Calcium in PDB 5vr0: Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus

All present enzymatic activity of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus:
5.3.1.5;

The structure of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus, PDB code: 5vr0 was solved by D.Borek, Z.Otwinowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.90 / 1.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.854, 98.061, 102.279, 90.00, 90.00, 90.00
R / Rfree (%)	11.9 / 14.2

The structure of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Chlorine	(Cl)	12 atoms

The binding sites of Calcium atom in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus (pdb code 5vr0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus, PDB code: 5vr0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca893 b:60.8 occ:1.00 OD2 A:ASP295 2.6 13.4 0.9 OD2 A:ASP297 2.9 20.0 0.8 O A:HOH829 3.4 27.0 1.0 CG A:ASP295 3.4 11.1 0.9 O A:HOH842 3.4 39.4 1.0 OD1 A:ASP295 3.6 11.8 0.9 O A:HOH783 3.7 15.7 1.0 CG A:ASP297 3.8 16.1 0.8 CB A:ASP297 3.9 13.6 1.0 CB A:ASP295 4.7 10.0 0.9 OD1 A:ASP297 4.9 17.9 0.8

Calcium binding site 2 out of 3 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca894 b:10.8 occ:0.50 O A:HOH622 2.3 23.5 0.7 O A:HOH573 2.3 14.8 0.9 O A:ALA339 2.4 10.3 1.0 O A:HOH594 2.6 15.4 0.9 O A:HOH666 2.6 30.5 0.6 C A:ALA339 3.6 9.6 1.0 CB A:ALA339 4.3 9.5 1.0 N A:ARG340 4.4 9.4 0.5 N A:ARG340 4.4 9.6 0.5 CA A:ARG340 4.4 9.8 0.5 CA A:ALA339 4.5 9.1 1.0 CA A:ARG340 4.5 10.2 0.5 O A:HOH574 4.7 22.0 1.0 O A:HOH641 4.7 34.8 0.9 CD A:PRO341 4.8 11.3 1.0 O A:HOH468 4.8 14.5 1.0 O A:HOH730 4.9 16.7 0.5

Calcium binding site 3 out of 3 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca895 b:40.5 occ:0.70 CL A:CL886 2.6 73.1 1.0 OD1 A:ASP110 4.4 18.6 0.5 O A:HOH453 4.6 17.1 1.0 NH1 A:ARG109 4.6 12.6 1.0 OD2 A:ASP110 4.9 19.2 0.5 O A:HOH553 4.9 20.6 1.0

D.Borek, R.Bromberg, J.Hattne, Z.Otwinowski. Real-Space Analysis of Radiation-Induced Specific Changes with Independent Component Analysis. J Synchrotron Radiat V. 25 451 2018.
ISSN: ESSN 1600-5775
PubMed: 29488925
DOI: 10.1107/S1600577517018148