SMTL ID : 3iaq.1

E. coli (lacz) beta-galactosidase (E416V)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

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: P.596, N.597 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.597 MG.3: 1 residues within 4Å: Chain A: Q.718 No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 7 residues within 4Å: Chain B: D.15, W.16, N.18, V.21, Y.161, 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.33: 1 residues within 4Å: Chain B: E.369 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain B: P.596, N.597 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.597, H2O.27, H2O.29 MG.35: 3 residues within 4Å: Chain B: H.622, Q.718, T.911 No protein-ligand interaction detected (PLIP) MG.63: 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.64: 2 residues within 4Å: Chain C: P.596, N.597 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:N.597, H2O.55 MG.65: 3 residues within 4Å: Chain C: Q.718, T.911 Ligands: DMS.94 No protein-ligand interaction detected (PLIP) MG.98: 7 residues within 4Å: Chain D: D.15, W.16, N.18, V.21, Y.161, Q.163, D.193 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.15, D:N.18, D:V.21, D:D.193 MG.99: 2 residues within 4Å: Chain D: Q.718, Q.719 No protein-ligand interaction detected (PLIP)

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

NA.5: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.559 NA.6: 5 residues within 4Å: Chain A: F.931, P.932, L.967, M.968, T.970 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.967 NA.7: 5 residues within 4Å: Chain A: D.201, W.568, F.601, N.604 Ligands: BTB.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.601, A:N.604 NA.36: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.556 NA.37: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.932 NA.38: 6 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.53 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.647, B:E.650, B:L.670 NA.39: 6 residues within 4Å: Chain B: Y.100, D.201, W.568, F.601, N.604 Ligands: BTB.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.201 NA.66: 5 residues within 4Å: Chain C: D.201, W.568, F.601, N.604 Ligands: BTB.97 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.201, C:N.604 NA.67: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.562 NA.68: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.968 NA.69: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.87 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.650, C:E.650 NA.100: 6 residues within 4Å: Chain D: L.350, F.556, Y.559, P.560, L.562, Q.563 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.562 NA.101: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.970 NA.102: 4 residues within 4Å: Chain D: D.201, W.568, F.601, N.604 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.201 Water bridges: D:N.604

