SMTL ID : 3dyp.1

E. coli (lacZ) beta-galactosidase (H418N)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: E.416, N.418, E.461 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.416, A:E.461, H2O.1, H2O.3, H2O.6 MG.2: 7 residues within 4Å: Chain A: D.15, W.16, N.18, V.21, Y.161, Q.163, D.193 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.15, A:N.18, A:V.21, A:D.193 MG.3: 1 residues within 4Å: Ligands: DMS.15 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: N.597 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:N.597, H2O.18, H2O.19, H2O.24, H2O.40 MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain B: E.416, N.418, E.461 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.416, B:E.461, H2O.43, H2O.46, H2O.49 MG.37: 5 residues within 4Å: Chain B: D.15, N.18, V.21, Q.163, D.193 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.15, B:N.18, B:V.21, B:D.193, B:D.193 MG.42: 2 residues within 4Å: Chain B: N.597, E.797 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:N.597, H2O.51, H2O.60, H2O.66 MG.70: 3 residues within 4Å: Chain C: E.416, N.418, E.461 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.416, C:E.461, H2O.85, H2O.88, H2O.91 MG.71: 6 residues within 4Å: Chain C: D.15, N.18, V.21, Y.161, Q.163, D.193 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.15, C:N.18, C:V.21, C:D.193, C:D.193 MG.72: 1 residues within 4Å: Chain C: Q.49 No protein-ligand interaction detected (PLIP) MG.73: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.78: 1 residues within 4Å: Chain C: N.597 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:N.597, H2O.93, H2O.102, H2O.103, H2O.108 MG.107: 3 residues within 4Å: Chain D: E.416, N.418, E.461 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.416, D:E.461, H2O.125, H2O.128, H2O.131 MG.108: 5 residues within 4Å: Chain D: D.15, N.18, V.21, Q.163, D.193 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.15, D:N.18, D:V.21, D:D.193, D:D.193 MG.113: 2 residues within 4Å: Chain D: N.597, E.797 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:N.597, H2O.142, H2O.144

16 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.5: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.6: 5 residues within 4Å: Chain A: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.7: 4 residues within 4Å: Chain A: S.647, E.650, L.670 Ligands: DMS.29 Ligand excluded by PLIP NA.38: 4 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.39: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.40: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.41: 6 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.63 Ligand excluded by PLIP NA.74: 4 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.75: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.76: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.77: 4 residues within 4Å: Chain C: S.647, E.650, L.670 Ligands: DMS.99 Ligand excluded by PLIP NA.109: 4 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.110: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.111: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.112: 5 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, L.670 Ligand excluded by PLIP

