Silver in PDB 6io4: Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A

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

The structure of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A, PDB code: 6io4 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)	87.77 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	87.991, 110.019, 139.712, 87.66, 86.94, 87.26
R / Rfree (%)	17.5 / 24

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Silver atom in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A (pdb code 6io4). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 16 binding sites of Silver where determined in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A, PDB code: 6io4:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 16 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag401 b:1.0 occ:0.86 NE2 A:HIS176 2.2 0.7 1.0 SG A:CYS149 2.4 0.7 1.0 CD2 A:HIS176 3.0 74.6 1.0 CE1 A:HIS176 3.3 92.0 1.0 OG1 A:THR150 3.4 59.6 1.0 CB A:ASN313 3.7 79.8 1.0 CB A:CYS149 3.7 96.5 1.0 OH A:TYR311 3.8 71.4 1.0 CE2 A:TYR311 4.0 64.9 1.0 N A:THR150 4.1 87.5 1.0 CG A:HIS176 4.2 63.4 1.0 ND1 A:HIS176 4.3 70.3 1.0 CZ A:TYR311 4.4 60.3 1.0 C A:CYS149 4.5 69.4 1.0 CA A:CYS149 4.5 81.8 1.0 CB A:THR150 4.6 59.4 1.0 CA A:ASN313 4.6 71.5 1.0 CG A:ASN313 4.7 83.6 1.0 N A:CYS149 4.8 76.5 1.0 CA A:THR150 4.8 77.1 1.0

Silver binding site 2 out of 16 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag401 b:0.2 occ:0.85 NE2 B:HIS176 2.1 90.8 1.0 SG B:CYS149 2.4 0.3 1.0 CE1 B:HIS176 3.0 74.8 1.0 CD2 B:HIS176 3.1 51.2 1.0 OG1 B:THR150 3.5 76.1 1.0 CB B:ASN313 3.7 72.7 1.0 CB B:CYS149 3.8 91.5 1.0 OH B:TYR311 4.0 55.1 1.0 N B:THR150 4.1 77.9 1.0 CE2 B:TYR311 4.1 65.3 1.0 ND1 B:HIS176 4.1 58.9 1.0 CG B:HIS176 4.2 68.7 1.0 CZ B:TYR311 4.6 58.4 1.0 C B:CYS149 4.6 86.2 1.0 CA B:CYS149 4.6 90.5 1.0 CG B:ASN313 4.7 69.0 1.0 CB B:THR150 4.7 78.3 1.0 CA B:ASN313 4.7 65.5 1.0 N B:CYS149 4.8 79.2 1.0 CA B:THR150 4.9 70.6 1.0

Silver binding site 3 out of 16 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag401 b:79.7 occ:0.76 NE2 C:HIS176 2.1 1.0 1.0 SG C:CYS149 2.4 92.6 1.0 CD2 C:HIS176 2.9 59.3 1.0 CE1 C:HIS176 3.2 94.0 1.0 OG1 C:THR150 3.4 95.4 1.0 CB C:CYS149 3.6 86.1 1.0 CB C:ASN313 3.7 60.8 1.0 OH C:TYR311 3.9 73.3 1.0 CE2 C:TYR311 4.1 52.7 1.0 CG C:HIS176 4.1 58.0 1.0 N C:THR150 4.1 77.1 1.0 ND1 C:HIS176 4.2 57.1 1.0 CZ C:TYR311 4.5 52.6 1.0 CA C:CYS149 4.6 66.6 1.0 C C:CYS149 4.6 68.1 1.0 CB C:THR150 4.7 81.8 1.0 CG C:ASN313 4.7 70.4 1.0 CA C:ASN313 4.8 62.4 1.0 CA C:THR150 4.8 76.5 1.0 N C:CYS149 4.9 64.4 1.0 OG C:SER238 5.0 55.6 1.0

