Cadmium in PDB 1t99: R106G KDO8PS Without Substrates

All present enzymatic activity of R106G KDO8PS Without Substrates:
2.5.1.55;

The structure of R106G KDO8PS Without Substrates, PDB code: 1t99 was solved by D.L.Gatti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.41 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.819, 84.819, 160.262, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 24.5

The binding sites of Cadmium atom in the R106G KDO8PS Without Substrates (pdb code 1t99). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the R106G KDO8PS Without Substrates, PDB code: 1t99:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the R106G KDO8PS Without Substrates


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of R106G KDO8PS Without Substrates within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1270 b:39.9 occ:0.50 OE1 A:GLU1222 2.3 45.9 1.0 OD2 A:ASP1233 2.3 55.9 1.0 OE2 A:GLU1222 2.4 45.0 1.0 SG A:CYS1011 2.4 46.5 1.0 NE2 A:HIS1185 2.5 41.9 1.0 CD A:GLU1222 2.6 45.5 1.0 O A:HOH3207 2.8 47.7 1.0 CE1 A:HIS1185 3.3 41.0 1.0 CG A:ASP1233 3.3 54.7 1.0 CB A:CYS1011 3.4 39.7 1.0 CD2 A:HIS1185 3.6 40.8 1.0 CB A:ASP1233 4.0 52.2 1.0 CG A:GLU1222 4.1 42.7 1.0 NZ A:LYS1046 4.1 37.5 1.0 OD1 A:ASP1233 4.1 56.0 1.0 CA A:CYS1011 4.3 37.0 1.0 O A:HOH3093 4.4 45.2 1.0 ND1 A:HIS1185 4.4 38.4 1.0 CG A:HIS1185 4.6 38.2 1.0 NZ A:LYS1041 4.8 30.4 1.0 CE A:LYS1046 4.9 38.3 1.0 CB A:GLU1222 5.0 35.5 1.0

Cadmium binding site 2 out of 2 in the R106G KDO8PS Without Substrates


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of R106G KDO8PS Without Substrates within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd2270 b:42.9 occ:0.50 OD2 B:ASP2233 2.2 57.5 1.0 OE1 B:GLU2222 2.3 49.9 1.0 NE2 B:HIS2185 2.3 50.2 1.0 OE2 B:GLU2222 2.4 50.5 1.0 CD B:GLU2222 2.6 48.8 1.0 SG B:CYS2011 2.6 44.7 1.0 O B:HOH3146 2.9 45.1 1.0 CE1 B:HIS2185 3.1 48.1 1.0 CG B:ASP2233 3.2 58.8 1.0 CD2 B:HIS2185 3.4 48.6 1.0 CB B:CYS2011 3.5 41.7 1.0 CB B:ASP2233 4.0 56.2 1.0 CG B:GLU2222 4.1 48.0 1.0 OD1 B:ASP2233 4.1 60.3 1.0 NZ B:LYS2046 4.2 40.4 1.0 CA B:CYS2011 4.3 39.3 1.0 ND1 B:HIS2185 4.3 48.4 1.0 CG B:HIS2185 4.5 47.0 1.0 O B:HOH3188 4.7 52.2 1.0 NZ B:LYS2041 4.7 38.8 1.0 OG B:SER2232 4.7 64.1 1.0 CB B:GLU2222 5.0 40.2 1.0

X.Xu, J.Wang, F.Kona, P.Divvela, T.Stemmler, D.L.Gatti. Effects of the ARG106==>Gly Mutation on the Catalytic and Conformational Cycle of Aquifex Aeolicus KDO8P Synthase. To Be Published.