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Cadmium in PDB 1pe1: Aquifex Aeolicus KDO8PS in Complex with Cadmium and 2-Pga

Enzymatic activity of Aquifex Aeolicus KDO8PS in Complex with Cadmium and 2-Pga

All present enzymatic activity of Aquifex Aeolicus KDO8PS in Complex with Cadmium and 2-Pga:
4.1.2.16;

Protein crystallography data

The structure of Aquifex Aeolicus KDO8PS in Complex with Cadmium and 2-Pga, PDB code: 1pe1 was solved by J.Wang, X.Xu, C.Grison, S.Petek, P.Coutrot, M.R.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) 43.05 / 1.74
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.434, 84.434, 159.751, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 23.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Aquifex Aeolicus KDO8PS in Complex with Cadmium and 2-Pga (pdb code 1pe1). 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 2-Pga, PDB code: 1pe1:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1pe1

Go back to Cadmium Binding Sites List in 1pe1
Cadmium binding site 1 out of 2 in the Aquifex Aeolicus KDO8PS in Complex with Cadmium and 2-Pga


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 2-Pga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1270

b:30.1
occ:0.25
OD2 A:ASP1233 2.2 49.1 1.0
OE1 A:GLU1222 2.3 50.3 1.0
OE2 A:GLU1222 2.4 46.6 1.0
O A:HOH3231 2.4 55.3 1.0
NE2 A:HIS1185 2.5 47.1 1.0
CD A:GLU1222 2.6 50.2 1.0
SG A:CYS1011 2.7 40.2 1.0
CE1 A:HIS1185 3.1 43.5 1.0
CG A:ASP1233 3.3 55.6 1.0
CD2 A:HIS1185 3.6 43.0 1.0
CB A:CYS1011 3.7 32.1 1.0
O2 A:2PG1268 3.7 36.6 0.6
NZ A:LYS1046 4.0 34.3 1.0
CB A:ASP1233 4.1 37.4 1.0
CG A:GLU1222 4.1 43.2 1.0
OD1 A:ASP1233 4.1 54.0 1.0
C1 A:2PG1268 4.2 31.4 0.6
C1 A:2PG1268 4.2 38.2 0.4
O1 A:2PG1268 4.3 35.9 0.4
ND1 A:HIS1185 4.3 35.1 1.0
CA A:CYS1011 4.5 29.6 1.0
C2 A:2PG1268 4.5 38.3 0.4
NZ A:LYS1041 4.6 29.3 1.0
O2 A:2PG1268 4.6 39.3 0.4
CG A:HIS1185 4.6 39.2 1.0
O1 A:2PG1268 4.7 33.2 0.6
NE2 A:GLN1188 4.8 56.5 1.0
CE A:LYS1046 4.8 33.1 1.0
C2 A:2PG1268 5.0 36.3 0.6

Cadmium binding site 2 out of 2 in 1pe1

Go back to Cadmium Binding Sites List in 1pe1
Cadmium binding site 2 out of 2 in the Aquifex Aeolicus KDO8PS in Complex with Cadmium and 2-Pga


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 2-Pga within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2270

b:33.4
occ:0.25
OD2 B:ASP2233 2.0 57.8 1.0
O B:HOH3252 2.4 57.7 1.0
OE1 B:GLU2222 2.5 46.6 1.0
NE2 B:HIS2185 2.5 53.9 1.0
OE2 B:GLU2222 2.6 50.0 1.0
SG B:CYS2011 2.7 40.0 1.0
CD B:GLU2222 2.8 42.2 1.0
CE1 B:HIS2185 3.1 54.9 1.0
CG B:ASP2233 3.2 60.2 1.0
CD2 B:HIS2185 3.7 46.5 1.0
CB B:CYS2011 3.7 40.0 1.0
OD1 B:ASP2233 3.9 59.1 1.0
O2 B:2PG2268 4.0 43.6 1.0
NZ B:LYS2046 4.0 27.9 1.0
CB B:ASP2233 4.1 33.3 1.0
C1 B:2PG2268 4.2 51.0 1.0
ND1 B:HIS2185 4.3 48.5 1.0
CG B:GLU2222 4.3 37.6 1.0
CA B:CYS2011 4.4 32.4 1.0
O1 B:2PG2268 4.6 38.9 1.0
NZ B:LYS2041 4.6 30.7 1.0
CG B:HIS2185 4.6 41.6 1.0
CE B:LYS2046 4.7 36.0 1.0
C2 B:2PG2268 4.8 40.1 1.0
OG B:SER2232 4.9 69.9 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: Wed Oct 28 09:55:25 2020
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