Cadmium in PDB 1zji: Aquifex Aeolicus KDO8PS R106G Mutant in Complex with 2PGA and R5P

All present enzymatic activity of Aquifex Aeolicus KDO8PS R106G Mutant in Complex with 2PGA and R5P:
2.5.1.55;

The structure of Aquifex Aeolicus KDO8PS R106G Mutant in Complex with 2PGA and R5P, PDB code: 1zji was solved by X.Xu, F.Kona, J.Wang, J.Lu, T.Stemmler, D.L.Gatti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.27 / 2.25
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.741, 84.741, 160.600, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 24.2

The binding sites of Cadmium atom in the Aquifex Aeolicus KDO8PS R106G Mutant in Complex with 2PGA and R5P (pdb code 1zji). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Aquifex Aeolicus KDO8PS R106G Mutant in Complex with 2PGA and R5P, PDB code: 1zji:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Aquifex Aeolicus KDO8PS R106G Mutant in Complex with 2PGA and R5P


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Aquifex Aeolicus KDO8PS R106G Mutant in Complex with 2PGA and R5P within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1270 b:55.7 occ:0.50 OD1 A:ASP1233 2.2 81.1 1.0 OE2 A:GLU1222 2.3 65.7 1.0 OE1 A:GLU1222 2.3 65.5 1.0 NE2 A:HIS1185 2.4 60.5 1.0 CD A:GLU1222 2.6 64.1 1.0 SG A:CYS1011 2.8 65.6 1.0 CE1 A:HIS1185 3.1 58.9 1.0 CG A:ASP1233 3.3 81.3 1.0 CD2 A:HIS1185 3.5 58.2 1.0 O3 A:R5P1269 3.5 0.4 1.0 CB A:CYS1011 3.7 61.1 1.0 O1 A:2PG1268 3.7 68.8 1.0 NZ A:LYS1046 4.0 68.5 1.0 CG A:GLU1222 4.0 61.0 1.0 OD2 A:ASP1233 4.1 82.5 1.0 CB A:ASP1233 4.3 80.0 1.0 ND1 A:HIS1185 4.3 57.4 1.0 C1 A:2PG1268 4.4 70.1 1.0 CA A:CYS1011 4.4 59.4 1.0 CG A:HIS1185 4.5 57.1 1.0 C3 A:R5P1269 4.7 0.8 1.0 NZ A:LYS1041 4.7 50.3 1.0 O2 A:2PG1268 4.7 68.7 1.0 OE1 A:GLN1188 4.8 77.0 1.0 CE A:LYS1046 4.8 69.4 1.0

Cadmium binding site 2 out of 2 in the Aquifex Aeolicus KDO8PS R106G Mutant in Complex with 2PGA and R5P


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Aquifex Aeolicus KDO8PS R106G Mutant in Complex with 2PGA and R5P within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd2270 b:48.3 occ:0.50 NE2 B:HIS2185 2.2 59.8 1.0 OD2 B:ASP2233 2.3 81.2 1.0 OE1 B:GLU2222 2.4 64.6 1.0 OE2 B:GLU2222 2.5 64.5 1.0 CD B:GLU2222 2.7 62.4 1.0 CE1 B:HIS2185 2.8 59.2 1.0 SG B:CYS2011 2.9 58.5 1.0 CD2 B:HIS2185 3.4 60.1 1.0 CG B:ASP2233 3.4 80.1 1.0 O1 B:2PG2268 3.6 85.0 1.0 CB B:CYS2011 3.8 59.9 1.0 ND1 B:HIS2185 4.0 60.0 1.0 CG B:GLU2222 4.2 62.5 1.0 C1 B:2PG2268 4.2 83.5 1.0 OD1 B:ASP2233 4.2 80.7 1.0 CB B:ASP2233 4.3 78.5 1.0 NZ B:LYS2046 4.3 58.5 1.0 CG B:HIS2185 4.3 58.4 1.0 CA B:CYS2011 4.6 58.7 1.0 O2 B:2PG2268 4.6 83.6 1.0 NZ B:LYS2041 4.8 56.3 1.0 CE B:LYS2046 5.0 59.4 1.0

X.Xu, F.Kona, J.Wang, J.Lu, T.Stemmler, D.L.Gatti. The Catalytic and Conformational Cycle of Aquifex Aeolicus KDO8P Synthase: Role of the L7 Loop Biochemistry V. 44 12434 2005.
ISSN: ISSN 0006-2960
PubMed: 16156656
DOI: 10.1021/BI051095Q