Silver binding site 4 out of 16 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag401 b:0.2 occ:0.78 NE2 D:HIS176 2.1 44.4 1.0 SG D:CYS149 2.4 68.5 1.0 CD2 D:HIS176 2.9 44.3 1.0 CE1 D:HIS176 3.2 81.9 1.0 OG1 D:THR150 3.5 53.5 1.0 CB D:ASN313 3.6 50.9 1.0 CB D:CYS149 3.7 77.6 1.0 OH D:TYR311 3.9 53.8 1.0 CG D:HIS176 4.1 44.3 1.0 ND1 D:HIS176 4.2 46.0 1.0 CE2 D:TYR311 4.2 76.2 1.0 N D:THR150 4.3 74.7 1.0 CZ D:TYR311 4.5 52.7 1.0 CG D:ASN313 4.5 51.2 1.0 CA D:CYS149 4.6 75.1 1.0 C D:CYS149 4.7 90.2 1.0 CB D:THR150 4.8 50.6 1.0 CA D:ASN313 4.8 51.4 1.0 N D:CYS149 4.9 83.2 1.0 ND2 D:ASN313 4.9 51.5 1.0 CA D:THR150 5.0 55.0 1.0 OG D:SER238 5.0 48.0 1.0

Silver binding site 5 out of 16 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A within 5.0Å range: probe atom residue distance (Å) B Occ E:Ag401 b:96.7 occ:0.77 NE2 E:HIS176 2.1 0.4 1.0 SG E:CYS149 2.4 0.6 1.0 CD2 E:HIS176 2.9 99.5 1.0 CE1 E:HIS176 3.2 0.8 1.0 OG1 E:THR150 3.5 76.6 1.0 CB E:CYS149 3.6 0.7 1.0 CB E:ASN313 3.7 72.4 1.0 OH E:TYR311 4.0 75.5 1.0 CG E:HIS176 4.1 92.6 1.0 CE2 E:TYR311 4.1 70.9 1.0 N E:THR150 4.1 72.8 1.0 ND1 E:HIS176 4.2 98.9 1.0 C E:CYS149 4.5 95.4 1.0 CA E:CYS149 4.5 0.4 1.0 CZ E:TYR311 4.6 81.8 1.0 CG E:ASN313 4.7 68.2 1.0 CB E:THR150 4.7 72.4 1.0 CA E:ASN313 4.8 70.0 1.0 N E:CYS149 4.8 99.5 1.0 OG E:SER238 4.9 79.7 1.0 CA E:THR150 4.9 72.9 1.0

Silver binding site 6 out of 16 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A within 5.0Å range: probe atom residue distance (Å) B Occ F:Ag401 b:0.7 occ:0.85 NE2 F:HIS176 2.1 99.4 1.0 SG F:CYS149 2.4 0.7 1.0 CE1 F:HIS176 3.1 0.7 1.0 CD2 F:HIS176 3.1 87.6 1.0 OG1 F:THR150 3.5 85.2 1.0 CB F:ASN313 3.6 68.0 1.0 CB F:CYS149 3.6 92.5 1.0 CE2 F:TYR311 4.1 69.3 1.0 OH F:TYR311 4.1 91.6 1.0 ND1 F:HIS176 4.2 90.9 1.0 CG F:HIS176 4.2 68.5 1.0 N F:THR150 4.3 84.9 1.0 CG F:ASN313 4.5 83.2 1.0 CA F:CYS149 4.6 85.2 1.0 CZ F:TYR311 4.6 69.9 1.0 C F:CYS149 4.6 89.3 1.0 CA F:ASN313 4.7 66.4 1.0 CB F:THR150 4.8 85.3 1.0 N F:CYS149 4.9 84.3 1.0 CA F:THR150 5.0 85.4 1.0 OG F:SER238 5.0 67.1 1.0

Silver binding site 7 out of 16 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A within 5.0Å range: probe atom residue distance (Å) B Occ G:Ag401 b:0.5 occ:0.81 NE2 G:HIS176 2.1 0.1 1.0 SG G:CYS149 2.5 0.3 1.0 CD2 G:HIS176 2.9 82.5 1.0 CE1 G:HIS176 3.2 97.5 1.0 OG1 G:THR150 3.4 91.6 1.0 CB G:CYS149 3.6 0.2 1.0 CB G:ASN313 3.7 85.5 1.0 OH G:TYR311 3.8 70.6 1.0 CE2 G:TYR311 4.0 55.4 1.0 N G:THR150 4.0 0.5 1.0 CG G:HIS176 4.1 74.7 1.0 ND1 G:HIS176 4.2 84.4 1.0 C G:CYS149 4.4 0.6 1.0 CZ G:TYR311 4.4 57.7 1.0 CA G:CYS149 4.5 96.0 1.0 CB G:THR150 4.6 75.8 1.0 CG G:ASN313 4.6 86.1 1.0 CA G:THR150 4.7 89.9 1.0 N G:CYS149 4.8 82.4 1.0 CA G:ASN313 4.9 68.0 1.0 OG G:SER238 4.9 77.9 1.0

