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Cadmium in PDB 1jcy: Aquifex Aeolicus KDO8P Synthase in Complex with R5P, Pep and Cadmium

Enzymatic activity of Aquifex Aeolicus KDO8P Synthase in Complex with R5P, Pep and Cadmium

All present enzymatic activity of Aquifex Aeolicus KDO8P Synthase in Complex with R5P, Pep and Cadmium:
4.1.2.16;

Protein crystallography data

The structure of Aquifex Aeolicus KDO8P Synthase in Complex with R5P, Pep and Cadmium, PDB code: 1jcy was solved by J.Wang, H.S.Duewel, 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) 27.00 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.316, 84.316, 159.569, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 23.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Aquifex Aeolicus KDO8P Synthase in Complex with R5P, Pep and Cadmium (pdb code 1jcy). 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 R5P, Pep and Cadmium, PDB code: 1jcy:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1jcy

Go back to Cadmium Binding Sites List in 1jcy
Cadmium binding site 1 out of 2 in the Aquifex Aeolicus KDO8P Synthase in Complex with R5P, 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 R5P, Pep and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1270

b:68.3
occ:0.50
NE2 A:HIS1185 2.3 41.7 1.0
OE2 A:GLU1222 2.4 49.3 1.0
OD2 A:ASP1233 2.4 57.9 1.0
OE1 A:GLU1222 2.5 45.6 1.0
SG A:CYS1011 2.6 43.1 1.0
CD A:GLU1222 2.7 46.3 1.0
CE1 A:HIS1185 2.9 40.1 1.0
CD2 A:HIS1185 3.5 39.1 1.0
CG A:ASP1233 3.6 54.0 1.0
CB A:CYS1011 3.7 36.9 1.0
O1 A:PEP1268 3.7 42.5 1.0
C1 A:PEP1268 3.9 42.6 1.0
NZ A:LYS1046 3.9 38.2 1.0
O2 A:R5P1269 4.1 72.0 1.0
ND1 A:HIS1185 4.1 38.7 1.0
CG A:GLU1222 4.1 42.2 1.0
O2' A:PEP1268 4.2 41.9 1.0
OD1 A:ASP1233 4.4 55.7 1.0
C2 A:R5P1269 4.4 70.7 1.0
C2 A:PEP1268 4.4 41.8 1.0
CG A:HIS1185 4.5 38.0 1.0
CB A:ASP1233 4.5 51.3 1.0
CA A:CYS1011 4.5 35.5 1.0
NZ A:LYS1041 4.6 31.3 1.0
CE A:LYS1046 4.7 36.4 1.0
C3 A:R5P1269 4.9 70.3 1.0

Cadmium binding site 2 out of 2 in 1jcy

Go back to Cadmium Binding Sites List in 1jcy
Cadmium binding site 2 out of 2 in the Aquifex Aeolicus KDO8P Synthase in Complex with R5P, 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 R5P, Pep and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2270

b:0.1
occ:0.50
OE2 B:GLU2222 2.2 49.7 1.0
SG B:CYS2011 2.5 43.5 1.0
OD2 B:ASP2233 2.6 65.7 1.0
CE1 B:HIS2185 2.8 47.6 1.0
NE2 B:HIS2185 2.9 49.0 1.0
CD B:GLU2222 3.0 46.3 1.0
OE1 B:GLU2222 3.1 48.0 1.0
NZ B:LYS2046 3.4 39.2 1.0
O1 B:PEP2268 3.5 44.6 1.0
CB B:CYS2011 3.6 39.7 1.0
C1 B:PEP2268 3.6 44.8 1.0
CG B:ASP2233 3.9 64.5 1.0
NZ B:LYS2041 4.0 36.2 1.0
O2' B:PEP2268 4.1 43.4 1.0
C2 B:PEP2268 4.1 42.5 1.0
CA B:CYS2011 4.1 38.2 1.0
ND1 B:HIS2185 4.1 47.4 1.0
CE B:LYS2046 4.3 38.4 1.0
CD2 B:HIS2185 4.3 47.8 1.0
C3 B:PEP2268 4.3 43.6 1.0
CG B:GLU2222 4.4 44.3 1.0
O B:CYS2011 4.6 37.8 1.0
C B:CYS2011 4.7 37.3 1.0
OD1 B:ASP2233 4.7 64.5 1.0
CB B:ASP2233 4.8 61.8 1.0
OG B:SER2232 4.9 63.0 1.0
CG B:HIS2185 4.9 45.3 1.0
O2 B:PEP2268 5.0 35.7 1.0

Reference:

J.Wang, H.S.Duewel, R.W.Woodard, D.L.Gatti. Structures of Aquifex Aeolicus KDO8P Synthase in Complex with R5P and Pep, and with A Bisubstrate Inhibitor: Role of Active Site Water in Catalysis. Biochemistry V. 40 15676 2001.
ISSN: ISSN 0006-2960
PubMed: 11747443
DOI: 10.1021/BI015568E
Page generated: Fri Aug 28 12:00:25 2020
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