SMTL ID : 4ztt.1

Crystal structures of ferritin mutants reveal diferric-peroxo intermediates

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-24-mer

Ligands

12 x FEO: MU-OXO-DIIRON(Non-covalent)(Covalent)

FEO.1: 10 residues within 4Å: Chain A: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.2, OH.3 8 PLIP interactions: 8 interactions with chain A, Hydrogen bonds: A:Q.128 Metal complexes: A:E.18, A:E.51, A:E.51, A:H.54, A:E.95, A:E.95, A:E.131 FEO.6: 10 residues within 4Å: Chain B: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.7, OH.8 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Water interactions, Hydrogen bonds: B:Q.128 Metal complexes: B:E.18, B:E.51, B:E.51, B:H.54, B:E.95, B:E.131, H2O.6 FEO.26: 9 residues within 4Å: Chain E: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.27 8 PLIP interactions: 7 interactions with chain E, 1 Ligand-Water interactions, Metal complexes: E:E.18, E:E.51, E:E.51, E:H.54, E:E.95, E:E.95, E:E.131, H2O.23 FEO.38: 10 residues within 4Å: Chain G: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.39, OH.40 8 PLIP interactions: 8 interactions with chain G, Hydrogen bonds: G:Q.128 Metal complexes: G:E.18, G:E.51, G:E.51, G:H.54, G:E.95, G:E.95, G:E.131 FEO.43: 10 residues within 4Å: Chain H: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.44, OH.45 8 PLIP interactions: 7 interactions with chain H, 1 Ligand-Water interactions, Hydrogen bonds: H:Q.128 Metal complexes: H:E.18, H:E.51, H:E.51, H:H.54, H:E.95, H:E.131, H2O.40 FEO.63: 9 residues within 4Å: Chain K: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.64 8 PLIP interactions: 7 interactions with chain K, 1 Ligand-Water interactions, Metal complexes: K:E.18, K:E.51, K:E.51, K:H.54, K:E.95, K:E.95, K:E.131, H2O.57 FEO.75: 10 residues within 4Å: Chain M: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.76, OH.77 8 PLIP interactions: 8 interactions with chain M, Hydrogen bonds: M:Q.128 Metal complexes: M:E.18, M:E.51, M:E.51, M:H.54, M:E.95, M:E.95, M:E.131 FEO.80: 10 residues within 4Å: Chain N: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.81, OH.82 8 PLIP interactions: 7 interactions with chain N, 1 Ligand-Water interactions, Hydrogen bonds: N:Q.128 Metal complexes: N:E.18, N:E.51, N:E.51, N:H.54, N:E.95, N:E.131, H2O.74 FEO.100: 9 residues within 4Å: Chain Q: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.101 8 PLIP interactions: 7 interactions with chain Q, 1 Ligand-Water interactions, Metal complexes: Q:E.18, Q:E.51, Q:E.51, Q:H.54, Q:E.95, Q:E.95, Q:E.131, H2O.91 FEO.112: 10 residues within 4Å: Chain S: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.113, OH.114 8 PLIP interactions: 8 interactions with chain S, Hydrogen bonds: S:Q.128 Metal complexes: S:E.18, S:E.51, S:E.51, S:H.54, S:E.95, S:E.95, S:E.131 FEO.117: 10 residues within 4Å: Chain T: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.118, OH.119 8 PLIP interactions: 7 interactions with chain T, 1 Ligand-Water interactions, Hydrogen bonds: T:Q.128 Metal complexes: T:E.18, T:E.51, T:E.51, T:H.54, T:E.95, T:E.131, H2O.108 FEO.137: 9 residues within 4Å: Chain W: E.18, H.47, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: OH.138 8 PLIP interactions: 7 interactions with chain W, 1 Ligand-Water interactions, Metal complexes: W:E.18, W:E.51, W:E.51, W:H.54, W:E.95, W:E.95, W:E.131, H2O.125

36 x OH: HYDROXIDE ION(Non-covalent)

