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Cadmium in PDB 1pcw: Aquifex Aeolicus KDO8PS in Complex with Cadmium and App, A Bisubstrate Inhibitor

Enzymatic activity of Aquifex Aeolicus KDO8PS in Complex with Cadmium and App, A Bisubstrate Inhibitor

All present enzymatic activity of Aquifex Aeolicus KDO8PS in Complex with Cadmium and App, A Bisubstrate Inhibitor:
4.1.2.16;

Protein crystallography data

The structure of Aquifex Aeolicus KDO8PS in Complex with Cadmium and App, A Bisubstrate Inhibitor, PDB code: 1pcw was solved by X.Xu, J.Wang, 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) 21.47 / 1.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.480, 84.480, 159.070, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 22.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Aquifex Aeolicus KDO8PS in Complex with Cadmium and App, A Bisubstrate Inhibitor (pdb code 1pcw). 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 Cadmium and App, A Bisubstrate Inhibitor, PDB code: 1pcw:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1pcw

Go back to Cadmium Binding Sites List in 1pcw
Cadmium binding site 1 out of 2 in the Aquifex Aeolicus KDO8PS in Complex with Cadmium and App, A Bisubstrate Inhibitor


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 Cadmium and App, A Bisubstrate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1270

b:32.9
occ:0.25
OD1 A:ASP1233 2.1 48.2 1.0
OE1 A:GLU1222 2.1 45.5 1.0
NE2 A:HIS1185 2.3 41.4 1.0
OE2 A:GLU1222 2.3 46.7 1.0
OA1 A:H4P1268 2.4 53.1 1.0
CD A:GLU1222 2.5 44.2 1.0
SG A:CYS1011 2.5 38.8 1.0
CE1 A:HIS1185 3.0 40.7 1.0
CG A:ASP1233 3.2 46.7 1.0
CD2 A:HIS1185 3.5 39.9 1.0
CA1 A:H4P1268 3.6 52.7 1.0
CB A:CYS1011 3.6 32.1 1.0
CG A:GLU1222 3.9 41.2 1.0
OD2 A:ASP1233 4.0 47.1 1.0
CB A:ASP1233 4.0 45.1 1.0
NZ A:LYS1046 4.1 31.3 1.0
ND1 A:HIS1185 4.2 39.4 1.0
CA A:CYS1011 4.3 30.1 1.0
CG A:HIS1185 4.5 37.1 1.0
C3 A:H4P1268 4.5 49.9 1.0
CA3 A:H4P1268 4.5 57.8 1.0
O A:HOH201 4.5 44.9 1.0
CA2 A:H4P1268 4.6 56.3 1.0
N A:H4P1268 4.7 45.7 1.0
CB A:GLU1222 4.8 35.4 1.0
NZ A:LYS1041 4.9 31.5 1.0
CE A:LYS1046 4.9 31.1 1.0

Cadmium binding site 2 out of 2 in 1pcw

Go back to Cadmium Binding Sites List in 1pcw
Cadmium binding site 2 out of 2 in the Aquifex Aeolicus KDO8PS in Complex with Cadmium and App, A Bisubstrate Inhibitor


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 Cadmium and App, A Bisubstrate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2270

b:40.7
occ:0.25
OE1 B:GLU2222 2.1 45.7 1.0
OD2 B:ASP2233 2.2 58.6 1.0
NE2 B:HIS2185 2.3 41.2 1.0
OE2 B:GLU2222 2.4 45.3 1.0
OA1 B:H4P2268 2.4 47.8 0.5
SG B:CYS2011 2.5 41.3 1.0
CD B:GLU2222 2.5 43.8 1.0
CE1 B:HIS2185 2.8 40.9 1.0
CG B:ASP2233 3.2 59.0 1.0
CB B:CYS2011 3.5 36.6 1.0
CA1 B:H4P2268 3.6 48.6 0.5
CD2 B:HIS2185 3.6 39.5 1.0
OA2 B:H4P2268 3.6 50.8 0.5
C3 B:H4P2268 3.9 42.9 0.5
OD1 B:ASP2233 3.9 60.8 1.0
CG B:GLU2222 4.0 42.8 1.0
CB B:ASP2233 4.0 56.9 1.0
ND1 B:HIS2185 4.1 39.4 1.0
NZ B:LYS2046 4.2 34.0 1.0
CA2 B:H4P2268 4.2 52.0 0.5
CA B:CYS2011 4.3 35.3 1.0
CA2 B:H4P2268 4.4 48.3 0.5
CG B:HIS2185 4.5 37.8 1.0
N B:H4P2268 4.5 40.1 0.5
C3 B:H4P2268 4.6 45.6 0.5
O B:HOH140 4.6 42.7 1.0
CA1 B:H4P2268 4.7 45.8 0.5
NZ B:LYS2041 4.9 31.0 1.0
CB B:GLU2222 4.9 39.0 1.0
OA2 B:H4P2268 4.9 52.7 0.5
CE B:LYS2046 4.9 36.2 1.0
N B:H4P2268 5.0 41.8 0.5
OG B:SER2232 5.0 59.7 1.0

Reference:

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
Page generated: Fri Aug 28 12:19:04 2020
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