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Cadmium in PDB 1fy6: Aquifex Aeolicus KDO8P Synthase in Complex with Cadmium and A5P

Enzymatic activity of Aquifex Aeolicus KDO8P Synthase in Complex with Cadmium and A5P

All present enzymatic activity of Aquifex Aeolicus KDO8P Synthase in Complex with Cadmium and A5P:
4.1.2.16;

Protein crystallography data

The structure of Aquifex Aeolicus KDO8P Synthase in Complex with Cadmium and A5P, PDB code: 1fy6 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) 43.14 / 1.89
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.671, 84.671, 160.036, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 25.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Aquifex Aeolicus KDO8P Synthase in Complex with Cadmium and A5P (pdb code 1fy6). 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 Cadmium and A5P, PDB code: 1fy6:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1fy6

Go back to Cadmium Binding Sites List in 1fy6
Cadmium binding site 1 out of 2 in the Aquifex Aeolicus KDO8P Synthase in Complex with Cadmium and A5P


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 Cadmium and A5P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1270

b:47.5
occ:0.50
NE2 A:HIS1185 2.2 32.2 1.0
OE1 A:GLU1222 2.3 43.1 1.0
OD2 A:ASP1233 2.3 47.0 1.0
OE2 A:GLU1222 2.6 41.9 1.0
SG A:CYS1011 2.7 33.1 1.0
CD A:GLU1222 2.7 41.4 1.0
CE1 A:HIS1185 2.8 32.9 1.0
O2 A:A5P1269 2.9 54.7 1.0
O3 A:A5P1269 3.2 56.7 1.0
CD2 A:HIS1185 3.5 31.8 1.0
CG A:ASP1233 3.5 45.5 1.0
CB A:CYS1011 3.8 24.8 1.0
NZ A:LYS1046 3.8 24.3 1.0
C2 A:A5P1269 3.8 55.9 1.0
ND1 A:HIS1185 4.1 31.0 1.0
C3 A:A5P1269 4.1 55.4 1.0
CG A:GLU1222 4.2 37.5 1.0
O A:HOH3334 4.3 37.8 1.0
OD1 A:ASP1233 4.4 47.8 1.0
CB A:ASP1233 4.4 42.9 1.0
CG A:HIS1185 4.4 29.3 1.0
CA A:CYS1011 4.5 23.5 1.0
CE A:LYS1046 4.7 23.0 1.0
NZ A:LYS1041 4.9 23.7 1.0
C4 A:A5P1269 5.0 54.0 1.0

Cadmium binding site 2 out of 2 in 1fy6

Go back to Cadmium Binding Sites List in 1fy6
Cadmium binding site 2 out of 2 in the Aquifex Aeolicus KDO8P Synthase in Complex with Cadmium and A5P


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 Cadmium and A5P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2270

b:57.9
occ:0.50
NE2 B:HIS2185 2.2 37.0 1.0
OD1 B:ASP2233 2.3 55.2 1.0
OE1 B:GLU2222 2.4 42.5 1.0
CE1 B:HIS2185 2.5 35.9 1.0
O B:HOH3094 2.8 27.6 1.0
OE2 B:GLU2222 2.9 40.1 1.0
CD B:GLU2222 3.0 39.1 1.0
SG B:CYS2011 3.1 30.9 1.0
CG B:ASP2233 3.3 55.9 1.0
CD2 B:HIS2185 3.5 34.5 1.0
ND1 B:HIS2185 3.8 34.8 1.0
CB B:CYS2011 4.0 28.1 1.0
OD2 B:ASP2233 4.0 56.3 1.0
O B:HOH3250 4.1 34.8 1.0
NZ B:LYS2046 4.2 25.8 1.0
O B:HOH3116 4.2 32.7 1.0
CG B:HIS2185 4.3 32.3 1.0
CB B:ASP2233 4.3 54.1 1.0
CG B:GLU2222 4.3 36.2 1.0
CA B:CYS2011 4.7 27.5 1.0
CE B:LYS2046 4.9 24.1 1.0
NZ B:LYS2041 4.9 25.4 1.0
O4 B:PO42268 4.9 26.5 1.0

Reference:

H.S.Duewel, S.Radaev, J.Wang, R.W.Woodard, D.L.Gatti. Substrate and Metal Complexes of 3-Deoxy-D-Manno-Octulosonate-8-Phosphate Synthase From Aquifex Aeolicus at 1.9-A Resolution. Implications For the Condensation Mechanism. J.Biol.Chem. V. 276 8393 2001.
ISSN: ISSN 0021-9258
PubMed: 11115499
DOI: 10.1074/JBC.M007884200
Page generated: Fri Aug 28 11:50:33 2020
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