Manganese 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:

Chlorine	(Cl)	12 atoms
Calcium	(Ca)	3 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus, PDB code: 5vr0:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn390 b:10.2 occ:0.90 OE2 A:GLU217 2.0 6.9 1.0 OD1 A:ASP257 2.2 9.6 1.0 O A:HOH837 2.2 14.3 1.0 OD1 A:ASP255 2.3 10.4 1.0 OD2 A:ASP255 2.3 11.2 1.0 NE2 A:HIS220 2.4 7.2 1.0 CG A:ASP255 2.7 9.8 1.0 CD A:GLU217 3.0 6.4 1.0 CG A:ASP257 3.1 9.7 1.0 CD2 A:HIS220 3.1 6.7 1.0 OD2 A:ASP257 3.3 12.2 1.0 OE1 A:GLU217 3.3 6.7 1.0 CE1 A:HIS220 3.4 7.0 1.0 O A:HOH503 3.6 18.0 0.9 ND2 A:ASN247 4.0 6.0 1.0 O A:HOH404 4.1 6.5 1.0 CB A:ASP255 4.2 9.3 1.0 CG A:HIS220 4.3 6.4 1.0 CG A:GLU217 4.4 6.1 1.0 ND1 A:HIS220 4.4 6.8 1.0 CB A:ASP257 4.5 8.9 1.0 NZ A:LYS183 4.6 8.0 1.0 O A:HOH631 4.7 11.2 1.0 CE A:LYS183 4.8 7.5 1.0 O A:HOH736 4.9 24.4 1.0 OD2 A:ASP287 4.9 9.4 1.0 CA A:ASP257 4.9 7.8 1.0 N A:ASP257 5.0 7.6 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn391 b:11.8 occ:0.90 OD2 A:ASP245 2.2 6.5 1.0 OE2 A:GLU181 2.3 11.4 1.0 OD2 A:ASP287 2.3 9.4 1.0 OE1 A:GLU217 2.3 6.7 1.0 O A:HOH630 2.4 5.7 0.7 O A:HOH631 2.5 11.2 1.0 OE1 A:GLU181 2.9 10.8 1.0 CD A:GLU181 2.9 9.8 1.0 CG A:ASP287 3.4 8.4 1.0 CG A:ASP245 3.4 6.4 1.0 CD A:GLU217 3.5 6.4 1.0 CB A:ASP287 3.8 8.0 1.0 O A:HOH755 3.9 27.0 1.0 O A:HOH837 3.9 14.3 1.0 O A:HOH401 4.0 11.0 0.9 CE1 A:HIS220 4.1 7.0 1.0 CB A:ASP245 4.1 6.2 1.0 CG A:GLU217 4.3 6.1 1.0 CB A:GLU217 4.3 5.8 1.0 CG A:GLU181 4.4 8.8 1.0 OD1 A:ASP245 4.4 6.5 1.0 OE2 A:GLU217 4.4 6.9 1.0 OD1 A:ASP287 4.5 8.6 1.0 ND2 A:ASN215 4.6 7.0 1.0 ND1 A:HIS220 4.7 6.8 1.0 NE2 A:HIS220 4.8 7.2 1.0 O A:HOH810 4.9 13.7 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