Cadmium in PDB 1t8x: R106G KDO8PS with Pep and A5P

All present enzymatic activity of R106G KDO8PS with Pep and A5P:
2.5.1.55;

The structure of R106G KDO8PS with Pep and A5P, PDB code: 1t8x 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)	54.02 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.375, 84.375, 160.459, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 24.2

The binding sites of Cadmium atom in the R106G KDO8PS with Pep and A5P (pdb code 1t8x). 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 and A5P, PDB code: 1t8x:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the R106G KDO8PS with Pep and A5P


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 and A5P within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1270 b:31.7 occ:0.50 OD1 A:ASP1233 2.1 49.6 1.0 OE1 A:GLU1222 2.3 40.4 1.0 O A:HOH3006 2.3 37.2 1.0 OE2 A:GLU1222 2.4 39.1 1.0 NE2 A:HIS1185 2.4 31.5 1.0 CD A:GLU1222 2.6 41.2 1.0 SG A:CYS1011 2.6 39.9 1.0 CE1 A:HIS1185 3.2 34.1 1.0 CG A:ASP1233 3.3 47.3 1.0 CD2 A:HIS1185 3.5 31.7 1.0 CB A:CYS1011 3.6 36.1 1.0 CB A:ASP1233 4.0 43.7 1.0 O1 A:PEP1268 4.1 38.1 1.0 CG A:GLU1222 4.1 39.7 1.0 NZ A:LYS1046 4.1 30.8 1.0 OD2 A:ASP1233 4.2 49.7 1.0 C1 A:PEP1268 4.3 39.1 1.0 CA A:CYS1011 4.4 29.7 1.0 ND1 A:HIS1185 4.4 30.4 1.0 OE1 A:GLN1188 4.5 70.9 1.0 CG A:HIS1185 4.5 29.5 1.0 O3 A:A5P1269 4.6 89.4 1.0 O2 A:A5P1269 4.6 87.4 1.0 O2' A:PEP1268 4.6 35.5 1.0 NZ A:LYS1041 4.6 24.9 1.0 C2 A:PEP1268 4.8 46.5 1.0 CE A:LYS1046 4.9 32.6 1.0 C3 A:A5P1269 5.0 85.9 1.0 CB A:GLU1222 5.0 30.6 1.0

Cadmium binding site 2 out of 2 in the R106G KDO8PS with Pep and A5P


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 and A5P within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd2270 b:33.8 occ:0.50 OD2 B:ASP2233 2.1 50.0 1.0 OE1 B:GLU2222 2.3 45.7 1.0 NE2 B:HIS2185 2.3 45.7 1.0 O B:HOH3056 2.6 33.3 1.0 OE2 B:GLU2222 2.6 44.1 1.0 SG B:CYS2011 2.7 35.8 1.0 CD B:GLU2222 2.7 42.2 1.0 CE1 B:HIS2185 3.1 36.3 1.0 CG B:ASP2233 3.2 52.5 1.0 CD2 B:HIS2185 3.4 39.2 1.0 CB B:CYS2011 3.6 40.6 1.0 CB B:ASP2233 3.9 41.6 1.0 O1 B:PEP2268 4.0 55.8 1.0 CG B:GLU2222 4.1 44.8 1.0 OD1 B:ASP2233 4.1 54.8 1.0 NZ B:LYS2046 4.2 31.7 1.0 ND1 B:HIS2185 4.3 40.4 1.0 C1 B:PEP2268 4.3 54.3 1.0 CA B:CYS2011 4.4 34.6 1.0 CG B:HIS2185 4.5 39.8 1.0 OG B:SER2232 4.7 51.0 1.0 O2' B:PEP2268 4.7 47.6 1.0 NZ B:LYS2041 4.8 32.5 1.0 C2 B:PEP2268 4.8 55.9 1.0 CE B:LYS2046 4.9 34.0 1.0 CG2 B:THR2184 5.0 36.3 1.0 CB B:GLU2222 5.0 35.7 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.