SMTL ID : 3iap.1

E. coli (lacZ) beta-galactosidase (E416Q)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.15, 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.2: 2 residues within 4Å: Chain A: T.911 Ligands: DMS.13 No protein-ligand interaction detected (PLIP) MG.40: 5 residues within 4Å: Chain B: D.15, N.18, V.21, Q.163, D.193 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.15, B:N.18, B:V.21, B:D.193 MG.41: 2 residues within 4Å: Chain B: Q.718 Ligands: DMS.75 No protein-ligand interaction detected (PLIP) MG.81: 5 residues within 4Å: Chain C: D.15, N.18, V.21, Q.163, D.193 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.15, C:N.18, C:V.21, C:D.193 MG.82: 3 residues within 4Å: Chain C: Q.718, T.911 Ligands: DMS.117 No protein-ligand interaction detected (PLIP) MG.119: 6 residues within 4Å: Chain D: D.15, N.18, V.21, Y.161, 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.120: 3 residues within 4Å: Chain D: Q.718, T.911 Ligands: DMS.150 No protein-ligand interaction detected (PLIP)

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

NA.3: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.4: 5 residues within 4Å: Chain A: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.5: 4 residues within 4Å: Chain A: S.647, D.648, E.650, L.670 Ligand excluded by PLIP NA.6: 6 residues within 4Å: Chain A: Y.100, D.201, W.568, F.601, N.604 Ligands: BTB.7 Ligand excluded by PLIP NA.42: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.43: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.44: 6 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.62 Ligand excluded by PLIP NA.45: 6 residues within 4Å: Chain B: Y.100, D.201, F.601, C.602, N.604 Ligands: BTB.46 Ligand excluded by PLIP NA.83: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.84: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.85: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.104 Ligand excluded by PLIP NA.86: 5 residues within 4Å: Chain C: D.201, W.568, F.601, N.604 Ligands: BTB.87 Ligand excluded by PLIP NA.121: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.122: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.123: 5 residues within 4Å: Chain D: D.201, W.568, F.601, N.604 Ligands: BTB.125 Ligand excluded by PLIP NA.124: 5 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, L.670 Ligand excluded by PLIP

4 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.7: 12 residues within 4Å: Chain A: N.102, D.201, H.391, Q.416, N.460, E.461, Y.503, E.537, H.540, W.568, W.999 Ligands: NA.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.416, A:Q.416, A:N.460, A:N.460, A:H.540, A:W.568 Water bridges: A:D.201, A:D.201 Salt bridges: A:D.201, A:E.461, A:E.537 BTB.46: 14 residues within 4Å: Chain B: N.102, Q.200, D.201, H.391, Q.416, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, W.999 Ligands: NA.45 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.201, B:H.391, B:Q.416, B:N.460, B:E.461, B:E.461 Salt bridges: B:D.201, B:E.461, B:E.537 BTB.87: 14 residues within 4Å: Chain C: N.102, V.103, Q.200, D.201, H.391, Q.416, H.418, N.460, E.461, M.502, Y.503, E.537, W.568 Ligands: NA.86 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:N.102, C:D.201, C:Q.416, C:Q.416, C:H.418, C:N.460, C:Y.503, C:E.537, C:W.568 Water bridges: C:E.461 Salt bridges: C:D.201, C:E.461, C:E.537 BTB.125: 13 residues within 4Å: Chain D: N.102, D.201, H.391, H.418, N.460, E.461, Y.503, E.537, H.540, W.568, N.604, W.999 Ligands: NA.123 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.102, D:D.201, D:N.460, D:E.461, D:Y.503, D:E.537, D:W.568, D:N.604 Salt bridges: D:D.201, D:E.461

