Cadmium in PDB 1t96: R106G KDO8PS with Pep

All present enzymatic activity of R106G KDO8PS with Pep:
2.5.1.55;

The structure of R106G KDO8PS with Pep, PDB code: 1t96 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)	41.11 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.028, 85.028, 161.151, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 24.6

The binding sites of Cadmium atom in the R106G KDO8PS with Pep (pdb code 1t96). 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 with Pep, PDB code: 1t96:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the R106G KDO8PS with Pep


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of R106G KDO8PS with Pep within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1270 b:26.0 occ:0.50 OD2 A:ASP1233 2.2 50.2 1.0 O A:HOH3419 2.3 36.5 1.0 OE2 A:GLU1222 2.3 35.8 1.0 OE1 A:GLU1222 2.3 38.0 1.0 NE2 A:HIS1185 2.5 27.6 1.0 SG A:CYS1011 2.5 35.5 1.0 CD A:GLU1222 2.6 39.1 1.0 CE1 A:HIS1185 3.2 24.5 1.0 CG A:ASP1233 3.4 47.5 1.0 CD2 A:HIS1185 3.6 32.9 1.0 CB A:CYS1011 3.6 32.2 1.0 NZ A:LYS1046 3.9 25.2 1.0 O1 A:PEP1268 4.1 20.9 1.0 CG A:GLU1222 4.1 35.8 1.0 CB A:ASP1233 4.2 45.1 1.0 C1 A:PEP1268 4.3 24.3 1.0 OD1 A:ASP1233 4.3 51.5 1.0 ND1 A:HIS1185 4.4 24.9 1.0 CA A:CYS1011 4.5 29.6 1.0 OE1 A:GLN1188 4.6 61.2 1.0 CG A:HIS1185 4.6 29.0 1.0 CE A:LYS1046 4.7 29.0 1.0 O2' A:PEP1268 4.7 24.5 1.0 NZ A:LYS1041 4.7 19.4 1.0 C2 A:PEP1268 4.8 24.1 1.0

Cadmium binding site 2 out of 2 in the R106G KDO8PS with Pep


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of R106G KDO8PS with Pep within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd2270 b:26.4 occ:0.50 OD2 B:ASP2233 2.0 43.0 1.0 OE1 B:GLU2222 2.4 38.9 1.0 NE2 B:HIS2185 2.4 37.3 1.0 OE2 B:GLU2222 2.5 37.2 1.0 O B:HOH3046 2.5 26.0 1.0 SG B:CYS2011 2.6 30.2 1.0 CD B:GLU2222 2.8 32.9 1.0 CE1 B:HIS2185 3.1 32.2 1.0 CG B:ASP2233 3.2 45.0 1.0 CD2 B:HIS2185 3.6 37.5 1.0 CB B:CYS2011 3.7 27.8 1.0 O1 B:PEP2268 3.9 29.6 1.0 CB B:ASP2233 4.0 40.5 1.0 OD1 B:ASP2233 4.1 46.0 1.0 NZ B:LYS2046 4.1 26.9 1.0 CG B:GLU2222 4.2 35.9 1.0 ND1 B:HIS2185 4.2 35.7 1.0 C1 B:PEP2268 4.3 30.1 1.0 CA B:CYS2011 4.4 25.1 1.0 CG B:HIS2185 4.5 28.9 1.0 NZ B:LYS2041 4.6 21.6 1.0 O2' B:PEP2268 4.7 22.4 1.0 O B:HOH3252 4.7 31.1 1.0 OG B:SER2232 4.7 44.0 1.0 C2 B:PEP2268 4.8 31.4 1.0 O B:HOH3335 4.8 57.3 1.0 CE B:LYS2046 4.8 31.1 1.0 CG2 B:THR2184 5.0 27.9 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.