Cadmium in PDB 1fww: Aquifex Aeolicus KDO8P Synthase in Complex with Pep, A5P and Cadmium

All present enzymatic activity of Aquifex Aeolicus KDO8P Synthase in Complex with Pep, A5P and Cadmium:
4.1.2.16;

The structure of Aquifex Aeolicus KDO8P Synthase in Complex with Pep, A5P and Cadmium, PDB code: 1fww was solved by H.S.Duewel, S.Radaev, J.Wang, R.W.Woodard, D.L.Gatti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.13 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.108, 84.108, 159.780, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 23.8

The binding sites of Cadmium atom in the Aquifex Aeolicus KDO8P Synthase in Complex with Pep, A5P and Cadmium (pdb code 1fww). 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 KDO8P Synthase in Complex with Pep, A5P and Cadmium, PDB code: 1fww:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Aquifex Aeolicus KDO8P Synthase in Complex with Pep, A5P and Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Aquifex Aeolicus KDO8P Synthase in Complex with Pep, A5P and Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1270 b:37.0 occ:0.50 OD2 A:ASP1233 2.2 50.3 1.0 O A:HOH3211 2.3 46.9 1.0 OE1 A:GLU1222 2.4 41.4 1.0 OE2 A:GLU1222 2.5 44.6 1.0 NE2 A:HIS1185 2.5 34.8 1.0 SG A:CYS1011 2.6 41.5 1.0 CD A:GLU1222 2.7 43.1 1.0 CE1 A:HIS1185 3.2 35.1 1.0 CG A:ASP1233 3.4 49.1 1.0 CB A:CYS1011 3.5 36.5 1.0 CD2 A:HIS1185 3.6 34.5 1.0 O A:HOH3189 3.8 47.5 1.0 NZ A:LYS1046 3.9 32.1 1.0 O2 A:A5P1269 4.0 67.2 1.0 CB A:ASP1233 4.0 46.5 1.0 O1 A:PEP1268 4.1 32.3 1.0 CG A:GLU1222 4.1 40.5 1.0 C1 A:PEP1268 4.3 31.6 1.0 CA A:CYS1011 4.3 34.9 1.0 ND1 A:HIS1185 4.4 33.8 1.0 OD1 A:ASP1233 4.4 53.5 1.0 CG A:HIS1185 4.6 33.9 1.0 O2' A:PEP1268 4.6 30.6 1.0 NZ A:LYS1041 4.6 27.7 1.0 CE A:LYS1046 4.7 30.2 1.0 C2 A:PEP1268 4.7 32.6 1.0 C2 A:A5P1269 4.9 66.5 1.0 O4 A:A5P1269 4.9 65.0 1.0

Cadmium binding site 2 out of 2 in the Aquifex Aeolicus KDO8P Synthase in Complex with Pep, A5P and Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Aquifex Aeolicus KDO8P Synthase in Complex with Pep, A5P and Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd2270 b:36.9 occ:0.50 OD2 B:ASP2233 2.2 51.0 1.0 OE1 B:GLU2222 2.3 44.0 1.0 NE2 B:HIS2185 2.3 42.3 1.0 OE2 B:GLU2222 2.4 43.2 1.0 O B:HOH3194 2.5 49.1 1.0 CD B:GLU2222 2.7 41.8 1.0 SG B:CYS2011 2.7 39.4 1.0 CE1 B:HIS2185 3.0 42.2 1.0 CG B:ASP2233 3.3 51.5 1.0 CD2 B:HIS2185 3.5 41.6 1.0 CB B:CYS2011 3.6 37.1 1.0 CB B:ASP2233 3.9 48.8 1.0 O1 B:PEP2268 4.1 35.1 1.0 NZ B:LYS2046 4.1 32.1 1.0 CG B:GLU2222 4.1 41.4 1.0 ND1 B:HIS2185 4.2 40.7 1.0 C1 B:PEP2268 4.3 35.6 1.0 OD1 B:ASP2233 4.3 51.9 1.0 CA B:CYS2011 4.4 35.1 1.0 CG B:HIS2185 4.4 40.9 1.0 O2' B:PEP2268 4.6 32.6 1.0 C2 B:PEP2268 4.6 34.2 1.0 NZ B:LYS2041 4.8 30.5 1.0 CE B:LYS2046 4.8 31.5 1.0 OG B:SER2232 4.8 52.8 1.0

F.Kona, P.Tao, P.Martin, X.Xu, D.L.Gatti. Electronic Structure of the Metal Center in the Cd(2+), Zn(2+), and Cu(2+) Substituted Forms of KDO8P Synthase: Implications For Catalysis. Biochemistry V. 48 3610 2009.
ISSN: ISSN 0006-2960
PubMed: 19228070
DOI: 10.1021/BI801955H