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Cadmium in PDB 1fws: Aquifex Aeolicus KDO8P Synthase in Complex with Pep and Cadmium

Enzymatic activity of Aquifex Aeolicus KDO8P Synthase in Complex with Pep and Cadmium

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

Protein crystallography data

The structure of Aquifex Aeolicus KDO8P Synthase in Complex with Pep and Cadmium, PDB code: 1fws 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) 24.04 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.230, 84.230, 159.330, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 21.7

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 2 in 1fws

Go back to Cadmium Binding Sites List in 1fws
Cadmium binding site 1 out of 2 in the Aquifex Aeolicus KDO8P Synthase in Complex with Pep 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 and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1270

b:30.9
occ:0.50
OD2 A:ASP1233 2.0 39.6 1.0
OE1 A:GLU1222 2.3 31.7 1.0
NE2 A:HIS1185 2.4 27.2 1.0
O A:HOH3140 2.5 37.5 1.0
OE2 A:GLU1222 2.5 32.6 1.0
SG A:CYS1011 2.6 31.4 1.0
CD A:GLU1222 2.7 32.9 1.0
CE1 A:HIS1185 3.1 28.6 1.0
CG A:ASP1233 3.2 38.1 1.0
CD2 A:HIS1185 3.5 29.4 1.0
CB A:CYS1011 3.5 27.8 1.0
O A:HOH3337 3.9 46.7 1.0
CB A:ASP1233 4.0 35.9 1.0
NZ A:LYS1046 4.0 24.1 1.0
O1 A:PEP1268 4.0 26.6 1.0
CG A:GLU1222 4.2 31.4 1.0
OD1 A:ASP1233 4.2 40.8 1.0
ND1 A:HIS1185 4.2 27.1 1.0
C1 A:PEP1268 4.3 25.8 1.0
CA A:CYS1011 4.4 27.1 1.0
CG A:HIS1185 4.5 28.1 1.0
NZ A:LYS1041 4.7 20.9 1.0
O2' A:PEP1268 4.7 25.5 1.0
CE A:LYS1046 4.7 25.4 1.0
C2 A:PEP1268 4.7 25.7 1.0

Cadmium binding site 2 out of 2 in 1fws

Go back to Cadmium Binding Sites List in 1fws
Cadmium binding site 2 out of 2 in the Aquifex Aeolicus KDO8P Synthase in Complex with Pep 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 and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2270

b:28.8
occ:0.50
OD2 B:ASP2233 2.0 40.6 1.0
OE1 B:GLU2222 2.3 33.6 1.0
NE2 B:HIS2185 2.4 32.0 1.0
OE2 B:GLU2222 2.4 31.2 1.0
SG B:CYS2011 2.5 30.7 1.0
O B:HOH3151 2.5 44.5 1.0
CD B:GLU2222 2.6 32.3 1.0
CE1 B:HIS2185 3.0 32.9 1.0
CG B:ASP2233 3.2 41.6 1.0
CB B:CYS2011 3.5 29.4 1.0
CD2 B:HIS2185 3.5 32.8 1.0
CB B:ASP2233 3.9 39.4 1.0
NZ B:LYS2046 4.1 25.6 1.0
CG B:GLU2222 4.1 31.4 1.0
O1 B:PEP2268 4.2 27.2 1.0
OD1 B:ASP2233 4.2 44.1 1.0
ND1 B:HIS2185 4.2 30.9 1.0
CA B:CYS2011 4.3 27.3 1.0
C1 B:PEP2268 4.4 28.2 1.0
CG B:HIS2185 4.5 31.8 1.0
NZ B:LYS2041 4.7 23.1 1.0
OG B:SER2232 4.7 42.8 1.0
O2' B:PEP2268 4.7 24.8 1.0
CE B:LYS2046 4.7 24.2 1.0
C2 B:PEP2268 4.8 26.0 1.0

Reference:

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
Page generated: Fri Aug 28 11:49:58 2020
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