107 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.10: 9 residues within 4Å: Chain A: V.227, T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.11: 6 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.13: 6 residues within 4Å: Chain A: P.32, F.33, W.36, D.45, A.327 Ligands: DMS.31 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.15: 6 residues within 4Å: Chain A: E.314, H.316, G.320, T.321, L.322 Ligands: MG.3 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain A: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: L.54, N.55, L.125, F.127 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain A: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: P.106, P.115, W.191 Ligands: DMS.25 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.21: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain A: G.593, D.594, T.595 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain A: V.84, V.85, H.93 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain A: L.250, R.251, D.252 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain A: Y.105, P.106, I.107, T.108, P.596 Ligands: DMS.19 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain A: D.428, P.430 Chain D: R.448, V.478 Ligand excluded by PLIP DMS.27: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain A: Y.926, Y.962, R.973, L.976 Ligand excluded by PLIP DMS.29: 6 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, N.704 Ligands: NA.7 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain A: W.695, Q.718, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.31: 7 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.13 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.33: 4 residues within 4Å: Chain A: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain A: R.37, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.43: 9 residues within 4Å: Chain B: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.44: 6 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.45: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.46: 7 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain B: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain B: E.314, H.316, G.320, T.321, L.322 Ligand excluded by PLIP DMS.49: 4 residues within 4Å: Chain B: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.50: 6 residues within 4Å: Chain B: L.54, N.55, G.56, E.57, W.58, L.125 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.52: 3 residues within 4Å: Chain B: P.106, P.115, W.191 Ligand excluded by PLIP DMS.53: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.54: 6 residues within 4Å: Chain B: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.55: 3 residues within 4Å: Chain B: G.593, D.594, T.595 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain B: V.84, V.85, H.93 Ligand excluded by PLIP DMS.57: 3 residues within 4Å: Chain B: K.621, R.699, W.717 Ligand excluded by PLIP DMS.58: 3 residues within 4Å: Chain B: L.250, R.251, D.252 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain B: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.60: 2 residues within 4Å: Chain B: D.428 Chain C: V.478 Ligand excluded by PLIP DMS.61: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.62: 4 residues within 4Å: Chain B: Y.926, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.63: 7 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.41 Ligand excluded by PLIP DMS.64: 4 residues within 4Å: Chain B: W.695, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain B: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.66: 4 residues within 4Å: Chain B: R.37, S.132, W.133, H.216 Ligand excluded by PLIP DMS.67: 3 residues within 4Å: Chain B: N.102, D.598, F.601 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain B: S.923, Y.926, R.961, Y.962, A.978 Ligand excluded by PLIP DMS.69: 4 residues within 4Å: Chain B: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.79: 9 residues within 4Å: Chain C: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.80: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.81: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.82: 7 residues within 4Å: Chain C: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligand excluded by PLIP DMS.83: 4 residues within 4Å: Chain C: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.84: 4 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.85: 6 residues within 4Å: Chain C: L.54, N.55, G.56, E.57, W.58, L.125 Ligand excluded by PLIP DMS.86: 4 residues within 4Å: Chain C: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.87: 4 residues within 4Å: Chain C: P.106, P.115, W.191 Ligands: DMS.95 Ligand excluded by PLIP DMS.88: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.89: 5 residues within 4Å: Chain C: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.90: 3 residues within 4Å: Chain C: G.593, D.594, T.595 Ligand excluded by PLIP DMS.91: 3 residues within 4Å: Chain C: V.84, V.85, H.93 Ligand excluded by PLIP DMS.92: 2 residues within 4Å: Chain C: K.621, W.717 Ligand excluded by PLIP DMS.93: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.94: 6 residues within 4Å: Chain C: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.95: 6 residues within 4Å: Chain C: Y.105, P.106, I.107, T.108, P.596 Ligands: DMS.87 Ligand excluded by PLIP DMS.96: 3 residues within 4Å: Chain B: R.448 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.97: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.98: 5 residues within 4Å: Chain C: Y.926, P.928, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.99: 7 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.77 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain C: W.695, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.101: 6 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.102: 4 residues within 4Å: Chain C: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.103: 5 residues within 4Å: Chain C: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.104: 4 residues within 4Å: Chain C: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.105: 4 residues within 4Å: Chain C: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.106: 4 residues within 4Å: Chain C: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.114: 8 residues within 4Å: Chain D: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.115: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.116: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.117: 7 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, A.327 Ligands: DMS.133 Ligand excluded by PLIP DMS.118: 3 residues within 4Å: Chain D: T.271, L.291, R.292 Ligand excluded by PLIP DMS.119: 4 residues within 4Å: Chain D: E.314, H.316, G.320 Ligands: DMS.137 Ligand excluded by PLIP DMS.120: 4 residues within 4Å: Chain D: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.121: 4 residues within 4Å: Chain D: L.54, N.55, G.56, E.57 Ligand excluded by PLIP DMS.122: 4 residues within 4Å: Chain D: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.123: 3 residues within 4Å: Chain D: P.106, P.115, W.191 Ligand excluded by PLIP DMS.124: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.125: 5 residues within 4Å: Chain D: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.126: 3 residues within 4Å: Chain D: G.593, D.594, T.595 Ligand excluded by PLIP DMS.127: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.128: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.129: 5 residues within 4Å: Chain D: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.130: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.131: 5 residues within 4Å: Chain D: Y.926, Y.962, R.973, L.976 Ligands: DMS.136 Ligand excluded by PLIP DMS.132: 5 residues within 4Å: Chain D: W.695, Q.718, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.133: 6 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.117 Ligand excluded by PLIP DMS.134: 4 residues within 4Å: Chain D: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.135: 4 residues within 4Å: Chain D: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.136: 5 residues within 4Å: Chain D: S.923, Y.926, R.961, Y.962 Ligands: DMS.131 Ligand excluded by PLIP DMS.137: 3 residues within 4Å: Chain D: G.320, L.322 Ligands: DMS.119 Ligand excluded by PLIP DMS.138: 5 residues within 4Å: Chain D: Q.49, Q.50, D.130, S.132, W.133 Ligand excluded by PLIP DMS.139: 6 residues within 4Å: Chain D: W.133, L.134, Q.135, E.136, G.137, S.174 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juers, D.H. et al., Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli). Protein Sci. (2009)

Release Date

2008-10-28

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-galactosidase

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