SMTL ID : 1jz2.1

E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE (ORTHORHOMBIC)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x 2FG: 2-deoxy-2-fluoro-beta-D-galactopyranose(Post Translational Modification)

2FG.1: 12 residues within 4Å: Chain A: D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.391, A:N.460 Water bridges: A:N.102, A:D.201, A:D.201, A:D.201 Halogen bonds: A:N.460 2FG.26: 15 residues within 4Å: Chain B: D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: MG.27, NA.29, BTB.32 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.201, B:H.391, B:N.460 Water bridges: B:D.201, B:D.201, B:H.391 2FG.53: 13 residues within 4Å: Chain C: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.56 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.102, C:H.391, C:N.460, C:Y.503 Water bridges: C:D.201, C:D.201, C:D.201 2FG.74: 13 residues within 4Å: Chain D: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.77 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:H.391, D:N.460, D:Y.503, D:H.540 Water bridges: D:N.102, D:D.201, D:D.201, D:D.201 Halogen bonds: D:N.460

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.416, A:H.418, A:E.461, H2O.1, H2O.3, H2O.6 MG.3: 7 residues within 4Å: Chain A: D.15, N.18, P.19, V.21, Y.161, Q.163, D.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.15, A:N.18, A:V.21, A:D.193, A:D.193 MG.27: 4 residues within 4Å: Chain B: E.416, H.418, E.461 Ligands: 2FG.26 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.416, B:H.418, B:E.461, H2O.30, H2O.33, H2O.36 MG.28: 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.54: 3 residues within 4Å: Chain C: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.416, C:H.418, C:E.461, H2O.59, H2O.61, H2O.64 MG.55: 6 residues within 4Å: Chain C: D.15, N.18, P.19, 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.75: 3 residues within 4Å: Chain D: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.416, D:H.418, D:E.461, H2O.87, H2O.89, H2O.92 MG.76: 6 residues within 4Å: Chain D: D.15, N.18, P.19, 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

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

NA.4: 5 residues within 4Å: Chain A: Y.100, D.201, F.601, N.604 Ligands: 2FG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.201, A:N.604 NA.5: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.562, A:L.562 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.29: 5 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligands: 2FG.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.601, B:N.604 NA.30: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.559, B:L.562 NA.31: 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.56: 4 residues within 4Å: Chain C: D.201, F.601, N.604 Ligands: 2FG.53 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.604, C:N.604 NA.57: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.560, C:L.562 NA.58: 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.77: 5 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligands: 2FG.74 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.100, D:W.568, D:N.604 NA.78: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.560, D:L.562 NA.79: 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:M.968

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

DMS.7: 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.8: 5 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.10: 7 residues within 4Å: Chain A: P.32, F.33, A.34, W.36, D.45, A.327 Ligands: DMS.23 Ligand excluded by PLIP DMS.11: 3 residues within 4Å: Chain A: T.271, L.291, R.292 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: E.314, H.316, G.320, L.322 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain A: R.505, E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.14: 6 residues within 4Å: Chain A: L.54, N.55, G.56, E.57, W.58, L.125 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain A: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain A: P.106, I.107, P.115, W.191 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: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.20: 6 residues within 4Å: Chain A: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain A: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.22: 2 residues within 4Å: Chain A: Y.926, R.973 Ligand excluded by PLIP DMS.23: 7 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.10 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain A: R.37, W.133, E.136, H.216 Ligand excluded by PLIP DMS.33: 10 residues within 4Å: Chain B: V.227, T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.34: 4 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.628 Ligand excluded by PLIP DMS.35: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.36: 6 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, A.327 Ligand excluded by PLIP DMS.37: 6 residues within 4Å: Chain B: G.270, T.271, T.290, L.291, R.292, L.293 Ligand excluded by PLIP DMS.38: 4 residues within 4Å: Chain B: E.314, H.316, G.320, T.321 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain B: R.505, E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain B: S.53, L.54, N.55, G.56, E.57 Ligand excluded by PLIP DMS.41: 4 residues within 4Å: Chain B: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.42: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.43: 6 residues within 4Å: Chain B: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.44: 4 residues within 4Å: Chain B: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.45: 5 residues within 4Å: Chain B: F.231, N.232, D.233, E.334, R.336 Ligand excluded by PLIP DMS.46: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain B: Y.926, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.48: 4 residues within 4Å: Chain B: D.648, N.649, E.650, N.704 Ligand excluded by PLIP DMS.49: 4 residues within 4Å: Chain B: E.57, R.59, L.125, T.126 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.51: 4 residues within 4Å: Chain B: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: L.922, S.923, R.961, Y.962 Ligand excluded by PLIP DMS.59: 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.60: 6 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.61: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.62: 6 residues within 4Å: Chain C: P.32, F.33, W.36, D.45, A.327, C.328 Ligand excluded by PLIP DMS.63: 3 residues within 4Å: Chain C: T.271, L.291, R.292 Ligand excluded by PLIP DMS.64: 6 residues within 4Å: Chain C: L.54, N.55, G.56, E.57, L.125, F.127 Ligand excluded by PLIP DMS.65: 4 residues within 4Å: Chain C: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.66: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.67: 6 residues within 4Å: Chain C: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.68: 3 residues within 4Å: Chain C: V.84, V.85, H.93 Ligand excluded by PLIP DMS.69: 5 residues within 4Å: Chain C: F.231, N.232, D.233, E.334, R.336 Ligand excluded by PLIP DMS.70: 5 residues within 4Å: Chain C: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.71: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.72: 5 residues within 4Å: Chain C: Y.926, Y.962, R.973, H.974, L.976 Ligand excluded by PLIP DMS.73: 5 residues within 4Å: Chain C: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.81: 10 residues within 4Å: Chain D: V.227, T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.82: 6 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.83: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.84: 3 residues within 4Å: Chain D: T.271, L.291, R.292 Ligand excluded by PLIP DMS.85: 3 residues within 4Å: Chain D: E.314, H.316, G.320 Ligand excluded by PLIP DMS.86: 6 residues within 4Å: Chain D: L.54, N.55, G.56, E.57, W.58, L.125 Ligand excluded by PLIP DMS.87: 4 residues within 4Å: Chain D: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.88: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.89: 6 residues within 4Å: Chain D: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.90: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.91: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.92: 2 residues within 4Å: Chain D: H.93, G.94 Ligand excluded by PLIP DMS.93: 5 residues within 4Å: Chain D: Y.926, P.928, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain D: W.695, Q.718, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.95: 5 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47 Ligand excluded by PLIP

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

BTB.32: 9 residues within 4Å: Chain B: N.102, H.418, M.423, E.461, M.502, F.601, W.999 Chain C: E.281 Ligands: 2FG.26 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.102, B:N.102, B:E.461 Water bridges: B:H.418, B:E.461 Salt bridges: B:E.461 BTB.80: 5 residues within 4Å: Chain A: E.281 Chain D: N.102, H.418, K.517, W.999 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.102, D:N.102, D:E.461, D:E.461, D:K.517 Water bridges: D:W.999 pi-Cation interactions: D:W.999

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juers, D.H. et al., A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase. Biochemistry (2001)

Release Date

2001-12-07

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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