SMTL ID : 4v45.3 (3 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

2FG.1: 13 residues within 4Å: Chain A: N.102, D.201, H.391, N.460, E.461, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: MG.2, NA.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.102, A:H.391, A:N.460, A:H.540 Water bridges: A:D.201, A:N.604 2FG.6: 13 residues within 4Å: Chain B: N.102, D.201, H.391, N.460, E.461, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: MG.7, NA.9 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.102, B:D.201, B:H.391, B:N.460, B:H.540 Water bridges: B:D.201, B:N.604 2FG.11: 13 residues within 4Å: Chain C: N.102, D.201, H.391, N.460, E.461, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: MG.12, NA.14 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.102, C:D.201, C:H.391, C:N.460, C:Y.503, C:H.540 Water bridges: C:D.201, C:N.604 2FG.16: 13 residues within 4Å: Chain D: N.102, D.201, H.391, N.460, E.461, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: MG.17, NA.19 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.102, D:H.391, D:N.460, D:H.540 Water bridges: D:D.201, D:N.604

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: N.102, D.201, E.416, H.418, E.461 Ligands: 2FG.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.416, A:H.418, A:E.461 MG.3: 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.7: 6 residues within 4Å: Chain B: N.102, D.201, E.416, H.418, E.461 Ligands: 2FG.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.416, B:H.418, B:E.461 MG.8: 6 residues within 4Å: Chain B: D.15, N.18, P.19, 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.12: 6 residues within 4Å: Chain C: N.102, D.201, E.416, H.418, E.461 Ligands: 2FG.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.416, C:H.418, C:E.461 MG.13: 6 residues within 4Å: Chain C: D.15, N.18, P.19, V.21, 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.17: 6 residues within 4Å: Chain D: N.102, D.201, E.416, H.418, E.461 Ligands: 2FG.16 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.416, D:H.418, D:E.461 MG.18: 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

8 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:F.601, A:N.604 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:P.560 NA.9: 5 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligands: 2FG.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.601, B:N.604 NA.10: 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:L.562 NA.14: 5 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligands: 2FG.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.100, C:D.201, C:N.604 NA.15: 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:P.560 NA.19: 5 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligands: 2FG.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.100, D:N.604, D:N.604 NA.20: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.562

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

2014-07-09

Peptides

Beta-Galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

Beta-Galactosidase

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