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Magnesium in PDB 6k0g: Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp

Enzymatic activity of Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp

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

Protein crystallography data

The structure of Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp, PDB code: 6k0g 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) 40.17 / 1.80
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.235, 70.235, 320.578, 90.00, 90.00, 120.00
R / Rfree (%) 14.9 / 18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp (pdb code 6k0g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp, PDB code: 6k0g:

Magnesium binding site 1 out of 1 in 6k0g

Go back to Magnesium Binding Sites List in 6k0g
Magnesium binding site 1 out of 1 in the Crystal Structure of Udp-Glucose 4-Epimerase From Bifidobacterium Longum in Complex with Nad+ and Udp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:27.6
occ:1.00
 NE2 A:HIS115 2.0 22.9 1.0
OE2 A:GLU67 2.3 29.8 1.0
O A:HOH809 2.5 35.3 1.0
CE1 A:HIS115 2.6 19.4 1.0
CD2 A:HIS115 3.1 19.9 1.0
CD A:GLU67 3.2 31.9 1.0
OE1 A:GLU67 3.5 26.6 1.0
ND1 A:HIS115 3.8 20.1 1.0
CE A:LYS114 4.0 40.3 1.0
CG A:HIS115 4.1 18.9 1.0
CB A:ALA71 4.2 24.2 1.0
O A:HOH614 4.2 35.5 1.0
O A:HOH555 4.4 34.5 1.0
CA A:ALA71 4.5 27.2 1.0
CG A:GLU67 4.6 27.4 1.0
N A:ALA71 4.7 22.4 1.0
NZ A:LYS114 4.7 46.3 1.0
O A:GLU67 4.8 20.9 1.0
O A:HOH722 4.9 34.9 1.0
CD A:LYS114 4.9 34.1 1.0

Reference:

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
Page generated: Tue Oct 1 06:21:41 2024

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