Silver in PDB 7cb6: The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)

All present enzymatic activity of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman):
1.1.1.44;

The structure of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman), PDB code: 7cb6 was solved by H.Wang, M.Wang, H.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.34 / 2.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.86, 133.86, 171.32, 90, 90, 90
R / Rfree (%)	20.4 / 24.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Silver atom in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) (pdb code 7cb6). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 20 binding sites of Silver where determined in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman), PDB code: 7cb6:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 20 in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag501 b:60.9 occ:0.84 ND1 A:HIS185 2.2 57.4 1.0 SD A:MET140 2.6 58.3 1.0 CE1 A:HIS185 3.1 57.4 1.0 CG A:HIS185 3.3 53.0 1.0 CE A:MET140 3.5 43.7 1.0 CB A:HIS185 3.6 52.5 1.0 CG A:MET140 3.7 47.6 1.0 O A:MET357 3.7 59.5 1.0 AG A:AG504 4.2 67.1 0.6 NE2 A:HIS185 4.3 51.5 1.0 OG A:SER127 4.3 54.4 1.0 CD2 A:HIS185 4.3 51.1 1.0 CA A:LYS182 4.5 54.1 1.0 O A:VAL181 4.6 42.1 1.0 CG1 A:VAL181 4.6 43.8 1.0 C A:MET357 4.6 57.5 1.0 CA A:ILE358 4.7 67.0 1.0 OG A:SER138 4.9 65.4 1.0 N A:LYS182 4.9 44.7 1.0 C A:VAL181 5.0 49.6 1.0

Silver binding site 2 out of 20 in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag502 b:64.9 occ:0.97 SG A:CYS363 2.4 76.8 1.0 SG A:CYS168 2.5 74.8 1.0 AG A:AG503 2.8 72.6 0.9 CB A:CYS363 3.0 80.7 1.0 CB A:CYS168 3.3 56.7 1.0 C A:CYS363 3.7 87.2 1.0 N A:ILE364 3.8 99.0 1.0 CB A:SER138 3.8 53.9 1.0 CA A:CYS363 3.9 85.9 1.0 AG A:AG504 3.9 67.1 0.6 O A:CYS363 4.0 89.7 1.0 CA A:ILE364 4.3 100.7 1.0 CA A:CYS168 4.5 65.4 1.0 OG A:SER138 4.6 65.4 1.0 CB A:MET357 4.7 59.3 1.0 CB A:ILE364 4.8 98.1 1.0 CE A:MET357 4.8 69.5 1.0

Silver binding site 3 out of 20 in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag503 b:72.6 occ:0.95 SG A:CYS168 2.5 74.8 1.0 SD A:MET357 2.6 63.4 1.0 CE A:MET357 2.8 69.5 1.0 AG A:AG502 2.8 64.9 1.0 CB A:CYS168 3.3 56.7 1.0 CA A:CYS168 3.5 65.4 1.0 CG A:MET357 3.9 60.6 1.0 CB A:MET357 3.9 59.3 1.0 SG A:CYS363 4.0 76.8 1.0 N A:CYS168 4.3 63.8 1.0 C A:CYS168 4.6 64.8 1.0 O A:CYS363 4.7 89.7 1.0 CB A:ALA162 4.7 84.9 1.0 O A:SER167 4.7 65.7 1.0 C A:SER167 4.8 67.1 1.0

Silver binding site 4 out of 20 in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag504 b:67.1 occ:0.55 O A:MET357 2.3 59.5 1.0 SG A:CYS363 2.4 76.8 1.0 OG A:SER138 3.0 65.4 1.0 C A:MET357 3.2 57.5 1.0 N A:TRP359 3.2 68.0 1.0 C A:ILE358 3.5 66.9 1.0 CA A:TRP359 3.5 67.0 1.0 CB A:CYS363 3.6 80.7 1.0 CB A:SER138 3.6 53.9 1.0 CB A:TRP359 3.8 69.0 1.0 CA A:ILE358 3.8 67.0 1.0 N A:ILE358 3.8 59.2 1.0 AG A:AG502 3.9 64.9 1.0 CB A:MET357 4.1 59.3 1.0 O A:ILE358 4.1 71.0 1.0 CA A:MET357 4.2 58.2 1.0 AG A:AG501 4.2 60.9 0.8 CD1 A:TRP359 4.4 71.5 1.0 CG A:TRP359 4.5 72.9 1.0 CB A:SER127 4.9 54.1 1.0 CA A:CYS363 4.9 85.9 1.0

