Magnesium in PDB 6k0h: Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp-Glcnac

All present enzymatic activity of Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp-Glcnac:
5.1.3.2;

The structure of Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp-Glcnac, PDB code: 6k0h was solved by Y.-W.Nam, M.Nishimoto, T.Arakawa, M.Kitaoka, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.75 / 2.00
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	69.450, 69.450, 321.986, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 22.1

The binding sites of Magnesium atom in the Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp-Glcnac (pdb code 6k0h). 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 Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp-Glcnac, PDB code: 6k0h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp-Glcnac


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 Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp-Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:29.3 occ:1.00 O A:HOH683 2.2 41.5 1.0 O A:LYS308 2.5 31.0 1.0 C A:LYS308 3.5 35.5 1.0 CA A:LYS308 4.0 33.0 1.0 O A:GLU307 4.4 33.9 1.0 O A:HOH621 4.4 47.1 1.0 N A:GLU309 4.7 38.2 1.0 CG A:LYS308 4.8 41.7 1.0 CB A:LYS308 4.9 38.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp-Glcnac


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 Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp-Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:40.8 occ:1.00 O A:HOH710 2.3 43.9 1.0 O A:GLY266 2.3 32.3 1.0 O A:HOH690 2.4 47.7 1.0 O A:HOH525 2.5 39.5 1.0 O A:HOH663 2.5 51.1 1.0 O A:HOH661 2.6 44.2 1.0 C A:GLY266 3.4 37.3 1.0 CA A:GLY266 4.0 37.2 1.0 N A:GLY266 4.0 33.5 1.0 N A:TYR267 4.5 30.6 1.0 OE1 A:GLU271 4.8 33.6 1.0 CA A:TYR267 4.9 30.3 1.0

Y.W.Nam, M.Nishimoto, T.Arakawa, M.Kitaoka, S.Fushinobu. Structural Basis For Broad Substrate Specificity of Udp-Glucose 4-Epimerase in the Human Milk Oligosaccharide Catabolic Pathway of Bifidobacterium Longum. Sci Rep V. 9 11081 2019.
ISSN: ESSN 2045-2322
PubMed: 31366978
DOI: 10.1038/S41598-019-47591-W