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

DMS.8: 8 residues within 4Å: Chain A: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.9: 4 residues within 4Å: Chain A: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.10: 3 residues within 4Å: Chain A: V.84, V.85, H.93 Ligand excluded by PLIP DMS.11: 7 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.20 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: S.53, L.54, N.55, L.125, F.127 Ligand excluded by PLIP DMS.13: 3 residues within 4Å: Chain A: Q.719, R.721 Ligands: MG.2 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: Y.472, T.494, T.496, R.531 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: P.907, L.910, C.939, G.940, Q.956 Ligand excluded by PLIP DMS.17: 6 residues within 4Å: Chain A: L.377, T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: R.282, G.283, G.284, A.286 Chain D: V.421 Ligand excluded by PLIP DMS.19: 2 residues within 4Å: Chain A: R.404, Y.405 Ligand excluded by PLIP DMS.20: 8 residues within 4Å: Chain A: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.11 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain A: L.250, R.251, D.252 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain A: R.37, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain A: Q.266, V.267, S.269 Ligand excluded by PLIP DMS.24: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain A: Q.783, F.784, T.785, H.815 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain A: F.629, R.630, L.631, Q.718, W.720 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain A: R.699, I.714, W.717, C.914 Ligand excluded by PLIP DMS.28: 6 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.29: 5 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain A: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.31: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.32: 6 residues within 4Å: Chain A: R.230, F.231, N.232, R.237, A.238, V.239 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain A: R.630, S.632, T.635, E.637, L.679 Ligand excluded by PLIP DMS.34: 4 residues within 4Å: Chain A: I.737, E.750, L.751, G.752 Ligand excluded by PLIP DMS.35: 5 residues within 4Å: Chain A: D.428, A.466 Chain D: H.226, W.474, V.478 Ligand excluded by PLIP DMS.36: 4 residues within 4Å: Chain A: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.37: 4 residues within 4Å: Chain A: E.314, H.316, G.320, L.322 Ligand excluded by PLIP DMS.38: 3 residues within 4Å: Chain A: E.40, W.261, E.264 Ligand excluded by PLIP DMS.39: 3 residues within 4Å: Chain A: I.305, P.306, N.307 Ligand excluded by PLIP DMS.47: 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.48: 6 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.50: 8 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.70 Ligand excluded by PLIP DMS.51: 4 residues within 4Å: Chain B: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.52: 5 residues within 4Å: Chain B: E.314, H.316, T.317, G.320, L.322 Ligand excluded by PLIP DMS.53: 4 residues within 4Å: Chain B: E.334, V.335, P.480, S.481 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.55: 5 residues within 4Å: Chain B: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.56: 4 residues within 4Å: Chain B: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.57: 2 residues within 4Å: Chain B: R.251, D.252 Ligand excluded by PLIP DMS.58: 4 residues within 4Å: Chain B: F.231, N.232, D.233, E.334 Ligand excluded by PLIP DMS.59: 6 residues within 4Å: Chain B: D.428, P.430 Chain C: H.226, Q.445, R.448, V.478 Ligand excluded by PLIP DMS.60: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain B: Y.926, P.928, Y.962, R.973 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain B: D.648, N.649, E.650, N.704 Ligands: NA.44 Ligand excluded by PLIP DMS.63: 4 residues within 4Å: Chain B: R.37, S.132, W.133, H.216 Ligand excluded by PLIP DMS.64: 5 residues within 4Å: Chain B: S.923, Y.926, R.961, Y.962, A.978 Ligand excluded by PLIP DMS.65: 4 residues within 4Å: Chain B: E.369, L.401, R.404 Ligands: DMS.66 Ligand excluded by PLIP DMS.66: 4 residues within 4Å: Chain B: R.404, Y.405, A.707 Ligands: DMS.65 Ligand excluded by PLIP DMS.67: 3 residues within 4Å: Chain B: I.305, P.306, N.307 Ligand excluded by PLIP DMS.68: 7 residues within 4Å: Chain B: L.377, Q.381, T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.69: 4 residues within 4Å: Chain B: R.630, S.632, T.635, E.637 Ligand excluded by PLIP DMS.70: 6 residues within 4Å: Chain B: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.50 Ligand excluded by PLIP DMS.71: 3 residues within 4Å: Chain B: N.102, V.103, V.795 Ligand excluded by PLIP DMS.72: 2 residues within 4Å: Chain B: E.41, Q.49 Ligand excluded by PLIP DMS.73: 6 residues within 4Å: Chain B: R.52, S.53, L.54, N.55, L.125, F.127 Ligand excluded by PLIP DMS.74: 4 residues within 4Å: Chain B: P.662, L.663, A.664, S.665 Ligand excluded by PLIP DMS.75: 4 residues within 4Å: Chain B: W.695, Q.719, R.721 Ligands: MG.41 Ligand excluded by PLIP DMS.76: 4 residues within 4Å: Chain B: T.618, K.621, I.714, W.717 Ligand excluded by PLIP DMS.77: 6 residues within 4Å: Chain B: E.57, W.58, R.59, S.124, L.125, T.126 Ligand excluded by PLIP DMS.78: 4 residues within 4Å: Chain B: Y.472, T.494, T.496, D.497 Ligand excluded by PLIP DMS.79: 4 residues within 4Å: Chain B: R.230, F.231, N.232, V.239 Ligand excluded by PLIP DMS.80: 5 residues within 4Å: Chain B: Q.23 Chain C: P.19, P.112, R.431, W.432 Ligand excluded by PLIP DMS.88: 8 