Silver binding site 5 out of 20 in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag505 b:67.4 occ:0.46 ND1 A:HIS211 2.2 74.4 1.0 SD A:MET239 2.5 89.3 1.0 O A:PHE238 2.6 79.6 1.0 CE1 A:HIS211 2.7 75.5 1.0 O A:HIS211 3.1 74.1 1.0 CE A:MET239 3.4 90.0 1.0 CG A:HIS211 3.4 78.0 1.0 C A:HIS211 3.4 75.9 1.0 CA A:MET239 3.6 73.9 1.0 C A:PHE238 3.6 73.7 1.0 N A:GLU212 3.6 78.2 1.0 CA A:GLU212 3.6 74.4 1.0 CG A:MET239 3.8 74.7 1.0 CG A:GLU212 3.9 81.8 1.0 NE2 A:HIS211 4.0 77.6 1.0 N A:MET239 4.0 69.6 1.0 CB A:HIS211 4.0 81.4 1.0 CB A:MET239 4.2 76.8 1.0 CB A:GLU212 4.3 79.1 1.0 CD2 A:HIS211 4.3 81.4 1.0 CA A:HIS211 4.4 80.8 1.0 CB A:ALA215 4.5 72.4 1.0 C A:MET239 4.6 82.7 1.0 OE1 A:GLU212 4.7 87.5 1.0 CD A:GLU212 4.8 90.5 1.0 O A:MET239 4.8 86.9 1.0 C A:GLU212 4.9 76.0 1.0 CA A:PHE238 4.9 72.9 1.0 CB A:PHE238 5.0 72.7 1.0

Silver binding site 6 out of 20 in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag501 b:66.5 occ:1.00 ND1 B:HIS185 2.4 51.8 1.0 SD B:MET140 2.6 48.9 1.0 CE1 B:HIS185 3.2 57.0 1.0 CG B:HIS185 3.4 43.1 1.0 O B:MET357 3.4 61.8 1.0 CE B:MET140 3.4 39.1 1.0 CG B:MET140 3.7 45.7 1.0 CB B:HIS185 3.7 46.4 1.0 AG B:AG503 4.4 71.8 0.8 NE2 B:HIS185 4.4 52.3 1.0 CD2 B:HIS185 4.5 54.8 1.0 C B:MET357 4.5 56.5 1.0 OG B:SER127 4.5 59.7 1.0 CA B:LYS182 4.6 50.0 1.0 CA B:ILE358 4.6 52.3 1.0 CG1 B:VAL181 4.6 47.7 1.0 O B:VAL181 4.7 52.7 1.0 OG B:SER138 4.8 68.3 1.0 N B:LYS182 5.0 39.3 1.0 N B:ILE358 5.0 53.8 1.0

Silver binding site 7 out of 20 in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag502 b:59.9 occ:1.00 SG B:CYS363 2.4 73.6 1.0 SG B:CYS168 2.8 72.9 1.0 AG B:AG504 3.0 68.8 1.0 CB B:CYS363 3.0 53.1 1.0 CB B:CYS168 3.2 62.2 1.0 AG B:AG503 3.4 71.8 0.8 C B:CYS363 3.6 62.2 1.0 N B:ILE364 3.7 63.1 1.0 O B:CYS363 3.9 59.0 1.0 CA B:CYS363 3.9 64.4 1.0 OG B:SER138 4.0 68.3 1.0 CA B:ILE364 4.1 71.5 1.0 CB B:SER138 4.4 48.2 1.0 CB B:MET357 4.4 58.7 1.0 CE3 B:TRP359 4.4 64.9 1.0 CZ3 B:TRP359 4.5 69.3 1.0 CB B:ILE364 4.6 60.6 1.0 CA B:CYS168 4.7 63.1 1.0 SD B:MET357 5.0 61.5 1.0