OH.2: 7 residues within 4Å: Chain A: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.1, OH.3 Ligand excluded by PLIP OH.3: 6 residues within 4Å: Chain A: E.18, E.51, H.54, I.98 Ligands: FEO.1, OH.2 Ligand excluded by PLIP OH.7: 7 residues within 4Å: Chain B: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.6, OH.8 Ligand excluded by PLIP OH.8: 7 residues within 4Å: Chain B: E.18, A.21, E.51, H.54, I.98 Ligands: FEO.6, OH.7 Ligand excluded by PLIP OH.14: 7 residues within 4Å: Chain C: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.11, OXY.13 Ligand excluded by PLIP OH.23: 7 residues within 4Å: Chain D: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.20, PER.22 Ligand excluded by PLIP OH.27: 6 residues within 4Å: Chain E: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.26 Ligand excluded by PLIP OH.35: 9 residues within 4Å: Chain F: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.32, O.33, O.34, OH.36 Ligand excluded by PLIP OH.36: 8 residues within 4Å: Chain F: E.18, A.21, E.51, H.54, I.98 Ligands: FE.32, O.33, OH.35 Ligand excluded by PLIP OH.39: 7 residues within 4Å: Chain G: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.38, OH.40 Ligand excluded by PLIP OH.40: 6 residues within 4Å: Chain G: E.18, E.51, H.54, I.98 Ligands: FEO.38, OH.39 Ligand excluded by PLIP OH.44: 7 residues within 4Å: Chain H: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.43, OH.45 Ligand excluded by PLIP OH.45: 7 residues within 4Å: Chain H: E.18, A.21, E.51, H.54, I.98 Ligands: FEO.43, OH.44 Ligand excluded by PLIP OH.51: 7 residues within 4Å: Chain I: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.48, OXY.50 Ligand excluded by PLIP OH.60: 7 residues within 4Å: Chain J: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.57, PER.59 Ligand excluded by PLIP OH.64: 6 residues within 4Å: Chain K: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.63 Ligand excluded by PLIP OH.72: 9 residues within 4Å: Chain L: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.69, O.70, O.71, OH.73 Ligand excluded by PLIP OH.73: 8 residues within 4Å: Chain L: E.18, A.21, E.51, H.54, I.98 Ligands: FE.69, O.70, OH.72 Ligand excluded by PLIP OH.76: 7 residues within 4Å: Chain M: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.75, OH.77 Ligand excluded by PLIP OH.77: 6 residues within 4Å: Chain M: E.18, E.51, H.54, I.98 Ligands: FEO.75, OH.76 Ligand excluded by PLIP OH.81: 7 residues within 4Å: Chain N: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.80, OH.82 Ligand excluded by PLIP OH.82: 7 residues within 4Å: Chain N: E.18, A.21, E.51, H.54, I.98 Ligands: FEO.80, OH.81 Ligand excluded by PLIP OH.88: 7 residues within 4Å: Chain O: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.85, OXY.87 Ligand excluded by PLIP OH.97: 7 residues within 4Å: Chain P: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.94, PER.96 Ligand excluded by PLIP OH.101: 6 residues within 4Å: Chain Q: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.100 Ligand excluded by PLIP OH.109: 9 residues within 4Å: Chain R: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.106, O.107, O.108, OH.110 Ligand excluded by PLIP OH.110: 8 residues within 4Å: Chain R: E.18, A.21, E.51, H.54, I.98 Ligands: FE.106, O.107, OH.109 Ligand excluded by PLIP OH.113: 7 residues within 4Å: Chain S: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.112, OH.114 Ligand excluded by PLIP OH.114: 6 residues within 4Å: Chain S: E.18, E.51, H.54, I.98 Ligands: FEO.112, OH.113 Ligand excluded by PLIP OH.118: 7 residues within 4Å: Chain T: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.117, OH.119 Ligand excluded by PLIP OH.119: 7 residues within 4Å: Chain T: E.18, A.21, E.51, H.54, I.98 Ligands: FEO.117, OH.118 Ligand excluded by PLIP OH.125: 7 residues within 4Å: Chain U: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.122, OXY.124 Ligand excluded by PLIP OH.134: 7 residues within 4Å: Chain V: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.131, PER.133 Ligand excluded by PLIP OH.138: 6 residues within 4Å: Chain W: E.18, H.54, I.98, Y.124, Q.128 Ligands: FEO.137 Ligand excluded by PLIP OH.146: 9 residues within 4Å: Chain X: E.18, H.54, I.98, Y.124, Q.128 Ligands: FE.143, O.144, O.145, OH.147 Ligand excluded by PLIP OH.147: 8 residues within 4Å: Chain X: E.18, A.21, E.51, H.54, I.98 Ligands: FE.143, O.144, OH.146 Ligand excluded by PLIP

