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Cadmium in PDB 1zha: A. Aeolicus KDO8PS R106G Mutant in Complex with Pep and R5P

Enzymatic activity of A. Aeolicus KDO8PS R106G Mutant in Complex with Pep and R5P

All present enzymatic activity of A. Aeolicus KDO8PS R106G Mutant in Complex with Pep and R5P:
2.5.1.55;

Protein crystallography data

The structure of A. Aeolicus KDO8PS R106G Mutant in Complex with Pep and R5P, PDB code: 1zha was solved by X.Xu, F.Kona, J.Wang, J.Lu, T.Stemmler, D.L.Gatti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.22 / 1.74
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.726, 84.726, 160.433, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 23.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the A. Aeolicus KDO8PS R106G Mutant in Complex with Pep and R5P (pdb code 1zha). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the A. Aeolicus KDO8PS R106G Mutant in Complex with Pep and R5P, PDB code: 1zha:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1zha

Go back to Cadmium Binding Sites List in 1zha
Cadmium binding site 1 out of 2 in the A. Aeolicus KDO8PS R106G Mutant in Complex with Pep and R5P


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of A. Aeolicus KDO8PS R106G Mutant in Complex with Pep and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1270

b:33.9
occ:0.50
OD2 A:ASP1233 2.1 46.3 1.0
OE1 A:GLU1222 2.2 37.9 1.0
O A:HOH3233 2.3 41.3 1.0
NE2 A:HIS1185 2.4 31.8 1.0
OE2 A:GLU1222 2.5 38.6 1.0
CD A:GLU1222 2.6 37.7 1.0
SG A:CYS1011 2.6 39.4 1.0
CE1 A:HIS1185 3.2 30.4 1.0
CG A:ASP1233 3.3 45.5 1.0
CD2 A:HIS1185 3.5 31.2 1.0
CB A:CYS1011 3.6 34.6 1.0
CG A:GLU1222 4.1 36.9 1.0
O3 A:R5P1269 4.1 77.2 1.0
CB A:ASP1233 4.1 44.6 1.0
NZ A:LYS1046 4.1 32.9 1.0
O1 A:PEP1268 4.3 30.4 1.0
OD1 A:ASP1233 4.3 47.1 1.0
ND1 A:HIS1185 4.3 29.8 1.0
CA A:CYS1011 4.3 34.0 1.0
NE2 A:GLN1188 4.5 50.0 1.0
C1 A:PEP1268 4.5 29.9 1.0
C3 A:R5P1269 4.5 75.7 1.0
CG A:HIS1185 4.5 30.6 1.0
NZ A:LYS1041 4.7 28.4 1.0
O2' A:PEP1268 4.8 28.0 1.0
CB A:GLU1222 4.9 32.9 1.0
CE A:LYS1046 4.9 33.5 1.0
C2 A:R5P1269 4.9 75.6 1.0

Cadmium binding site 2 out of 2 in 1zha

Go back to Cadmium Binding Sites List in 1zha
Cadmium binding site 2 out of 2 in the A. Aeolicus KDO8PS R106G Mutant in Complex with Pep and R5P


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of A. Aeolicus KDO8PS R106G Mutant in Complex with Pep and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2270

b:30.4
occ:0.50
OD2 B:ASP2233 2.1 43.1 1.0
OE1 B:GLU2222 2.2 34.9 1.0
NE2 B:HIS2185 2.4 36.4 1.0
OE2 B:GLU2222 2.4 36.0 1.0
O B:HOH3148 2.6 40.5 1.0
CD B:GLU2222 2.6 33.1 1.0
SG B:CYS2011 2.7 37.2 1.0
CE1 B:HIS2185 3.1 35.3 1.0
CG B:ASP2233 3.2 43.4 1.0
CD2 B:HIS2185 3.5 35.3 1.0
CB B:CYS2011 3.6 35.9 1.0
CB B:ASP2233 4.0 40.7 1.0
OD1 B:ASP2233 4.0 43.3 1.0
CG B:GLU2222 4.1 34.7 1.0
O1 B:PEP2268 4.1 37.5 1.0
NZ B:LYS2046 4.2 28.1 1.0
ND1 B:HIS2185 4.3 35.4 1.0
CA B:CYS2011 4.3 34.0 1.0
C1 B:PEP2268 4.4 37.0 1.0
CG B:HIS2185 4.5 33.1 1.0
OE1 B:GLN2188 4.5 47.0 1.0
NZ B:LYS2041 4.7 30.6 1.0
O B:HOH3494 4.8 57.6 1.0
O2' B:PEP2268 4.8 34.0 1.0
C2 B:PEP2268 4.9 35.7 1.0
CG2 B:THR2184 4.9 32.8 1.0
CB B:GLU2222 4.9 33.1 1.0
CE B:LYS2046 5.0 29.4 1.0

Reference:

X.Xu, F.Kona, J.Wang, J.Lu, T.Stemmler, D.L.Gatti. The Catalytic and Conformational Cycle of Aquifex Aeolicus KDO8P Synthase: Role of the L7 Loop. Biochemistry V. 44 12434 2005.
ISSN: ISSN 0006-2960
PubMed: 16156656
DOI: 10.1021/BI051095Q
Page generated: Fri Aug 28 12:45:01 2020
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