Magnesium in PDB 8fdb: Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution.

The structure of Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution., PDB code: 8fdb was solved by A.Rodriguez-Romero, A.Rodriguez-Hernandez, J.Marcos-Viquez, I.Bustos-Jaimes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.95 / 3.06
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.885, 113.142, 171.008, 90, 90, 90
R / Rfree (%)	20.6 / 24.2

The binding sites of Magnesium atom in the Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution. (pdb code 8fdb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution., PDB code: 8fdb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution.


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 Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:31.1 occ:1.00 O A:ILE96 2.8 27.5 1.0 O2P A:AGP501 2.8 32.0 1.0 N A:ARG49 3.1 32.1 1.0 CA A:GLY48 3.3 25.9 1.0 CB A:SER97 3.5 30.4 1.0 C A:GLY48 3.6 32.6 1.0 O A:ARG49 3.6 33.7 1.0 CB A:SER52 3.6 25.4 1.0 CA A:SER97 3.7 31.3 1.0 OG A:SER97 3.7 30.7 1.0 O1P A:AGP501 3.9 37.9 1.0 P A:AGP501 3.9 46.7 1.0 C A:ILE96 3.9 23.1 1.0 OG A:SER52 3.9 19.8 1.0 CG1 A:ILE105 4.0 41.8 1.0 CA A:ARG49 4.0 37.4 1.0 CB A:ARG49 4.1 41.6 1.0 C6 A:AGP501 4.2 37.5 1.0 C A:ARG49 4.3 34.7 1.0 N A:SER97 4.3 26.3 1.0 N A:GLY48 4.5 33.0 1.0 O6 A:AGP501 4.6 46.5 1.0 CD1 A:ILE105 4.6 43.3 1.0 O A:VAL47 4.6 25.5 1.0 O A:GLY48 4.7 36.6 1.0 CB A:ILE105 4.8 37.9 1.0 CG2 A:ILE105 4.9 37.8 1.0 C A:VAL47 5.0 25.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Nagb-II Phosphosugar Isomerase From Shewanella Denitrificans OS217 in Complex with Glucitolamine-6-Phosphate at 3.06 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:29.7 occ:1.00 O1P B:AGP702 2.6 34.0 1.0 OH A:TYR61 2.9 25.2 1.0 CB A:TYR215 3.0 23.0 1.0 N A:GLY212 3.2 25.2 1.0 CG A:TYR215 3.2 26.9 1.0 CD2 A:TYR215 3.2 27.1 1.0 CB A:SER237 3.4 23.4 1.0 P B:AGP702 3.6 38.4 1.0 O3P B:AGP702 3.7 38.9 1.0 CA A:ARG211 3.8 23.8 1.0 CZ A:TYR61 3.8 26.1 1.0 C A:ARG211 3.9 25.0 1.0 C6 B:AGP702 4.0 44.3 1.0 CA A:GLY212 4.0 20.4 1.0 CA A:SER237 4.1 20.8 1.0 CD1 A:TYR215 4.1 27.1 1.0 CE2 A:TYR215 4.1 26.6 1.0 O A:GLY210 4.1 24.9 1.0 O A:GLY212 4.2 21.8 1.0 O6 B:AGP702 4.3 42.1 1.0 CE2 A:TYR61 4.4 28.6 1.0 CG A:ARG211 4.4 23.6 1.0 NH1 A:ARG211 4.5 36.5 1.0 CA A:TYR215 4.5 23.0 1.0 CE1 A:TYR61 4.5 26.9 1.0 OG A:SER237 4.6 36.8 1.0 N A:ARG211 4.6 27.8 1.0 C A:GLY212 4.6 26.2 1.0 C A:GLY210 4.7 25.7 1.0 CB A:ARG211 4.7 20.6 1.0 OG B:SER77 4.8 37.1 1.0 CE1 A:TYR215 4.8 28.0 1.0 CZ A:TYR215 4.8 29.0 1.0 O4 B:AGP702 4.9 55.5 1.0 N A:SER237 4.9 21.8 1.0 O2P B:AGP702 4.9 32.6 1.0 N A:TYR215 5.0 22.5 1.0

J.Marcos-Viquez, A.Rodriguez-Hernandez, L.I.Alvarez-Anorve, A.Medina-Garcia, J.Plumbridge, M.L.Calcagno, A.Rodriguez-Romero, I.Bustos-Jaimes. Substrate Binding in the Allosteric Site Mimics Homotropic Cooperativity in the Sis-Fold Glucosamine-6-Phosphate Deaminases. Protein Sci. E4651 2023.
ISSN: ESSN 1469-896X
PubMed: 37145875
DOI: 10.1002/PRO.4651