Silver in PDB 5z3w: Malate Dehydrogenase Binds Silver at C113

All present enzymatic activity of Malate Dehydrogenase Binds Silver at C113:
1.1.1.37;

The structure of Malate Dehydrogenase Binds Silver at C113, PDB code: 5z3w 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)	53.57 / 2.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.648, 124.564, 85.503, 90.00, 107.10, 90.00
R / Rfree (%)	19.6 / 22.9

The binding sites of Silver atom in the Malate Dehydrogenase Binds Silver at C113 (pdb code 5z3w). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 4 binding sites of Silver where determined in the Malate Dehydrogenase Binds Silver at C113, PDB code: 5z3w:
Jump to Silver binding site number: 1; 2; 3; 4;

Silver binding site 1 out of 4 in the Malate Dehydrogenase Binds Silver at C113


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Malate Dehydrogenase Binds Silver at C113 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag401 b:64.5 occ:1.00 SG A:CYS113 2.5 26.3 1.0 O A:HOH515 2.6 30.0 1.0 N A:CYS113 3.1 24.0 1.0 CB A:CYS113 3.5 24.9 1.0 O A:LYS111 3.6 30.3 1.0 O A:ASP71 3.6 23.2 1.0 C A:ALA112 3.7 18.1 1.0 CA A:CYS113 3.7 23.7 1.0 CD2 A:LEU242 3.9 24.2 1.0 CD1 A:LEU242 4.1 23.3 1.0 CA A:ALA112 4.1 19.1 1.0 CE A:LYS142 4.1 25.2 1.0 CD A:LYS142 4.3 24.2 1.0 CG A:LYS142 4.5 23.1 1.0 O A:ALA112 4.5 17.3 1.0 C A:LYS111 4.6 30.1 1.0 CG A:LEU242 4.7 23.0 1.0 NZ A:LYS142 4.7 26.2 1.0 O A:ASN273 4.8 25.6 1.0 C A:ASP71 4.8 24.0 1.0 N A:ALA112 4.9 18.9 1.0 C A:ASN273 4.9 27.1 1.0 N A:GLY274 5.0 23.3 1.0

Silver binding site 2 out of 4 in the Malate Dehydrogenase Binds Silver at C113


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Malate Dehydrogenase Binds Silver at C113 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag401 b:50.5 occ:1.00 SG B:CYS113 2.5 30.4 1.0 O B:HOH510 3.0 30.0 1.0 N B:CYS113 3.1 30.1 1.0 CB B:CYS113 3.3 28.3 1.0 CA B:CYS113 3.6 29.0 1.0 O B:ASP71 3.7 23.1 1.0 CD2 B:LEU242 3.7 21.7 1.0 O B:LYS111 3.7 34.5 1.0 CD1 B:LEU242 3.7 20.3 1.0 C B:ALA112 3.8 21.6 1.0 CE B:LYS142 4.2 25.9 1.0 CA B:ALA112 4.2 22.3 1.0 CD B:LYS142 4.2 24.7 1.0 CG B:LEU242 4.4 21.3 1.0 CG B:LYS142 4.5 24.5 1.0 O B:ALA112 4.5 21.4 1.0 NZ B:LYS142 4.6 25.9 1.0 C B:LYS111 4.7 33.8 1.0 N B:GLY274 4.8 30.3 1.0 C B:ASP71 4.8 23.1 1.0 C B:ASN273 4.9 24.1 1.0

Silver binding site 3 out of 4 in the Malate Dehydrogenase Binds Silver at C113


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Malate Dehydrogenase Binds Silver at C113 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag401 b:54.4 occ:1.00 SG C:CYS113 2.5 25.5 1.0 N C:CYS113 3.0 26.2 1.0 CB C:CYS113 3.4 24.8 1.0 O C:HOH505 3.4 30.0 1.0 O C:ASP71 3.6 26.3 1.0 CD C:LYS142 3.6 22.3 1.0 CA C:CYS113 3.7 25.6 1.0 O C:LYS111 3.7 29.5 1.0 C C:ALA112 3.7 23.8 1.0 CD2 C:LEU242 3.7 25.6 1.0 CD1 C:LEU242 3.8 25.6 1.0 NZ C:LYS142 4.0 25.0 1.0 CA C:ALA112 4.2 24.9 1.0 CE C:LYS142 4.4 24.2 1.0 CG C:LEU242 4.4 25.6 1.0 O C:ALA112 4.5 24.1 1.0 C C:LYS111 4.7 30.5 1.0 C C:ASP71 4.8 25.6 1.0 N C:GLY274 4.8 29.4 1.0 CG C:LYS142 4.8 21.9 1.0 C C:ASN273 4.9 24.0 1.0 N C:ALA112 5.0 25.5 1.0

Silver binding site 4 out of 4 in the Malate Dehydrogenase Binds Silver at C113


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Malate Dehydrogenase Binds Silver at C113 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag401 b:40.1 occ:1.00 SG D:CYS113 2.4 21.8 1.0 O D:HOH511 3.0 30.0 1.0 N D:CYS113 3.1 22.1 1.0 CB D:CYS113 3.2 21.0 1.0 NZ D:LYS142 3.3 25.9 1.0 CA D:CYS113 3.6 21.1 1.0 O D:ASP71 3.7 22.0 1.0 C D:ALA112 3.7 19.0 1.0 CD2 D:LEU242 3.8 24.2 1.0 O D:LYS111 3.8 30.9 1.0 CD1 D:LEU242 3.9 25.0 1.0 CD D:LYS142 3.9 24.4 1.0 CE D:LYS142 4.1 25.8 1.0 CA D:ALA112 4.3 20.1 1.0 O D:ALA112 4.4 18.7 1.0 CG D:LYS142 4.5 23.5 1.0 CG D:LEU242 4.5 24.0 1.0 C D:LYS111 4.8 31.4 1.0 C D:ASP71 4.9 23.0 1.0 N D:GLY274 4.9 20.8 1.0

H.Wang, M.Wang, H.Sun. Structure of Silver-Bound Malate Dehydrogenase To Be Published.