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Cadmium in PDB 1fwt: Aquifex Aeolicus KDO8P Synthase in Complex with Pep, E4P and Cadmium

Enzymatic activity of Aquifex Aeolicus KDO8P Synthase in Complex with Pep, E4P and Cadmium

All present enzymatic activity of Aquifex Aeolicus KDO8P Synthase in Complex with Pep, E4P and Cadmium:
4.1.2.16;

Protein crystallography data

The structure of Aquifex Aeolicus KDO8P Synthase in Complex with Pep, E4P and Cadmium, PDB code: 1fwt 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) 25.45 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.164, 84.164, 159.737, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 22.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Aquifex Aeolicus KDO8P Synthase in Complex with Pep, E4P and Cadmium (pdb code 1fwt). 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, E4P and Cadmium, PDB code: 1fwt:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1fwt

Go back to Cadmium Binding Sites List in 1fwt
Cadmium binding site 1 out of 2 in the Aquifex Aeolicus KDO8P Synthase in Complex with Pep, E4P 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, E4P and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1270

b:31.1
occ:0.50
OD2 A:ASP1233 2.0 43.9 1.0
O A:HOH3097 2.3 38.3 1.0
OE1 A:GLU1222 2.3 38.5 1.0
NE2 A:HIS1185 2.4 31.4 1.0
OE2 A:GLU1222 2.4 38.1 1.0
SG A:CYS1011 2.5 39.3 1.0
CD A:GLU1222 2.7 36.6 1.0
CE1 A:HIS1185 3.2 32.2 1.0
CG A:ASP1233 3.2 42.9 1.0
CD2 A:HIS1185 3.5 33.8 1.0
CB A:CYS1011 3.5 34.6 1.0
NZ A:LYS1046 3.9 28.1 1.0
CB A:ASP1233 4.0 40.4 1.0
O1 A:PEP1268 4.1 29.4 1.0
CG A:GLU1222 4.2 36.4 1.0
OD1 A:ASP1233 4.2 45.6 1.0
C1 A:PEP1268 4.3 29.3 1.0
CA A:CYS1011 4.3 32.7 1.0
ND1 A:HIS1185 4.3 32.0 1.0
CG A:HIS1185 4.5 31.5 1.0
NZ A:LYS1041 4.6 23.7 1.0
O2' A:PEP1268 4.7 27.7 1.0
C2 A:PEP1268 4.7 31.1 1.0
CE A:LYS1046 4.8 29.1 1.0
O1 A:E4P1269 4.8 57.1 1.0

Cadmium binding site 2 out of 2 in 1fwt

Go back to Cadmium Binding Sites List in 1fwt
Cadmium binding site 2 out of 2 in the Aquifex Aeolicus KDO8P Synthase in Complex with Pep, E4P 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, E4P and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2270

b:32.5
occ:0.50
OD2 B:ASP2233 1.9 46.0 1.0
OE1 B:GLU2222 2.3 38.2 1.0
NE2 B:HIS2185 2.4 39.2 1.0
O B:HOH3192 2.4 41.3 1.0
OE2 B:GLU2222 2.5 37.6 1.0
SG B:CYS2011 2.6 36.0 1.0
CD B:GLU2222 2.7 37.8 1.0
CE1 B:HIS2185 3.0 39.0 1.0
CG B:ASP2233 3.2 46.4 1.0
CB B:CYS2011 3.5 35.2 1.0
CD2 B:HIS2185 3.6 39.1 1.0
CB B:ASP2233 3.9 43.8 1.0
OD1 B:ASP2233 4.1 47.5 1.0
NZ B:LYS2046 4.1 31.8 1.0
O1 B:PEP2268 4.1 32.7 1.0
CG B:GLU2222 4.1 37.3 1.0
ND1 B:HIS2185 4.2 38.2 1.0
C1 B:PEP2268 4.3 34.3 1.0
CA B:CYS2011 4.3 33.3 1.0
CG B:HIS2185 4.5 37.9 1.0
OG B:SER2232 4.7 51.2 1.0
NZ B:LYS2041 4.7 27.2 1.0
O2' B:PEP2268 4.7 33.1 1.0
C2 B:PEP2268 4.7 32.9 1.0
CE B:LYS2046 4.8 29.8 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: Wed Oct 28 09:53:11 2020
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