Silver binding site 8 out of 20 in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag503 b:71.8 occ:0.80 O B:MET357 2.4 61.8 1.0 OG B:SER138 2.8 68.3 1.0 SG B:CYS363 2.9 73.6 1.0 C B:MET357 3.1 56.5 1.0 CB B:CYS363 3.2 53.1 1.0 N B:TRP359 3.3 70.2 1.0 AG B:AG502 3.4 59.9 1.0 CB B:SER138 3.5 48.2 1.0 C B:ILE358 3.5 68.3 1.0 CA B:TRP359 3.6 57.4 1.0 N B:ILE358 3.8 53.8 1.0 CB B:MET357 3.8 58.7 1.0 CA B:ILE358 3.9 52.3 1.0 CB B:TRP359 4.0 64.0 1.0 CA B:MET357 4.0 57.6 1.0 O B:ILE358 4.1 67.3 1.0 CE3 B:TRP359 4.2 64.9 1.0 AG B:AG501 4.4 66.5 1.0 CA B:CYS363 4.7 64.4 1.0 CG B:TRP359 4.9 68.6 1.0 CD2 B:TRP359 4.9 70.5 1.0 CA B:SER138 5.0 51.8 1.0

Silver binding site 9 out of 20 in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag504 b:68.8 occ:0.99 SG B:CYS168 2.4 72.9 1.0 SD B:MET357 2.6 61.5 1.0 CB B:CYS168 2.7 62.2 1.0 AG B:AG502 3.0 59.9 1.0 CE B:MET357 3.3 69.7 1.0 CA B:CYS168 3.3 63.1 1.0 CG B:MET357 3.4 53.1 1.0 CB B:MET357 3.7 58.7 1.0 N B:CYS168 4.2 60.7 1.0 CB B:ALA162 4.2 84.7 1.0 C B:CYS168 4.5 61.1 1.0 O B:CYS363 4.5 59.0 1.0 CB B:CYS363 4.8 53.1 1.0 C B:SER167 5.0 61.3 1.0 O B:CYS168 5.0 56.6 1.0 C B:CYS363 5.0 62.2 1.0

Silver binding site 10 out of 20 in the The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of The Silver-Bound 6-Phosphogluconate Dehydrogenase From Staphylococcus Aureus (Strain Newman) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag505 b:70.5 occ:0.60 ND1 B:HIS211 2.4 80.1 1.0 SD B:MET239 2.4 79.5 1.0 O B:PHE238 2.4 76.0 1.0 CE1 B:HIS211 2.6 75.4 1.0 O B:HIS211 3.3 81.9 1.0 C B:PHE238 3.4 70.7 1.0 CA B:MET239 3.4 66.5 1.0 CA B:GLU212 3.6 82.0 1.0 C B:HIS211 3.7 84.6 1.0 CG B:HIS211 3.7 80.4 1.0 N B:GLU212 3.7 82.7 1.0 N B:MET239 3.8 70.4 1.0 CG B:MET239 3.8 62.9 1.0 CE B:MET239 3.8 83.0 1.0 NE2 B:HIS211 3.9 69.6 1.0 CB B:GLU212 3.9 85.0 1.0 CB B:MET239 4.1 65.0 1.0 CB B:ALA215 4.2 78.9 1.0 CD2 B:HIS211 4.4 78.8 1.0 C B:MET239 4.4 69.1 1.0 CB B:HIS211 4.5 75.5 1.0 CA B:PHE238 4.7 71.0 1.0 CA B:HIS211 4.7 76.4 1.0 O B:MET239 4.8 67.1 1.0 CB B:PHE238 4.8 61.0 1.0 CD2 B:LEU241 4.9 78.4 1.0 OE2 B:GLU212 5.0 87.0 1.0 C B:GLU212 5.0 78.0 1.0 CD B:GLU212 5.0 89.7 1.0

H.Wang, M.Wang, X.Xu, P.Gao, Z.Xu, Q.Zhang, H.Li, A.Yan, R.Y.-T.Kao, H.Sun. Multi-Target Mode of Action of Silver Against Staphylococcus Aureus Enables Its Potential For Combating Antibiotic Resistance. To Be Published.