56 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: N.16, L.19, Y.20, T.73, V.74, E.75 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: Q.100, N.103, E.104, H.107 Chain C: Q.113, Y.115 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain B: S.22, L.23, Q.26, A.48, Q.49, M.52 Chain E: M.52, M.55 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain B: L.3, D.114, P.116 Chain W: T.99, N.103 Ligand excluded by PLIP GOL.15: 9 residues within 4Å: Chain C: S.22, L.23, Q.26, A.48, Q.49, M.52 Chain D: M.52, M.55, Q.56 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain C: I.8, E.9, N.12, L.68, P.69, R.70 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain C: T.36, E.38 Chain N: S.137, D.140, K.141, L.144 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain C: A.42, R.45, R.46 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain C: R.70, N.72, T.73 Chain D: S.76 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain D: Q.100, N.103, H.107 Chain E: Q.113, Y.115 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain A: K.147 Chain D: S.148, G.149, E.150 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain E: I.8, E.9, N.12, L.68, R.70 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain B: S.76 Chain E: R.70, N.72, T.73 Ligand excluded by PLIP GOL.37: 9 residues within 4Å: Chain A: M.52, M.55, Q.56 Chain F: S.22, L.23, Q.26, A.48, Q.49, M.52 Ligand excluded by PLIP GOL.41: 6 residues within 4Å: Chain G: N.16, L.19, Y.20, T.73, V.74, E.75 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain G: Q.100, N.103, E.104, H.107 Chain I: Q.113, Y.115 Ligand excluded by PLIP GOL.46: 8 residues within 4Å: Chain H: S.22, L.23, Q.26, A.48, Q.49, M.52 Chain K: M.52, M.55 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain H: L.3, D.114, P.116 Chain Q: T.99, N.103 Ligand excluded by PLIP GOL.52: 9 residues within 4Å: Chain I: S.22, L.23, Q.26, A.48, Q.49, M.52 Chain J: M.52, M.55, Q.56 Ligand excluded by PLIP GOL.53: 6 residues within 4Å: Chain I: I.8, E.9, N.12, L.68, P.69, R.70 Ligand excluded by PLIP GOL.54: 6 residues within 4Å: Chain I: T.36, E.38 Chain T: S.137, D.140, K.141, L.144 Ligand excluded by PLIP GOL.55: 3 residues within 4Å: Chain I: A.42, R.45, R.46 Ligand excluded by PLIP GOL.56: 4 residues within 4Å: Chain I: R.70, N.72, T.73 Chain J: S.76 Ligand excluded by PLIP GOL.61: 5 residues within 4Å: Chain J: Q.100, N.103, H.107 Chain K: Q.113, Y.115 Ligand excluded by PLIP GOL.62: 4 residues within 4Å: Chain G: K.147 Chain J: S.148, G.149, E.150 Ligand excluded by PLIP GOL.65: 5 residues within 4Å: Chain K: I.8, E.9, N.12, L.68, R.70 Ligand excluded by PLIP GOL.66: 4 residues within 4Å: Chain H: S.76 Chain K: R.70, N.72, T.73 Ligand excluded by PLIP GOL.74: 9 residues within 4Å: Chain G: M.52, M.55, Q.56 Chain L: S.22, L.23, Q.26, A.48, Q.49, M.52 Ligand excluded by PLIP GOL.78: 6 residues