SMTL ID : 3dym.1

E. coli (lacZ) beta-galactosidase (H418E)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: E.416, E.418, E.461 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.416, A:E.418, A:E.461, H2O.1, H2O.3, H2O.6 MG.2: 6 residues within 4Å: Chain A: D.15, N.18, P.19, V.21, 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.3: 1 residues within 4Å: Ligands: DMS.13 No protein-ligand interaction detected (PLIP) MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain B: N.102, E.416, E.418, E.461 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.416, B:E.418, B:E.461, H2O.35, H2O.37, H2O.40 MG.27: 7 residues within 4Å: Chain B: D.15, W.16, N.18, V.21, Y.161, 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.51: 3 residues within 4Å: Chain C: E.416, E.418, E.461 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.416, C:E.418, C:E.461, H2O.69, H2O.71, H2O.74 MG.52: 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.81: 3 residues within 4Å: Chain D: E.416, E.418, E.461 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.416, D:E.418, D:E.461, H2O.101, H2O.104, H2O.107 MG.82: 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

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.21 Ligand excluded by PLIP NA.28: 4 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.29: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.30: 4 residues within 4Å: Chain B: F.931, P.932, L.967, T.970 Ligand excluded by PLIP NA.31: 4 residues within 4Å: Chain B: S.647, E.650, L.670 Ligands: DMS.47 Ligand excluded by PLIP NA.53: 4 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.54: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.55: 4 residues within 4Å: Chain C: F.931, P.932, L.967, T.970 Ligand excluded by PLIP NA.56: 4 residues within 4Å: Chain C: S.647, E.650, L.670 Ligands: DMS.74 Ligand excluded by PLIP NA.83: 4 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.84: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.85: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.86: 5 residues within 4Å: Chain D: S.647, N.649, E.650, L.670 Ligands: DMS.102 Ligand excluded by PLIP

82 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: 5 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.11: 6 residues within 4Å: Chain A: P.32, F.33, A.34, W.36, D.45, A.327 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.13: 6 residues within 4Å: Chain A: E.314, H.316, G.320, T.321, L.322 Ligands: MG.3 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: L.54, N.55, G.56, L.125 Ligand excluded by PLIP DMS.15: 3 residues within 4Å: Chain A: E.334, V.335, P.480 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.17: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain A: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.19: 2 residues within 4Å: Chain A: R.251, D.252 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.21: 7 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.7 Ligand excluded by PLIP DMS.22: 6 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain A: R.37, Q.50, E.136, H.216 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.32: 8 residues within 4Å: Chain B: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.35: 6 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, A.327 Ligand excluded by PLIP DMS.36: 3 residues within 4Å: Chain B: T.271, L.291, R.292 Ligand excluded by PLIP DMS.37: 5 residues within 4Å: Chain B: E.314, H.316, G.320, T.321, L.322 Ligand excluded by PLIP DMS.38: 4 residues within 4Å: Chain B: L.54, N.55, G.56, E.57 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain B: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.41: 5 residues within 4Å: Chain B: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.42: 4 residues within 4Å: Chain B: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.43: 3 residues within 4Å: Chain B: L.250, R.251, D.252 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain B: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.45: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.46: 4 residues within 4Å: Chain B: Y.926, Y.962, R.973, L.976 Ligand excluded by PLIP DMS.47: 7 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.31 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain B: R.37, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain B: S.923, Y.926, R.961, Y.962, A.978 Ligand excluded by PLIP DMS.50: 4 residues within 4Å: Chain B: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.57: 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.58: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.60: 6 residues within 4Å: Chain C: P.32, F.33, W.36, D.45, R.310, A.327 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain C: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.63: 4 residues within 4Å: Chain C: S.53, L.54, N.55, L.125 Ligand excluded by PLIP DMS.64: 4 residues within 4Å: Chain C: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.66: 5 residues within 4Å: Chain C: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain C: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.68: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.69: 5 residues within 4Å: Chain C: F.231, N.232, D.233, F.235, E.334 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: 2 residues within 4Å: Chain C: D.428, P.430 Ligand excluded by PLIP DMS.72: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.73: 3 residues within 4Å: Chain C: Y.926, Y.962, R.973 Ligand excluded by PLIP DMS.74: 7 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.56 Ligand excluded by PLIP DMS.75: 6 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.76: 5 residues within 4Å: Chain C: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.77: 4 residues within 4Å: Chain C: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.78: 4 residues within 4Å: Chain C: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.79: 3 residues within 4Å: Chain C: Q.266, V.267, A.268 Ligand excluded by PLIP DMS.80: 3 residues within 4Å: Chain A: D.428 Chain D: W.474, V.478 Ligand excluded by PLIP DMS.87: 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.88: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.89: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.90: 8 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.103 Ligand excluded by PLIP DMS.91: 4 residues within 4Å: Chain D: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.92: 4 residues within 4Å: Chain D: E.314, H.316, G.320 Ligands: DMS.106 Ligand excluded by PLIP DMS.93: 6 residues within 4Å: Chain D: L.54, N.55, G.56, E.57, W.58, L.125 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain D: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.95: 6 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, D.610, R.973 Ligand excluded by PLIP DMS.96: 6 residues within 4Å: Chain D: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.97: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.98: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.99: 5 residues within 4Å: Chain D: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain D: D.82, H.93, G.94, Y.95 Ligand excluded by PLIP DMS.101: 5 residues within 4Å: Chain D: Y.926, Y.962, R.973, L.976 Ligands: DMS.105 Ligand excluded by PLIP DMS.102: 7 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.86 Ligand excluded by PLIP DMS.103: 7 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.90 Ligand excluded by PLIP DMS.104: 4 residues within 4Å: Chain D: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.105: 5 residues within 4Å: Chain D: S.923, Y.926, R.961, Y.962 Ligands: DMS.101 Ligand excluded by PLIP DMS.106: 3 residues within 4Å: Chain D: G.320, L.322 Ligands: DMS.92 Ligand excluded by PLIP DMS.107: 5 residues within 4Å: Chain D: Q.49, Q.50, D.130, S.132, W.133 Ligand excluded by PLIP DMS.108: 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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