Silver in PDB 6ka0: Silver-Bound E.Coli Malate Dehydrogenase

All present enzymatic activity of Silver-Bound E.Coli Malate Dehydrogenase:
1.1.1.37;

The structure of Silver-Bound E.Coli Malate Dehydrogenase, PDB code: 6ka0 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)	48.16 / 2.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.860, 152.830, 78.500, 90.00, 108.75, 90.00
R / Rfree (%)	22 / 27.2

The binding sites of Silver atom in the Silver-Bound E.Coli Malate Dehydrogenase (pdb code 6ka0). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 5 binding sites of Silver where determined in the Silver-Bound E.Coli Malate Dehydrogenase, PDB code: 6ka0:
Jump to Silver binding site number: 1; 2; 3; 4; 5;

Silver binding site 1 out of 5 in the Silver-Bound E.Coli Malate Dehydrogenase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag401 b:52.0 occ:0.96 N A:TRS403 2.1 37.3 1.0 SG A:CYS113 2.7 56.8 1.0 CB A:CYS113 3.1 39.8 1.0 N A:CYS113 3.1 41.3 1.0 C A:TRS403 3.1 47.5 1.0 C1 A:TRS403 3.2 43.9 1.0 O1 A:TRS403 3.3 48.6 1.0 CA A:CYS113 3.6 42.5 1.0 CD2 A:LEU242 3.7 46.2 1.0 O A:ASP71 3.7 50.7 1.0 CD A:LYS142 3.8 46.6 1.0 O A:LYS111 3.9 57.4 1.0 C2 A:TRS403 3.9 30.5 1.0 C A:ALA112 3.9 42.5 1.0 CD1 A:LEU242 4.0 48.6 1.0 CE A:LYS142 4.2 51.2 1.0 NZ A:LYS142 4.2 48.1 1.0 C3 A:TRS403 4.4 47.5 1.0 CA A:ALA112 4.4 48.7 1.0 CG A:LEU242 4.5 51.4 1.0 CG A:LYS142 4.5 56.1 1.0 N A:GLY274 4.6 50.7 1.0 O A:ALA112 4.7 48.4 1.0 C A:ASN273 4.8 62.7 1.0 CB A:LYS142 4.9 49.1 1.0 C A:ASP71 4.9 37.0 1.0 C A:LYS111 4.9 53.7 1.0 CA A:GLY274 5.0 45.3 1.0

Silver binding site 2 out of 5 in the Silver-Bound E.Coli Malate Dehydrogenase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag402 b:63.9 occ:0.43 SG A:CYS251 2.7 65.5 1.0 O A:HOH501 2.8 60.6 1.0 N A:CYS251 3.6 37.5 1.0 CB A:CYS251 3.8 46.2 1.0 CB A:PRO267 4.1 67.6 1.0 CA A:CYS251 4.2 48.6 1.0 CG A:PRO267 4.2 63.7 1.0 C A:GLU250 4.3 43.1 1.0 CA A:PRO267 4.3 61.0 1.0 CG1 A:VAL249 4.3 42.6 1.0 CA A:PRO172 4.5 35.7 1.0 CB A:PRO172 4.5 41.3 1.0 CA A:GLU250 4.5 38.2 1.0 N A:GLU250 4.9 48.3 1.0 O A:VAL249 4.9 45.2 1.0

Silver binding site 3 out of 5 in the Silver-Bound E.Coli Malate Dehydrogenase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag401 b:50.0 occ:0.77 SG B:CYS113 2.2 66.6 1.0 N B:TRS402 2.2 55.0 1.0 N B:CYS113 3.1 41.3 1.0 CB B:CYS113 3.2 64.5 1.0 C B:TRS402 3.3 59.5 1.0 C1 B:TRS402 3.4 60.4 1.0 O B:ASP71 3.6 57.7 1.0 O1 B:TRS402 3.6 59.0 1.0 CA B:CYS113 3.6 56.1 1.0 CD B:LYS142 3.7 61.2 1.0 CD2 B:LEU242 3.8 54.1 1.0 CD1 B:LEU242 3.8 48.9 1.0 O B:LYS111 3.8 65.9 1.0 C B:ALA112 3.9 46.4 1.0 C2 B:TRS402 4.0 56.6 1.0 CA B:ALA112 4.3 52.7 1.0 CE B:LYS142 4.4 65.4 1.0 CG B:LEU242 4.4 48.4 1.0 CG B:LYS142 4.4 64.3 1.0 N B:GLY274 4.5 66.0 1.0 C3 B:TRS402 4.5 48.9 1.0 NZ B:LYS142 4.6 53.3 1.0 O B:ALA112 4.7 53.0 1.0 C B:ASP71 4.8 54.5 1.0 C B:LYS111 4.9 71.6 1.0 CA B:GLY274 4.9 64.2 1.0 CB B:LYS142 4.9 64.6 1.0