residues within 4Å: Chain C: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.89: 6 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.90: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.91: 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.92: 4 residues within 4Å: Chain C: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.93: 4 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain C: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.95: 3 residues within 4Å: Chain C: I.99, P.106 Ligands: DMS.107 Ligand excluded by PLIP DMS.96: 6 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, D.610, R.973 Ligand excluded by PLIP DMS.97: 6 residues within 4Å: Chain C: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.98: 4 residues within 4Å: Chain C: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.99: 4 residues within 4Å: Chain C: T.618, K.621, W.717 Ligands: DMS.113 Ligand excluded by PLIP DMS.100: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.101: 3 residues within 4Å: Chain B: V.478 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.102: 2 residues within 4Å: Chain C: H.93, G.94 Ligand excluded by PLIP DMS.103: 3 residues within 4Å: Chain C: Y.926, Y.962, R.973 Ligand excluded by PLIP DMS.104: 4 residues within 4Å: Chain C: E.650, P.703, N.704 Ligands: NA.85 Ligand excluded by PLIP DMS.105: 4 residues within 4Å: Chain C: W.36, D.45, R.46, P.47 Ligand excluded by PLIP DMS.106: 2 residues within 4Å: Chain C: Q.266, V.267 Ligand excluded by PLIP DMS.107: 3 residues within 4Å: Chain C: I.107, T.108 Ligands: DMS.95 Ligand excluded by PLIP DMS.108: 4 residues within 4Å: Chain C: R.630, S.632, T.635, E.637 Ligand excluded by PLIP DMS.109: 7 residues within 4Å: Chain C: L.377, Q.381, T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.110: 2 residues within 4Å: Chain C: R.404, Y.405 Ligand excluded by PLIP DMS.111: 5 residues within 4Å: Chain C: E.314, H.316, G.320, T.321, L.322 Ligand excluded by PLIP DMS.112: 6 residues within 4Å: Chain C: R.37, Q.50, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.113: 5 residues within 4Å: Chain C: T.697, R.699, I.714, W.717 Ligands: DMS.99 Ligand excluded by PLIP DMS.114: 5 residues within 4Å: Chain C: R.230, F.231, N.232, R.237, V.239 Ligand excluded by PLIP DMS.115: 6 residues within 4Å: Chain C: L.54, N.55, G.56, E.57, L.125, F.127 Ligand excluded by PLIP DMS.116: 6 residues within 4Å: Chain C: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.117: 5 residues within 4Å: Chain C: W.695, Q.718, Q.719, R.721 Ligands: MG.82 Ligand excluded by PLIP DMS.118: 2 residues within 4Å: Chain C: P.306, N.307 Ligand excluded by PLIP DMS.126: 9 residues within 4Å: Chain D: V.227, T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.127: 6 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.128: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.129: 8 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.139 Ligand excluded by PLIP DMS.130: 3 residues within 4Å: Chain D: T.271, L.291, R.292 Ligand excluded by PLIP DMS.131: 4 residues within 4Å: Chain D: E.314, H.316, G.320, L.322 Ligand excluded by PLIP DMS.132: 5 residues within 4Å: Chain D: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.133: 4 residues within 4Å: Chain D: P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.134: 5 residues within 4Å: Chain D: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.135: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.136: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.137: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.138: 4 residues within 4Å: Chain D: Y.926, P.928, Y.962, R.973 Ligand excluded by PLIP DMS.139: 7 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.129 Ligand excluded by PLIP DMS.140: 4 residues within 4Å: Chain D: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.141: 6 residues within 4Å: Chain D: L.922, S.923, Y.926, R.961, Y.962, A.978 Ligand excluded by PLIP DMS.142: 6 residues within 4Å: Chain D: W.133, L.134, Q.135, E.136, G.137, S.174 Ligand excluded by PLIP DMS.143: 3 residues within 4Å: Chain D: H.739, L.751, G.752 Ligand excluded by PLIP DMS.144: 4 residues within 4Å: Chain D: K.621, I.714, W.717 Ligands: DMS.148 Ligand excluded by PLIP DMS.145: 6 residues within 4Å: Chain D: R.630, L.631, S.632, T.635, E.637, L.679 Ligand excluded by PLIP DMS.146: 6 residues within 4Å: Chain D: L.377, T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.147: 5 residues within 4Å: Chain D: R.505, E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.148: 5 residues within 4Å: Chain D: T.697, I.714, W.717, C.914 Ligands: DMS.144 Ligand excluded by PLIP DMS.149: 5 residues within 4Å: Chain D: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.150: 4 residues within 4Å: Chain D: Q.719, W.720, R.721 Ligands: MG.120 Ligand excluded by PLIP DMS.151: 5 residues within 4Å: Chain D: Y.472, T.494, T.496, D.497, R.531 Ligand excluded by PLIP DMS.152: 4 residues within 4Å: Chain D: L.822, L.823, Q.824, C.825 Ligand excluded by PLIP DMS.153: 5 residues within 4Å: Chain D: E.689, A.691, L.726, V.728, T.729 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lo, S. et al., Studies of Glu-416 variants of beta-galactosidase (E. coli) show that the active site Mg(2+) is not important for structure and indicate that the main role of Mg (2+) is to mediate optimization of active site chemistry. Protein J. (2010)

Release Date

2009-12-29

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-galactosidase