Silver in PDB 6io6: Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A at Non- Catalytic Site

All present enzymatic activity of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A at Non- Catalytic Site:
1.2.1.12;

The structure of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A at Non- Catalytic Site, PDB code: 6io6 was solved by H.Wang, H.Sun, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.32 / 2.64
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	122.260, 122.260, 157.780, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.3

The binding sites of Silver atom in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A at Non- Catalytic Site (pdb code 6io6). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 2 binding sites of Silver where determined in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A at Non- Catalytic Site, PDB code: 6io6:
Jump to Silver binding site number: 1; 2;

Silver binding site 1 out of 2 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A at Non- Catalytic Site


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A at Non- Catalytic Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag401 b:99.3 occ:0.81 SG A:CYS289 2.7 77.5 1.0 O A:HOH501 2.7 77.4 1.0 AG A:AG402 3.2 84.3 0.6 OE2 A:GLU287 3.3 0.5 1.0 CB A:CYS289 3.6 73.0 1.0 CD A:GLU287 3.9 94.6 1.0 CA A:GLY273 4.2 54.8 1.0 OE1 A:GLU287 4.2 92.8 1.0 CG2 A:VAL292 4.7 58.5 1.0 N A:CYS289 4.8 69.5 1.0 O A:HOH502 4.8 99.5 1.0 CG A:GLU287 4.8 84.2 1.0 CA A:CYS289 4.8 62.4 1.0 N A:GLY273 5.0 57.7 1.0

Silver binding site 2 out of 2 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A at Non- Catalytic Site


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A at Non- Catalytic Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag402 b:84.3 occ:0.57 SG A:CYS289 2.4 77.5 1.0 O A:HOH502 2.8 99.5 1.0 AG A:AG401 3.2 99.3 0.8 N A:CYS289 3.4 69.5 1.0 OE2 A:GLU287 3.5 0.5 1.0 CB A:CYS289 3.6 73.0 1.0 CA A:CYS289 3.9 62.4 1.0 O A:GLY270 3.9 84.8 1.0 CA A:GLY270 4.0 79.5 1.0 CB A:VAL288 4.1 67.7 1.0 C A:VAL288 4.2 63.4 1.0 CG1 A:VAL288 4.2 61.4 1.0 C A:GLY270 4.3 81.1 1.0 CA A:VAL288 4.5 67.4 1.0 N A:VAL288 4.7 69.5 1.0 CD A:GLU287 4.7 94.6 1.0 N A:GLY270 4.8 82.8 1.0

H.Wang, M.Wang, X.Yang, X.Xu, Q.Hao, A.Yan, M.Hu, R.Lobinski, H.Li, H.Sun. Antimicrobial Silver Targets Glyceraldehyde-3-Phosphate Dehydrogenase in Glycolysis Ofe. Coli. Chem Sci V. 10 7193 2019.
ISSN: ISSN 2041-6520
PubMed: 31588287
DOI: 10.1039/C9SC02032B