Silver binding site 8 out of 16 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A within 5.0Å range: probe atom residue distance (Å) B Occ H:Ag401 b:82.2 occ:0.88 NE2 H:HIS176 2.1 0.4 1.0 SG H:CYS149 2.4 0.6 1.0 CD2 H:HIS176 3.0 73.0 1.0 CE1 H:HIS176 3.2 92.2 1.0 OG1 H:THR150 3.4 94.1 1.0 CB H:CYS149 3.6 0.4 1.0 CB H:ASN313 3.6 76.7 1.0 OH H:TYR311 3.8 72.2 1.0 CE2 H:TYR311 4.0 76.4 1.0 N H:THR150 4.1 1.0 1.0 CG H:HIS176 4.2 78.5 1.0 ND1 H:HIS176 4.3 68.9 1.0 CZ H:TYR311 4.4 72.3 1.0 C H:CYS149 4.5 0.9 1.0 CA H:CYS149 4.5 0.7 1.0 CB H:THR150 4.6 92.3 1.0 CG H:ASN313 4.6 71.9 1.0 CA H:ASN313 4.7 82.0 1.0 CA H:THR150 4.8 0.8 1.0 N H:CYS149 4.8 0.1 1.0 OG H:SER238 5.0 88.9 1.0

Silver binding site 9 out of 16 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A within 5.0Å range: probe atom residue distance (Å) B Occ I:Ag401 b:92.5 occ:0.70 NE2 I:HIS176 2.2 0.9 1.0 SG I:CYS149 2.4 0.1 1.0 CD2 I:HIS176 3.0 98.7 1.0 CE1 I:HIS176 3.3 0.3 1.0 OG1 I:THR150 3.3 0.5 1.0 CB I:CYS149 3.6 0.8 1.0 CB I:ASN313 3.7 97.4 1.0 OH I:TYR311 3.8 86.0 1.0 CE2 I:TYR311 3.9 90.9 1.0 N I:THR150 4.0 0.5 1.0 CG I:HIS176 4.2 82.2 1.0 ND1 I:HIS176 4.3 94.8 1.0 CZ I:TYR311 4.4 93.5 1.0 C I:CYS149 4.4 0.9 1.0 CA I:CYS149 4.4 0.6 1.0 CB I:THR150 4.5 1.0 1.0 CG I:ASN313 4.6 0.3 1.0 CA I:THR150 4.6 0.0 1.0 N I:CYS149 4.7 0.3 1.0 CA I:ASN313 4.8 89.5 1.0

Silver binding site 10 out of 16 in the Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of Silver-Bound Glyceraldehyde-3-Phosphate Dehydrogenase A within 5.0Å range: probe atom residue distance (Å) B Occ J:Ag401 b:0.9 occ:0.80 NE2 J:HIS176 2.1 0.2 1.0 SG J:CYS149 2.4 0.7 1.0 CD2 J:HIS176 3.1 88.9 1.0 CE1 J:HIS176 3.2 99.5 1.0 OG1 J:THR150 3.4 84.4 1.0 CB J:ASN313 3.6 85.3 1.0 CB J:CYS149 3.6 0.0 1.0 N J:THR150 4.0 0.6 1.0 OH J:TYR311 4.0 75.2 1.0 CE2 J:TYR311 4.0 57.7 1.0 CG J:HIS176 4.2 84.0 1.0 ND1 J:HIS176 4.3 83.6 1.0 C J:CYS149 4.4 99.8 1.0 CA J:CYS149 4.5 0.8 1.0 CZ J:TYR311 4.5 58.5 1.0 CB J:THR150 4.5 82.2 1.0 CA J:ASN313 4.6 72.0 1.0 CG J:ASN313 4.6 84.8 1.0 CA J:THR150 4.7 95.6 1.0 N J:CYS149 4.7 0.1 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