Silver binding site 4 out of 5 in the Silver-Bound E.Coli Malate Dehydrogenase


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag401 b:48.0 occ:0.83 SG C:CYS113 2.1 54.7 1.0 N C:TRS402 2.2 34.7 1.0 C1 C:TRS402 3.0 68.8 1.0 C C:TRS402 3.1 54.8 1.0 N C:CYS113 3.3 46.8 1.0 O1 C:TRS402 3.3 70.2 1.0 CB C:CYS113 3.4 59.4 1.0 CD2 C:LEU242 3.6 40.5 1.0 CD1 C:LEU242 3.6 45.7 1.0 C2 C:TRS402 3.6 62.7 1.0 CA C:CYS113 3.7 57.2 1.0 O C:ASP71 3.8 58.9 1.0 O C:LYS111 3.9 63.2 1.0 C C:ALA112 3.9 49.7 1.0 CE C:LYS142 4.2 68.3 1.0 CG C:LEU242 4.2 52.4 1.0 CD C:LYS142 4.3 56.7 1.0 CA C:ALA112 4.4 45.8 1.0 C3 C:TRS402 4.4 53.9 1.0 NZ C:LYS142 4.4 58.8 1.0 N C:GLY274 4.5 65.6 1.0 CG C:LYS142 4.6 53.8 1.0 O C:ALA112 4.6 44.6 1.0 O2 C:TRS402 4.7 57.4 1.0 C C:LYS111 4.9 62.9 1.0 O C:LYS272 4.9 59.8 1.0 CA C:GLY274 5.0 68.4 1.0 C C:ASP71 5.0 52.7 1.0 C C:ASN273 5.0 69.9 1.0

Silver binding site 5 out of 5 in the Silver-Bound E.Coli Malate Dehydrogenase


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag401 b:61.6 occ:0.76 N D:TRS402 2.3 50.3 1.0 SG D:CYS113 2.4 74.2 1.0 C1 D:TRS402 2.8 72.2 1.0 N D:CYS113 3.0 53.3 1.0 O1 D:TRS402 3.0 80.2 1.0 C D:TRS402 3.0 64.9 1.0 CB D:CYS113 3.2 49.3 1.0 CD1 D:LEU242 3.4 75.3 1.0 CA D:CYS113 3.5 51.6 1.0 O D:ASP71 3.7 64.8 1.0 C2 D:TRS402 3.8 73.4 1.0 C D:ALA112 3.8 56.3 1.0 CD D:LYS142 3.8 74.7 1.0 O D:LYS111 3.8 65.2 1.0 CE D:LYS142 4.1 69.7 1.0 NZ D:LYS142 4.2 66.3 1.0 CA D:ALA112 4.2 66.3 1.0 CD2 D:LEU242 4.2 78.5 1.0 C3 D:TRS402 4.3 55.1 1.0 CG D:LEU242 4.5 76.1 1.0 CG D:LYS142 4.6 74.2 1.0 C D:ASN273 4.6 83.1 1.0 O D:ALA112 4.6 66.3 1.0 N D:GLY274 4.7 77.1 1.0 C D:LYS111 4.8 64.5 1.0 O D:ASN273 4.8 90.6 1.0 O D:LYS272 4.9 81.7 1.0 CA D:ASN273 4.9 78.3 1.0 C D:ASP71 4.9 69.3 1.0 C D:CYS113 4.9 53.1 1.0

H.Wang, M.Wang, H.Sun. Mdh Is A Major Silver Target in E. Coli To Be Published.