Silver in PDB 7cgc: Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251)

All present enzymatic activity of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251):
1.1.1.37;

The structure of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251), PDB code: 7cgc 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)	40.71 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.222, 125.129, 85.195, 90.00, 107.10, 90.00
R / Rfree (%)	24.3 / 29

Pages:

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

Binding sites:

The binding sites of Silver atom in the Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) (pdb code 7cgc). 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 E. Coli Malate Dehydrogenase (C113 and C251), PDB code: 7cgc:
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 E. Coli Malate Dehydrogenase (C113 and C251)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag401 b:58.8 occ:0.89 AG A:AG402 2.7 49.6 0.8 SG A:CYS113 2.8 38.5 1.0 O A:HOH502 2.8 30.3 1.0 O A:ASP71 3.0 23.9 1.0 N A:CYS113 3.2 36.5 1.0 CD2 A:LEU242 3.3 39.0 1.0 CB A:CYS113 3.5 36.1 1.0 CA A:CYS113 3.9 35.8 1.0 CG A:LEU242 4.0 38.9 1.0 C A:ASP71 4.0 23.2 1.0 C A:ALA112 4.0 22.9 1.0 CA A:ALA112 4.2 23.7 1.0 O A:LYS111 4.2 25.2 1.0 CD1 A:LEU242 4.3 39.0 1.0 NZ A:LYS142 4.5 24.8 1.0 CA A:ASP71 4.6 23.5 1.0 CB A:ASP71 4.7 23.9 1.0 CG2 A:VAL72 5.0 28.1 1.0 O A:ALA112 5.0 23.1 1.0

Silver binding site 2 out of 16 in the Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag402 b:49.6 occ:0.85 NZ A:LYS142 2.2 24.8 1.0 SG A:CYS113 2.5 38.5 1.0 AG A:AG401 2.7 58.8 0.9 CG A:LYS142 2.7 21.0 1.0 CE A:LYS142 3.1 23.6 1.0 CD A:LYS142 3.4 21.7 1.0 O A:ASN273 3.5 46.2 1.0 C A:ASN273 3.6 45.8 1.0 N A:CYS113 3.7 36.5 1.0 CB A:CYS113 3.8 36.1 1.0 N A:GLY274 3.8 40.9 1.0 CA A:CYS113 3.9 35.8 1.0 O A:LYS111 3.9 25.2 1.0 CB A:LYS142 4.1 20.2 1.0 CA A:GLY274 4.1 39.8 1.0 C A:ALA112 4.1 22.9 1.0 O A:HOH502 4.2 30.3 1.0 CA A:ASN273 4.3 47.4 1.0 O A:ALA112 4.5 23.1 1.0 CA A:LYS142 4.6 19.6 1.0 CA A:ALA112 4.8 23.7 1.0 C A:LYS111 4.9 24.6 1.0

Silver binding site 3 out of 16 in the Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag403 b:27.1 occ:0.67 N A:VAL173 2.2 27.5 1.0 SG A:CYS251 2.3 46.5 1.0 O A:VAL173 2.7 24.8 1.0 CB A:CYS251 2.9 44.9 1.0 C A:PRO172 3.0 40.6 1.0 CA A:PRO172 3.0 40.6 1.0 AG A:AG404 3.2 50.4 0.9 C A:VAL173 3.2 25.6 1.0 CA A:VAL173 3.2 26.3 1.0 CD1 A:ILE151 3.3 25.4 1.0 CB A:PRO172 3.4 41.0 1.0 CB A:VAL173 4.0 25.6 1.0 O A:PRO172 4.2 41.4 1.0 N A:ILE174 4.3 24.8 1.0 CA A:CYS251 4.3 42.9 1.0 N A:PRO172 4.4 41.2 1.0 O A:VAL171 4.5 26.6 1.0 CG2 A:VAL173 4.6 26.6 1.0 CG2 A:ILE174 4.7 25.8 1.0 CG1 A:ILE151 4.8 24.8 1.0 O A:HOH504 4.8 35.3 1.0 N A:CYS251 4.8 42.2 1.0 CG A:PRO172 4.9 42.0 1.0 C A:VAL171 4.9 27.7 1.0