within 4Å: Chain M: N.16, L.19, Y.20, T.73, V.74, E.75 Ligand excluded by PLIP GOL.79: 6 residues within 4Å: Chain M: Q.100, N.103, E.104, H.107 Chain O: Q.113, Y.115 Ligand excluded by PLIP GOL.83: 8 residues within 4Å: Chain N: S.22, L.23, Q.26, A.48, Q.49, M.52 Chain Q: M.52, M.55 Ligand excluded by PLIP GOL.84: 5 residues within 4Å: Chain E: T.99, N.103 Chain N: L.3, D.114, P.116 Ligand excluded by PLIP GOL.89: 9 residues within 4Å: Chain O: S.22, L.23, Q.26, A.48, Q.49, M.52 Chain P: M.52, M.55, Q.56 Ligand excluded by PLIP GOL.90: 6 residues within 4Å: Chain O: I.8, E.9, N.12, L.68, P.69, R.70 Ligand excluded by PLIP GOL.91: 6 residues within 4Å: Chain H: S.137, D.140, K.141, L.144 Chain O: T.36, E.38 Ligand excluded by PLIP GOL.92: 3 residues within 4Å: Chain O: A.42, R.45, R.46 Ligand excluded by PLIP GOL.93: 4 residues within 4Å: Chain O: R.70, N.72, T.73 Chain P: S.76 Ligand excluded by PLIP GOL.98: 5 residues within 4Å: Chain P: Q.100, N.103, H.107 Chain Q: Q.113, Y.115 Ligand excluded by PLIP GOL.99: 4 residues within 4Å: Chain M: K.147 Chain P: S.148, G.149, E.150 Ligand excluded by PLIP GOL.102: 5 residues within 4Å: Chain Q: I.8, E.9, N.12, L.68, R.70 Ligand excluded by PLIP GOL.103: 4 residues within 4Å: Chain N: S.76 Chain Q: R.70, N.72, T.73 Ligand excluded by PLIP GOL.111: 9 residues within 4Å: Chain M: M.52, M.55, Q.56 Chain R: S.22, L.23, Q.26, A.48, Q.49, M.52 Ligand excluded by PLIP GOL.115: 6 residues within 4Å: Chain S: N.16, L.19, Y.20, T.73, V.74, E.75 Ligand excluded by PLIP GOL.116: 6 residues within 4Å: Chain S: Q.100, N.103, E.104, H.107 Chain U: Q.113, Y.115 Ligand excluded by PLIP GOL.120: 8 residues within 4Å: Chain T: S.22, L.23, Q.26, A.48, Q.49, M.52 Chain W: M.52, M.55 Ligand excluded by PLIP GOL.121: 5 residues within 4Å: Chain K: T.99, N.103 Chain T: L.3, D.114, P.116 Ligand excluded by PLIP GOL.126: 9 residues within 4Å: Chain U: S.22, L.23, Q.26, A.48, Q.49, M.52 Chain V: M.52, M.55, Q.56 Ligand excluded by PLIP GOL.127: 6 residues within 4Å: Chain U: I.8, E.9, N.12, L.68, P.69, R.70 Ligand excluded by PLIP GOL.128: 6 residues within 4Å: Chain B: S.137, D.140, K.141, L.144 Chain U: T.36, E.38 Ligand excluded by PLIP GOL.129: 3 residues within 4Å: Chain U: A.42, R.45, R.46 Ligand excluded by PLIP GOL.130: 4 residues within 4Å: Chain U: R.70, N.72, T.73 Chain V: S.76 Ligand excluded by PLIP GOL.135: 5 residues within 4Å: Chain V: Q.100, N.103, H.107 Chain W: Q.113, Y.115 Ligand excluded by PLIP GOL.136: 4 residues within 4Å: Chain S: K.147 Chain V: S.148, G.149, E.150 Ligand excluded by PLIP GOL.139: 5 residues within 4Å: Chain W: I.8, E.9, N.12, L.68, R.70 Ligand excluded by PLIP GOL.140: 4 residues within 4Å: Chain T: S.76 Chain W: R.70, N.72, T.73 Ligand excluded by PLIP GOL.148: 9 residues within 4Å: Chain S: M.52, M.55, Q.56 Chain X: S.22, L.23, Q.26, A.48, Q.49, M.52 Ligand excluded by PLIP

