å: Chain U: E.18, E.51, H.54, E.127 Ligands: FE2.81 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:E.18, U:E.18, U:E.51, U:H.54, U:E.127 FE2.81: 5 residues within 4Å: Chain U: E.51, E.94, E.127, H.130 Ligands: FE2.80 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:E.51, U:E.94, U:E.94, U:E.127, U:H.130 FE2.84: 5 residues within 4Å: Chain V: E.18, E.51, H.54, E.127 Ligands: FE2.85 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.18, V:E.18, V:E.51, V:H.54, V:E.127 FE2.85: 5 residues within 4Å: Chain V: E.51, E.94, E.127, H.130 Ligands: FE2.84 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.51, V:E.94, V:E.94, V:E.127, V:H.130 FE2.87: 5 residues within 4Å: Chain W: E.18, E.51, H.54, E.127 Ligands: FE2.88 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:E.18, W:E.18, W:E.51, W:H.54, W:E.127 FE2.88: 5 residues within 4Å: Chain W: E.51, E.94, E.127, H.130 Ligands: FE2.87 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:E.51, W:E.94, W:E.94, W:E.127, W:H.130 FE2.90: 5 residues within 4Å: Chain X: E.18, E.51, H.54, E.127 Ligands: FE2.91 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.18, X:E.18, X:E.51, X:H.54, X:E.127 FE2.91: 5 residues within 4Å: Chain X: E.51, E.94, E.127, H.130 Ligands: FE2.90 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.51, X:E.94, X:E.94, X:E.127, X:H.130

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

HEM.5: 16 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 17 PLIP interactions: 8 interactions with chain B, 9 interactions with chain A, Hydrophobic interactions: B:L.19, B:I.22, B:F.26, B:F.26, B:F.26, B:I.49, B:I.49, B:M.52, A:L.19, A:I.22, A:F.26, A:F.26, A:I.49, A:I.49, A:M.52, A:A.55 Salt bridges: A:K.53 HEM.16: 16 residues within 4Å: Chain C: 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 16 PLIP interactions: 7 interactions with chain C, 9 interactions with chain D, Hydrophobic interactions: 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.24: 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 15 PLIP interactions: 7 interactions with chain E, 8 interactions with chain F, Hydrophobic interactions: E:I.22, E:F.26, E:F.26, E:I.49, E:M.52, E:A.55, F:L.19, F:I.22, F:F.26, F:F.26, F:Y.45, F:I.49, F:I.49, F:M.52 Salt bridges: E:K.53 HEM.29: 17 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, D.56 18 PLIP interactions: 8 interactions with chain H, 10 interactions with chain G, Hydrophobic interactions: H:L.19, H:I.22, H:I.22, H:F.26, H:F.26, H:F.26, 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:M.52, G:A.55 Salt bridges: G:K.53 HEM.36: 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 17 PLIP interactions: 9 interactions with chain I, 8 interactions with chain J, Hydrophobic interactions: I:L.19, I:I.22, I:I.22, I:F.26, I:F.26, I:I.49, I:M.52, I:A.55, J:L.19, J:I.22, J:F.26, J:F.26, J:F.26, J:I.49, J:I.49, J:M.52 Salt bridges: I:K.53 HEM.46: 15 residues within 4Å: Chain K: 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 16 PLIP interactions: 7 interactions with chain K, 9 interactions with chain L, Hydrophobic interactions: K:I.22, K:F.26, K:F.26, K:I.49, K:M.52, K:A.55, L:L.19, L:I.22, L:I.22, L:F.26, L:F.26, L:F.26, L:I.49, L:I.49, L:M.52 Salt bridges: K:K.53 HEM.51: 16 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 17 PLIP interactions: 9 interactions with chain M, 8 interactions with chain N, Hydrophobic interactions: M:L.19, M:I.22, 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:F.26, N:F.26, N:F.26, N:I.49, N:I.49, N:M.52 Salt bridges: M:K.53 HEM.62: 16 residues within 4Å: Chain O: 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 16 PLIP interactions: 9 interactions with chain P, 7 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:F.26, O:F.26, O:I.49, O:I.49, O:M.52, O:A.55 Salt bridges: O:K.53 HEM.70: 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 15 PLIP interactions: 8 interactions with chain R, 7 interactions with chain Q, Hydrophobic interactions: R:L.19, R:I.22, R:F.26, R:F.26, R:Y.45, R:I.49, R:I.49, R:M.52, Q:I.22, Q:F.26, Q:F.26, Q:I.49, Q:M.52, Q:A.55 Salt bridges: Q:K.53 HEM.75: 17 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, D.56 18 PLIP interactions: 10 interactions with chain S, 8 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:M.52, S:A.55, T:L.19, T:I.22, T:I.22, T:F.26, T:F.26, T:F.26, T:I.49, T:M.52 Salt bridges: S:K.53 HEM.82: 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 17 PLIP interactions: 9 interactions with chain U, 8 interactions with chain V, Hydrophobic interactions: U:L.19, U:I.22, U:I.22, U:F.26, U:F.26, U:I.49, U:M.52, U:A.55, V:L.19, V:I.22, V:F.26, V:F.26, V:F.26, V:I.49, V:I.49, V:M.52 Salt bridges: U:K.53 HEM.92: 15 residues within 4Å: Chain W: 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 16 PLIP interactions: 7 interactions with chain W, 9 interactions with chain X, Hydrophobic interactions: W:I.22, W:F.26, W:F.26, W:I.49, W:M.52, W:A.55, X:L.19, X:I.22, X:I.22, X:F.26, X:F.26, X:F.26, X:I.49, X:I.49, X:M.52 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

2009-08-18

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