Zinc in PDB 6dnt: Udp-N-Acetylglucosamine 4-Epimerase From Methanobrevibacter Ruminantium M1 in Complex with Udp-N-Acetylmuramic Acid

The structure of Udp-N-Acetylglucosamine 4-Epimerase From Methanobrevibacter Ruminantium M1 in Complex with Udp-N-Acetylmuramic Acid, PDB code: 6dnt was solved by V.Carbone, L.R.Schofield, C.Sang, A.J.Sutherland-Smith, R.S.Ronimus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.36 / 1.66
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.497, 89.497, 82.717, 90.00, 90.00, 120.00
R / Rfree (%)	15.2 / 17.2

The binding sites of Zinc atom in the Udp-N-Acetylglucosamine 4-Epimerase From Methanobrevibacter Ruminantium M1 in Complex with Udp-N-Acetylmuramic Acid (pdb code 6dnt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Udp-N-Acetylglucosamine 4-Epimerase From Methanobrevibacter Ruminantium M1 in Complex with Udp-N-Acetylmuramic Acid, PDB code: 6dnt:

Zinc binding site 1 out of 1 in the Udp-N-Acetylglucosamine 4-Epimerase From Methanobrevibacter Ruminantium M1 in Complex with Udp-N-Acetylmuramic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Udp-N-Acetylglucosamine 4-Epimerase From Methanobrevibacter Ruminantium M1 in Complex with Udp-N-Acetylmuramic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:13.7 occ:0.50 OE1 A:GLU209 2.1 14.7 1.0 NE2 A:HIS275 2.1 12.2 1.0 CD A:GLU209 2.8 14.3 1.0 OE2 A:GLU209 2.9 15.4 1.0 CE1 A:HIS275 3.0 12.7 1.0 CD2 A:HIS275 3.2 12.7 1.0 CG A:LYS274 4.0 13.5 1.0 ND1 A:HIS275 4.2 12.4 1.0 CE A:LYS274 4.2 14.7 1.0 CG A:GLU209 4.3 14.0 1.0 CG A:HIS275 4.3 12.4 1.0 O A:GLU209 4.7 13.2 1.0 CD A:LYS274 4.7 13.9 1.0 CB A:GLU209 5.0 13.7 1.0

V.Carbone, L.R.Schofield, C.Sang, A.J.Sutherland-Smith, R.S.Ronimus. Structural Determination of Archaeal Udp-N-Acetylglucosamine 4-Epimerase From Methanobrevibacter Ruminantium M1 in Complex with the Bacterial Cell Wall Intermediate Udp-N-Acetylmuramic Acid. Proteins V. 86 1306 2018.
ISSN: ESSN 1097-0134
PubMed: 30242905
DOI: 10.1002/PROT.25606