Cadmium in PDB 1pck: Aquifex Aeolicus KDO8PS in Complex with Z-Methyl-Pep

All present enzymatic activity of Aquifex Aeolicus KDO8PS in Complex with Z-Methyl-Pep:
4.1.2.16;

The structure of Aquifex Aeolicus KDO8PS in Complex with Z-Methyl-Pep, PDB code: 1pck was solved by J.Wang, X.Xu, C.Grison, S.Petek, P.Coutrot, M.Birck, 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)	22.12 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.254, 84.254, 159.599, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 23.4

The binding sites of Cadmium atom in the Aquifex Aeolicus KDO8PS in Complex with Z-Methyl-Pep (pdb code 1pck). 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 in Complex with Z-Methyl-Pep, PDB code: 1pck:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Aquifex Aeolicus KDO8PS in Complex with Z-Methyl-Pep


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 in Complex with Z-Methyl-Pep within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1270 b:48.8 occ:0.25 NE2 A:HIS1185 2.3 40.4 1.0 OE1 A:GLU1222 2.3 46.5 1.0 OE2 A:GLU1222 2.4 49.9 1.0 OD2 A:ASP1233 2.4 47.5 1.0 O A:HOH276 2.4 47.8 1.0 CD A:GLU1222 2.6 44.7 1.0 SG A:CYS1011 2.7 39.7 1.0 CE1 A:HIS1185 2.9 40.6 1.0 CG A:ASP1233 3.4 47.7 1.0 CD2 A:HIS1185 3.5 39.7 1.0 CB A:CYS1011 3.7 32.8 1.0 O1 A:PEZ1268 3.9 41.4 1.0 CG A:GLU1222 4.0 41.1 1.0 NZ A:LYS1046 4.0 30.1 1.0 C1 A:PEZ1268 4.1 40.9 1.0 OD1 A:ASP1233 4.1 48.0 1.0 ND1 A:HIS1185 4.2 37.7 1.0 CB A:ASP1233 4.3 45.4 1.0 O2' A:PEZ1268 4.4 39.2 1.0 CG A:HIS1185 4.5 37.4 1.0 CA A:CYS1011 4.5 32.2 1.0 C2 A:PEZ1268 4.7 39.8 1.0 NZ A:LYS1041 4.7 34.1 1.0 CE A:LYS1046 4.8 30.6 1.0

Cadmium binding site 2 out of 2 in the Aquifex Aeolicus KDO8PS in Complex with Z-Methyl-Pep


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 in Complex with Z-Methyl-Pep within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd2270 b:70.7 occ:0.25 OE2 B:GLU2222 2.3 53.0 1.0 NE2 B:HIS2185 2.3 45.6 1.0 OD2 B:ASP2233 2.4 60.3 1.0 SG B:CYS2011 2.6 42.7 1.0 OE1 B:GLU2222 2.7 50.6 1.0 CD B:GLU2222 2.7 49.1 1.0 CE1 B:HIS2185 2.8 45.9 1.0 CG B:ASP2233 3.6 57.4 1.0 CD2 B:HIS2185 3.6 44.1 1.0 O1 B:PEZ2268 3.7 44.5 1.0 CB B:CYS2011 3.8 38.4 1.0 NZ B:LYS2046 3.8 34.8 1.0 C1 B:PEZ2268 3.9 44.1 1.0 ND1 B:HIS2185 4.0 43.5 1.0 CG B:GLU2222 4.2 45.6 1.0 O2' B:PEZ2268 4.2 41.2 1.0 CB B:ASP2233 4.4 54.6 1.0 OD1 B:ASP2233 4.4 58.6 1.0 C2 B:PEZ2268 4.4 42.2 1.0 CG B:HIS2185 4.5 41.7 1.0 CA B:CYS2011 4.5 36.7 1.0 CE B:LYS2046 4.6 34.1 1.0 NZ B:LYS2041 4.6 35.3 1.0 C3 B:PEZ2268 4.8 43.8 1.0 OG B:SER2232 4.9 54.2 1.0

X.Xu, J.Wang, C.Grison, S.Petek, P.Coutrot, M.R.Birck, R.W.Woodard, D.L.Gatti. Structure-Based Design of Novel Inhibitors of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase. Drug Des.Discovery V. 18 91 2003.
ISSN: ISSN 1055-9612
PubMed: 14675946