Silver binding site 4 out of 16 in the Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag404 b:50.4 occ:0.92 SG A:CYS251 2.8 46.5 1.0 O A:HOH504 2.9 35.3 1.0 AG A:AG403 3.2 27.1 0.7 CB A:CYS251 3.2 44.9 1.0 N A:CYS251 3.3 42.2 1.0 CA A:CYS251 3.8 42.9 1.0 C A:GLU250 4.0 34.3 1.0 CA A:GLU250 4.3 33.7 1.0 CB A:PRO172 4.5 41.0 1.0 CA A:PRO172 4.5 40.6 1.0 CD1 A:ILE151 4.6 25.4 1.0 CA A:PRO267 4.7 27.9 1.0 O A:GLU250 4.7 34.4 1.0 CB A:PRO267 4.8 29.1 1.0 CG A:PRO267 4.8 29.3 1.0 N A:GLU250 4.9 34.2 1.0 CG1 A:VAL249 4.9 22.0 1.0 O A:VAL249 4.9 20.7 1.0

Silver binding site 5 out of 16 in the Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag401 b:47.2 occ:0.79 O B:HOH502 2.8 30.3 1.0 AG B:AG402 2.9 47.9 0.9 SG B:CYS113 3.0 40.5 1.0 O B:ASP71 3.1 29.6 1.0 N B:CYS113 3.3 39.0 1.0 CB B:CYS113 3.4 37.9 1.0 CD2 B:LEU242 3.4 35.6 1.0 CD1 B:LEU242 3.6 34.0 1.0 CA B:CYS113 3.9 38.1 1.0 O B:LYS111 4.1 48.9 1.0 C B:ALA112 4.1 46.8 1.0 O B:HOH503 4.1 32.0 1.0 CG B:LEU242 4.2 34.3 1.0 C B:ASP71 4.2 29.8 1.0 CA B:ALA112 4.2 48.0 1.0 CA B:ASP71 4.7 32.1 1.0 CB B:ASP71 4.8 32.1 1.0

Silver binding site 6 out of 16 in the Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag402 b:47.9 occ:0.87 SG B:CYS113 2.4 40.5 1.0 AG B:AG401 2.9 47.2 0.8 CB B:LYS142 3.4 23.6 1.0 O B:ASN273 3.5 38.9 1.0 C B:ASN273 3.5 37.7 1.0 N B:GLY274 3.7 29.8 1.0 CB B:CYS113 3.7 37.9 1.0 O B:LYS111 3.7 48.9 1.0 N B:CYS113 3.8 39.0 1.0 CA B:CYS113 3.8 38.1 1.0 CA B:GLY274 3.9 28.9 1.0 CA B:LYS142 4.1 22.4 1.0 CA B:ASN273 4.2 38.2 1.0 C B:ALA112 4.2 46.8 1.0 O B:HOH503 4.3 32.0 1.0 O B:ALA112 4.5 47.6 1.0 O B:HOH502 4.5 30.3 1.0 C B:LYS111 4.8 48.9 1.0 O B:ASN141 4.8 32.5 1.0 CD2 B:LEU242 4.9 35.6 1.0 CA B:ALA112 5.0 48.0 1.0 N B:LYS142 5.0 22.3 1.0

Silver binding site 7 out of 16 in the Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag403 b:32.9 occ:0.76 SG B:CYS251 2.2 33.7 1.0 N B:VAL173 2.2 20.9 1.0 O B:VAL173 2.5 19.9 1.0 CB B:CYS251 3.0 31.1 1.0 C B:VAL173 3.0 20.4 1.0 C B:PRO172 3.1 35.3 1.0 CA B:VAL173 3.1 20.7 1.0 CD1 B:ILE151 3.1 20.6 1.0 CA B:PRO172 3.2 36.6 1.0 AG B:AG404 3.3 49.6 0.9 CB B:PRO172 3.8 37.1 1.0 CB B:VAL173 3.9 20.2 1.0 N B:ILE174 4.2 28.5 1.0 O B:PRO172 4.3 37.3 1.0 CG2 B:VAL173 4.3 20.4 1.0 O B:VAL171 4.4 29.2 1.0 CA B:CYS251 4.4 31.0 1.0 N B:PRO172 4.5 38.2 1.0 CG2 B:ILE174 4.5 29.7 1.0 CG1 B:ILE151 4.6 20.2 1.0 CA B:ILE174 4.9 28.5 1.0 C B:VAL171 4.9 30.1 1.0 N B:CYS251 4.9 31.6 1.0