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

DMS.8: 9 residues within 4Å: Chain A: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.10: 6 residues within 4Å: Chain A: K.380, N.383, F.384, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.11: 7 residues within 4Å: Chain A: F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.23 Ligand excluded by PLIP DMS.12: 6 residues within 4Å: Chain A: G.270, T.271, A.272, T.290, L.291, R.292 Ligand excluded by PLIP DMS.13: 3 residues within 4Å: Chain A: R.505, E.508, P.1001 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: S.53, L.54, N.55, G.56, F.127 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain A: P.106, I.107, P.115 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: A.272, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.19: 3 residues within 4Å: Chain A: G.593, D.594, T.595 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain A: K.621, I.714, W.717 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain A: D.428, P.430 Chain D: H.226, R.448, V.478 Ligand excluded by PLIP DMS.22: 2 residues within 4Å: Chain A: H.93, G.94 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain A: D.45, P.47, L.51 Ligands: DMS.11 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain A: E.57, R.59, S.124, L.125, T.126 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain A: R.37, Q.50, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.27: 3 residues within 4Å: Chain A: V.84, V.85, H.93 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain A: H.316, G.320, T.321, L.322 Ligand excluded by PLIP DMS.29: 6 residues within 4Å: Chain A: R.230, F.231, N.232, R.237, A.238, V.239 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain A: R.282, G.283, G.284, A.286 Ligand excluded by PLIP DMS.40: 9 residues within 4Å: Chain B: T.229, D.329, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.41: 5 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.42: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.43: 7 residues within 4Å: Chain B: F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.54 Ligand excluded by PLIP DMS.44: 3 residues within 4Å: Chain B: T.271, L.291, R.292 Ligand excluded by PLIP DMS.45: 3 residues within 4Å: Chain B: E.314, H.316, G.320 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain B: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.47: 5 residues within 4Å: Chain B: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.48: 4 residues within 4Å: Chain B: P.106, I.107, P.115, W.191 Ligand excluded by PLIP DMS.49: 6 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, D.610, R.973 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: G.275, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.51: 4 residues within 4Å: Chain B: D.428 Chain C: H.226, Q.445, V.478 Ligand excluded by PLIP DMS.52: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.53: 4 residues within 4Å: Chain B: D.648, E.650, P.703 Ligands: NA.38 Ligand excluded by PLIP DMS.54: 7 residues within 4Å: Chain B: W.36, D.45, R.46, P.47, S.48, L.51 Ligands: DMS.43 Ligand excluded by PLIP DMS.55: 5 residues within 4Å: Chain B: E.57, R.59, S.124, L.125, T.126 Ligand excluded by PLIP DMS.56: 2 residues within 4Å: Chain B: Q.719, R.721 Ligand excluded by PLIP DMS.57: 1 residues within 4Å: Chain B: S.132 Ligand excluded by PLIP DMS.58: 6 residues within 4Å: Chain B: R.230, F.231, N.232, R.237, A.238, V.239 Ligand excluded by PLIP DMS.59: 3 residues within 4Å: Chain B: V.84, V.85, H.93 Ligand excluded by PLIP DMS.60: 2 residues within 4Å: Chain B: S.923, Y.962 Ligand excluded by PLIP DMS.62: 3 residues within 4Å: Chain B: R.425 Chain C: L.250, D.287 Ligand excluded by PLIP DMS.70: 10 residues within 4Å: Chain C: V.227, T.229, D.329, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.71: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.72: 6 residues within 4Å: Chain C: K.380, N.383, F.384, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.73: 7 residues within 4Å: Chain C: F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.88 Ligand excluded by PLIP DMS.74: 6 residues within 4Å: Chain C: G.270, T.271, T.290, L.291, R.292, L.293 Ligand excluded by PLIP DMS.75: 4 residues within 4Å: Chain C: E.314, H.316, G.320, L.322 Ligand excluded by PLIP DMS.76: 5 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.77: 6 residues within 4Å: Chain C: S.53, L.54, N.55, W.58, L.125, F.127 Ligand excluded by PLIP DMS.78: 4 residues within 4Å: Chain C: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.79: 5 residues within 4Å: Chain C: I.99, P.106, I.107, P.115 Ligands: DMS.93 Ligand excluded by PLIP DMS.80: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.81: 4 residues within 4Å: Chain C: G.275, G.276, V.289, T.290 Ligand excluded by PLIP DMS.82: 4 residues within 4Å: Chain C: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.83: 3 residues within 4Å: Chain C: K.621, I.714, W.717 Ligand excluded by PLIP DMS.84: 4 residues within 4Å: Chain B: Q.445, V.478 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.85: 4 residues within 4Å: Chain C: D.82, H.93, G.94, Y.95 Ligand excluded by PLIP DMS.86: 4 residues within 4Å: Chain C: I.793, V.807, E.808, K.811 Ligand excluded by PLIP DMS.87: 6 residues within 4Å: Chain C: N.649, E.650, L.651, P.703, N.704 Ligands: NA.69 Ligand excluded by PLIP DMS.88: 5 residues within 4Å: Chain C: D.45, R.46, P.47, L.51 Ligands: DMS.73 Ligand excluded by PLIP DMS.89: 3 residues within 4Å: Chain C: F.629, Q.718, W.720 Ligand excluded by PLIP DMS.90: 4 residues within 4Å: Chain C: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.91: 3 residues within 4Å: Chain C: R.721, L.722 Chain D: D.875 Ligand excluded by PLIP DMS.92: 5 residues within 4Å: Chain C: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.93: 4 residues within 4Å: Chain C: Y.105, T.108, P.596 Ligands: DMS.79 Ligand excluded by PLIP DMS.94: 4 residues within 4Å: Chain C: W.695, Q.719, R.721 Ligands: MG.65 Ligand excluded by PLIP DMS.95: 3 residues within 4Å: Chain C: I.305, P.306, N.307 Ligand excluded by PLIP DMS.96: 5 residues within 4Å: Chain C: Y.926, P.928, Y.962, R.973, L.976 Ligand excluded by PLIP DMS.103: 9 residues within 4Å: Chain D: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.104: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.105: 6 residues within 4Å: Chain D: K.380, N.383, F.384, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.106: 5 residues within 4Å: Chain D: G.270, T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.107: 6 residues within 4Å: Chain D: R.505, E.508, P.1001, S.1002, V.1003, Q.1008 Ligand excluded by PLIP DMS.108: 4 residues within 4Å: Chain D: S.53, L.54, N.55, L.125 Ligand excluded by PLIP DMS.109: 5 residues within 4Å: Chain D: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.110: 3 residues within 4Å: Chain D: P.106, I.107, P.115 Ligand excluded by PLIP DMS.111: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.112: 4 residues within 4Å: Chain D: G.275, G.276, V.289, T.290 Ligand excluded by PLIP DMS.113: 3 residues within 4Å: Chain D: G.593, D.594, T.595 Ligand excluded by PLIP DMS.114: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.115: 3 residues within 4Å: Chain D: R.699, I.714, W.717 Ligand excluded by PLIP DMS.116: 5 residues within 4Å: Chain D: N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.117: 6 residues within 4Å: Chain D: A.34, W.36, D.45, P.47, S.48, L.51 Ligand excluded by PLIP DMS.118: 3 residues within 4Å: Chain D: G.320, T.321, L.322 Ligand excluded by PLIP DMS.119: 5 residues within 4Å: Chain D: E.314, H.316, T.317, G.320, T.321 Ligand excluded by PLIP DMS.120: 2 residues within 4Å: Chain D: A.68, P.70 Ligand excluded by PLIP DMS.121: 4 residues within 4Å: Chain D: S.923, Y.926, R.961, Y.962 Ligand excluded by PLIP

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

BTB.30: 12 residues within 4Å: Chain A: N.102, D.201, H.391, H.418, N.460, E.461, Y.503, E.537, H.540, W.568, W.999 Ligands: NA.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.102, A:D.201, A:H.391, A:N.460, A:W.568 Salt bridges: A:D.201, A:E.461, A:E.537 BTB.61: 12 residues within 4Å: Chain B: N.102, V.103, D.201, H.391, H.418, E.461, Y.503, E.537, H.540, W.568, W.999 Ligands: NA.39 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.102, B:N.102, B:D.201, B:D.201, B:W.568 Water bridges: B:D.201, B:N.460, B:N.460, B:H.540 Salt bridges: B:D.201, B:E.461, B:E.537 BTB.97: 14 residues within 4Å: Chain C: N.102, D.201, H.391, H.418, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, N.604, W.999 Ligands: NA.66 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:N.102, C:D.201, C:N.460, C:Y.503, C:E.537, C:H.540, C:W.568 Water bridges: C:N.102, C:D.199, C:E.461 Salt bridges: C:D.201, C:E.461, C:E.537 BTB.122: 13 residues within 4Å: Chain D: N.102, Q.200, D.201, H.391, H.418, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, W.999 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:N.102, D:D.201, D:H.391, D:N.460, D:Y.503, D:H.540 Water bridges: D:E.461, D:E.461 Salt bridges: D:D.201, D:E.461, D:E.537

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