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

FE.11: 7 residues within 4Å: Chain C: E.18, E.51, H.54, Q.128 Ligands: FE2.12, OXY.13, OH.14 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.18, C:E.51, C:H.54, H2O.12 FE.20: 7 residues within 4Å: Chain D: E.18, E.51, H.54, Q.128 Ligands: FE.21, PER.22, OH.23 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.18, D:E.51, D:H.54, H2O.18 FE.21: 6 residues within 4Å: Chain D: H.47, E.51, E.95, E.131 Ligands: FE.20, PER.22 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.51, D:E.95, D:E.95, D:E.131 FE.31: 7 residues within 4Å: Chain F: H.47, E.51, E.95, E.131 Ligands: FE.32, O.33, O.34 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:E.51, F:E.95, F:E.95, F:E.131, O.33 FE.32: 9 residues within 4Å: Chain F: E.18, E.51, H.54, Q.128 Ligands: FE.31, O.33, O.34, OH.35, OH.36 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:E.18, F:E.51, F:H.54, O.33 FE.48: 7 residues within 4Å: Chain I: E.18, E.51, H.54, Q.128 Ligands: FE2.49, OXY.50, OH.51 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.18, I:E.51, I:H.54, H2O.46 FE.57: 7 residues within 4Å: Chain J: E.18, E.51, H.54, Q.128 Ligands: FE.58, PER.59, OH.60 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.18, J:E.51, J:H.54, H2O.52 FE.58: 6 residues within 4Å: Chain J: H.47, E.51, E.95, E.131 Ligands: FE.57, PER.59 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.51, J:E.95, J:E.95, J:E.131 FE.68: 7 residues within 4Å: Chain L: H.47, E.51, E.95, E.131 Ligands: FE.69, O.70, O.71 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Ligand interactions Metal complexes: L:E.51, L:E.95, L:E.95, L:E.131, O.70 FE.69: 9 residues within 4Å: Chain L: E.18, E.51, H.54, Q.128 Ligands: FE.68, O.70, O.71, OH.72, OH.73 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Ligand interactions Metal complexes: L:E.18, L:E.51, L:H.54, O.70 FE.85: 7 residues within 4Å: Chain O: E.18, E.51, H.54, Q.128 Ligands: FE2.86, OXY.87, OH.88 4 PLIP interactions: 3 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.18, O:E.51, O:H.54, H2O.80 FE.94: 7 residues within 4Å: Chain P: E.18, E.51, H.54, Q.128 Ligands: FE.95, PER.96, OH.97 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.18, P:E.51, P:H.54, H2O.86 FE.95: 6 residues within 4Å: Chain P: H.47, E.51, E.95, E.131 Ligands: FE.94, PER.96 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:E.51, P:E.95, P:E.95, P:E.131 FE.105: 7 residues within 4Å: Chain R: H.47, E.51, E.95, E.131 Ligands: FE.106, O.107, O.108 5 PLIP interactions: 4 interactions with chain R, 1 Ligand-Ligand interactions Metal complexes: R:E.51, R:E.95, R:E.95, R:E.131, O.107 FE.106: 9 residues within 4Å: Chain R: E.18, E.51, H.54, Q.128 Ligands: FE.105, O.107, O.108, OH.109, OH.110 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Ligand interactions Metal complexes: R:E.18, R:E.51, R:H.54, O.107 FE.122: 7 residues within 4Å: Chain U: E.18, E.51, H.54, Q.128 Ligands: FE2.123, OXY.124, OH.125 4 PLIP interactions: 3 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.18, U:E.51, U:H.54, H2O.114 FE.131: 7 residues within 4Å: Chain V: E.18, E.51, H.54, Q.128 Ligands: FE.132, PER.133, OH.134 4 PLIP interactions: 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.18, V:E.51, V:H.54, H2O.119 FE.132: 6 residues within 4Å: Chain V: H.47, E.51, E.95, E.131 Ligands: FE.131, PER.133 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:E.51, V:E.95, V:E.95, V:E.131 FE.142: 7 residues within 4Å: Chain X: H.47, E.51, E.95, E.131 Ligands: FE.143, O.144, O.145 5 PLIP interactions: 4 interactions with chain X, 1 Ligand-Ligand interactions Metal complexes: X:E.51, X:E.95, X:E.95, X:E.131, O.144 FE.143: 9 residues within 4Å: Chain X: E.18, E.51, H.54, Q.128 Ligands: FE.142, O.144, O.145, OH.146, OH.147 4 PLIP interactions: 3 interactions with chain X, 1 Ligand-Ligand interactions Metal complexes: X:E.18, X:E.51, X:H.54, O.144