Silver binding site 8 out of 16 in the Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag404 b:49.6 occ:0.89 SG B:CYS251 2.3 33.7 1.0 O B:HOH504 2.8 30.3 1.0 N B:CYS251 3.3 31.6 1.0 CB B:CYS251 3.3 31.1 1.0 AG B:AG403 3.3 32.9 0.8 CA B:CYS251 3.8 31.0 1.0 C B:GLU250 4.0 47.0 1.0 CB B:PRO267 4.4 37.9 1.0 CA B:GLU250 4.4 48.0 1.0 CG B:PRO267 4.4 38.2 1.0 CA B:PRO267 4.4 36.7 1.0 CD1 B:ILE151 4.4 20.6 1.0 CA B:PRO172 4.6 36.6 1.0 CB B:PRO172 4.8 37.1 1.0 O B:GLU250 4.8 47.0 1.0 CG1 B:VAL249 4.9 40.0 1.0 N B:GLU250 4.9 48.4 1.0 N B:PRO267 5.0 36.5 1.0 O B:VAL249 5.0 40.8 1.0

Silver binding site 9 out of 16 in the Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag401 b:42.8 occ:1.00 SG C:CYS113 2.4 36.2 1.0 NZ C:LYS142 2.4 33.7 1.0 N C:CYS113 3.2 34.8 1.0 NZ C:LYS111 3.3 53.4 1.0 CB C:CYS113 3.3 34.0 1.0 AG C:AG402 3.3 35.2 0.7 O C:ASP71 3.7 34.1 1.0 CA C:CYS113 3.7 33.7 1.0 CD1 C:LEU242 3.7 56.1 1.0 O C:LYS111 3.8 48.6 1.0 CE C:LYS142 3.8 35.0 1.0 CE C:LYS111 3.8 54.5 1.0 C C:ALA112 3.9 32.7 1.0 CD2 C:LEU242 3.9 59.0 1.0 CG C:LEU242 4.3 56.9 1.0 CA C:ALA112 4.3 33.8 1.0 CD C:LYS142 4.5 34.2 1.0 O C:ALA112 4.6 32.8 1.0 CD C:LYS111 4.8 53.7 1.0 CG C:LYS142 4.8 33.5 1.0 C C:LYS111 4.8 48.1 1.0 C C:ASP71 4.9 34.2 1.0 N C:GLY274 4.9 29.8 1.0

Silver binding site 10 out of 16 in the Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of Silver-Bound E. Coli Malate Dehydrogenase (C113 and C251) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag402 b:35.2 occ:0.65 SG C:CYS113 2.5 36.2 1.0 CG C:LEU242 3.2 56.9 1.0 CD2 C:LEU242 3.3 59.0 1.0 AG C:AG401 3.3 42.8 1.0 CB C:CYS113 3.5 34.0 1.0 CD2 C:LEU238 3.6 37.6 1.0 CA C:GLY274 3.7 28.7 1.0 CD1 C:LEU242 3.7 56.1 1.0 N C:GLY274 3.8 29.8 1.0 O C:GLY271 4.2 35.8 1.0 O C:LEU238 4.4 37.6 1.0 CD1 C:LEU238 4.4 34.8 1.0 CG C:LEU238 4.4 35.3 1.0 CB C:LEU242 4.5 55.8 1.0 CB C:LEU238 4.7 34.5 1.0 NZ C:LYS142 4.7 33.7 1.0 C C:GLY274 4.8 28.0 1.0 C C:ASN273 4.8 49.8 1.0 CA C:CYS113 4.9 33.7 1.0 CA C:LEU238 5.0 35.3 1.0 C C:LEU238 5.0 35.7 1.0

H.Wang, X.Yang, M.Wang, M.Hu, X.Xu, A.Yan, Q.Hao, H.Li, H.Sun. Atomic Differentiation of Silver Binding Preference in Protein Targets: Escherichia Coli Malate Dehydrogenase As A Paradigm Chem Sci 2020.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC04151C