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Calcium in PDB 7dmm: Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants

Enzymatic activity of Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants

All present enzymatic activity of Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants:
5.3.1.5;

Protein crystallography data

The structure of Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants, PDB code: 7dmm was solved by Y.Suzuki, N.Maita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.16 / 0.99
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.61, 98.46, 102.3, 90, 90, 90
R / Rfree (%) 15.7 / 16.6

Other elements in 7dmm:

The structure of Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants (pdb code 7dmm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants, PDB code: 7dmm:

Calcium binding site 1 out of 1 in 7dmm

Go back to Calcium Binding Sites List in 7dmm
Calcium binding site 1 out of 1 in the Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:23.3
occ:1.00
O A:GLY261 2.8 6.9 1.0
O A:GLY263 2.8 7.5 1.0
CA A:ALA262 3.4 6.8 1.0
N A:GLY263 3.4 6.5 1.0
C A:ALA262 3.4 5.9 1.0
CB A:LEU265 3.5 6.5 1.0
O A:HOH697 3.6 9.9 1.0
C A:GLY263 3.6 5.8 1.0
C A:GLY261 3.7 6.4 1.0
N A:LEU265 3.8 5.8 1.0
O A:HOH656 3.9 18.8 1.0
CA A:LEU265 4.0 5.7 1.0
N A:ALA262 4.0 6.5 1.0
CA A:GLY263 4.1 6.5 1.0
O A:ALA262 4.1 6.9 1.0
CG A:LEU265 4.5 6.9 1.0
N A:ASP264 4.5 5.4 1.0
C A:ASP264 4.6 5.2 1.0
CB A:ALA262 4.6 7.4 1.0
CD2 A:LEU265 4.6 8.3 1.0
CD1 A:LEU265 4.7 7.7 1.0
CA A:ASP264 4.9 5.4 1.0

Reference:

Y.Suzuki, N.Ikemitsu, N.Maita. Extraordinarily Fast Growth of High-Quality Glucose Isomerase Crystals Simply By Concentration in A Precipitant-Free Solution with A Cryoprotectant To Be Published.
Page generated: Wed Jul 9 21:38:10 2025

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