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Magnesium in PDB 3vkk: Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex

Enzymatic activity of Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex

All present enzymatic activity of Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex:
3.2.1.21;

Protein crystallography data

The structure of Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex, PDB code: 3vkk was solved by J.Noguchi, Y.Hayashi, N.Okino, M.Ito, M.Kimura, Y.Kakuta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.69 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.733, 83.519, 90.892, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.2

Other elements in 3vkk:

The structure of Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex (pdb code 3vkk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex, PDB code: 3vkk:

Magnesium binding site 1 out of 1 in 3vkk

Go back to Magnesium Binding Sites List in 3vkk
Magnesium binding site 1 out of 1 in the Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg478

b:23.9
occ:1.00
 NH1 A:ARG75 3.0 10.1 0.5
OG A:SER223 3.1 18.9 1.0
OG1 A:THR372 3.2 19.4 1.0
OE1 A:GLN165 3.2 30.5 1.0
ND2 A:ASN164 3.2 17.1 1.0
NH2 A:ARG75 3.3 16.2 0.5
CB A:SER223 3.5 21.5 1.0
CZ A:ARG75 3.6 20.3 0.5
NH1 A:ARG75 3.6 28.8 0.5
CB A:GLN307 3.7 22.7 1.0
OE2 A:GLU373 3.7 25.2 1.0
CB A:GLU373 3.8 23.6 1.0
CB A:THR372 3.9 19.6 1.0
CD A:GLU373 3.9 24.1 1.0
CG A:GLN165 3.9 25.6 1.0
C A:THR372 4.0 20.9 1.0
CD A:GLN165 4.0 30.7 1.0
CG A:GLU373 4.1 25.1 1.0
N A:GLU373 4.1 20.4 1.0
CZ A:ARG75 4.1 27.5 0.5
NH2 A:ARG75 4.2 25.0 0.5
O A:THR372 4.3 18.4 1.0
CG A:ASN164 4.4 22.1 1.0
CG A:GLN307 4.4 25.2 1.0
CA A:GLN307 4.4 23.1 1.0
CA A:THR372 4.5 19.1 1.0
N A:GLN307 4.5 22.3 1.0
CA A:GLU373 4.6 23.2 1.0
OE1 A:GLU373 4.6 25.9 1.0
NE A:ARG75 4.8 19.5 0.5
C A:VAL306 4.8 21.8 1.0
O A:VAL306 4.9 21.6 1.0
OD1 A:ASN164 4.9 24.1 1.0
CA A:SER223 4.9 20.9 1.0

Reference:

J.Noguchi, Y.Hayashi, N.Okino, M.Ito, M.Kimura, Y.Kakuta. Structural Basis For Inhibition Mechanism of Human Cytosolic Beta-Glucosidase By Monnoside To Be Published.
Page generated: Mon Aug 11 04:38:48 2025

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