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

FE2.12: 7 residues within 4Å: Chain C: H.47, E.51, E.95, Q.128, E.131 Ligands: FE.11, OXY.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.51, C:E.95, C:E.95, C:E.131, H2O.12 FE2.30: 11 residues within 4Å: Chain E: E.150, F.154 Chain K: E.150, F.154 Chain Q: E.150, F.154 Chain W: E.150, F.154 Ligands: FE2.67, FE2.104, FE2.141 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain Q, 1 interactions with chain K, 1 interactions with chain W Metal complexes: E:E.150, Q:E.150, K:E.150, W:E.150 FE2.49: 7 residues within 4Å: Chain I: H.47, E.51, E.95, Q.128, E.131 Ligands: FE.48, OXY.50 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.51, I:E.95, I:E.95, I:E.131, H2O.46 FE2.67: 11 residues within 4Å: Chain E: E.150, F.154 Chain K: E.150, F.154 Chain Q: E.150, F.154 Chain W: E.150, F.154 Ligands: FE2.30, FE2.104, FE2.141 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain Q, 1 interactions with chain K, 1 interactions with chain W Metal complexes: E:E.150, Q:E.150, K:E.150, W:E.150 FE2.86: 7 residues within 4Å: Chain O: H.47, E.51, E.95, Q.128, E.131 Ligands: FE.85, OXY.87 5 PLIP interactions: 4 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.51, O:E.95, O:E.95, O:E.131, H2O.80 FE2.104: 11 residues within 4Å: Chain E: E.150, F.154 Chain K: E.150, F.154 Chain Q: E.150, F.154 Chain W: E.150, F.154 Ligands: FE2.30, FE2.67, FE2.141 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain Q, 1 interactions with chain E, 1 interactions with chain W Metal complexes: K:E.150, Q:E.150, E:E.150, W:E.150 FE2.123: 7 residues within 4Å: Chain U: H.47, E.51, E.95, Q.128, E.131 Ligands: FE.122, OXY.124 5 PLIP interactions: 4 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.51, U:E.95, U:E.95, U:E.131, H2O.114 FE2.141: 11 residues within 4Å: Chain E: E.150, F.154 Chain K: E.150, F.154 Chain Q: E.150, F.154 Chain W: E.150, F.154 Ligands: FE2.30, FE2.67, FE2.104 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain W, 1 interactions with chain E, 1 interactions with chain Q Metal complexes: K:E.150, W:E.150, E:E.150, Q:E.150

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.13: 10 residues within 4Å: Chain C: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.11, FE2.12, OH.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.128, C:E.131 OXY.50: 10 residues within 4Å: Chain I: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.48, FE2.49, OH.51 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.128 OXY.87: 10 residues within 4Å: Chain O: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.85, FE2.86, OH.88 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:Q.128 OXY.124: 10 residues within 4Å: Chain U: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.122, FE2.123, OH.125 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:Q.128, U:Q.128

4 x PER: PEROXIDE ION(Non-covalent)

PER.22: 10 residues within 4Å: Chain D: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.20, FE.21, OH.23 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.18, D:Q.128 PER.59: 10 residues within 4Å: Chain J: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.57, FE.58, OH.60 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:E.18, J:Q.128 PER.96: 10 residues within 4Å: Chain P: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.94, FE.95, OH.97 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:E.18, P:Q.128 PER.133: 10 residues within 4Å: Chain V: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.131, FE.132, OH.134 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:E.18, V:Q.128

8 x O: OXYGEN ATOM(Non-covalent)(Covalent)

O.33: 12 residues within 4Å: Chain F: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.31, FE.32, O.34, OH.35, OH.36 No protein-ligand interaction detected (PLIP) O.34: 8 residues within 4Å: Chain F: E.95, I.98, Q.128, E.131 Ligands: FE.31, FE.32, O.33, OH.35 No protein-ligand interaction detected (PLIP) O.70: 12 residues within 4Å: Chain L: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.68, FE.69, O.71, OH.72, OH.73 No protein-ligand interaction detected (PLIP) O.71: 8 residues within 4Å: Chain L: E.95, I.98, Q.128, E.131 Ligands: FE.68, FE.69, O.70, OH.72 No protein-ligand interaction detected (PLIP) O.107: 12 residues within 4Å: Chain R: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.105, FE.106, O.108, OH.109, OH.110 No protein-ligand interaction detected (PLIP) O.108: 8 residues within 4Å: Chain R: E.95, I.98, Q.128, E.131 Ligands: FE.105, FE.106, O.107, OH.109 No protein-ligand interaction detected (PLIP) O.144: 12 residues within 4Å: Chain X: E.18, E.51, H.54, E.95, I.98, Q.128, E.131 Ligands: FE.142, FE.143, O.145, OH.146, OH.147 No protein-ligand interaction detected (PLIP) O.145: 8 residues within 4Å: Chain X: E.95, I.98, Q.128, E.131 Ligands: FE.142, FE.143, O.144, OH.146 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S. et al., Structural Basis of Novel Iron-Uptake Route and Reaction Intermediates in Ferritins from Gram-Negative Bacteria. J. Mol. Biol. (2016)

Release Date

2016-06-15

Peptides

Bacterial non-heme ferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

M
A

N
B

O
C

P
D

Q
E

R
F

S
A

T
B

U
C

V
D

W
E

X
F

Bacterial non-heme ferritin