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Cadmium in PDB 1t96: R106G KDO8PS with Pep

Enzymatic activity of R106G KDO8PS with Pep

All present enzymatic activity of R106G KDO8PS with Pep:
2.5.1.55;

Protein crystallography data

The structure of R106G KDO8PS with Pep, PDB code: 1t96 was solved by D.L.Gatti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.11 / 1.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 85.028, 85.028, 161.151, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 24.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the R106G KDO8PS with Pep (pdb code 1t96). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the R106G KDO8PS with Pep, PDB code: 1t96:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1t96

Go back to Cadmium Binding Sites List in 1t96
Cadmium binding site 1 out of 2 in the R106G KDO8PS with Pep


Mono view


Stereo pair view

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

b:26.0
occ:0.50
OD2 A:ASP1233 2.2 50.2 1.0
O A:HOH3419 2.3 36.5 1.0
OE2 A:GLU1222 2.3 35.8 1.0
OE1 A:GLU1222 2.3 38.0 1.0
NE2 A:HIS1185 2.5 27.6 1.0
SG A:CYS1011 2.5 35.5 1.0
CD A:GLU1222 2.6 39.1 1.0
CE1 A:HIS1185 3.2 24.5 1.0
CG A:ASP1233 3.4 47.5 1.0
CD2 A:HIS1185 3.6 32.9 1.0
CB A:CYS1011 3.6 32.2 1.0
NZ A:LYS1046 3.9 25.2 1.0
O1 A:PEP1268 4.1 20.9 1.0
CG A:GLU1222 4.1 35.8 1.0
CB A:ASP1233 4.2 45.1 1.0
C1 A:PEP1268 4.3 24.3 1.0
OD1 A:ASP1233 4.3 51.5 1.0
ND1 A:HIS1185 4.4 24.9 1.0
CA A:CYS1011 4.5 29.6 1.0
OE1 A:GLN1188 4.6 61.2 1.0
CG A:HIS1185 4.6 29.0 1.0
CE A:LYS1046 4.7 29.0 1.0
O2' A:PEP1268 4.7 24.5 1.0
NZ A:LYS1041 4.7 19.4 1.0
C2 A:PEP1268 4.8 24.1 1.0

Cadmium binding site 2 out of 2 in 1t96

Go back to Cadmium Binding Sites List in 1t96
Cadmium binding site 2 out of 2 in the R106G KDO8PS with Pep


Mono view


Stereo pair view

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

b:26.4
occ:0.50
OD2 B:ASP2233 2.0 43.0 1.0
OE1 B:GLU2222 2.4 38.9 1.0
NE2 B:HIS2185 2.4 37.3 1.0
OE2 B:GLU2222 2.5 37.2 1.0
O B:HOH3046 2.5 26.0 1.0
SG B:CYS2011 2.6 30.2 1.0
CD B:GLU2222 2.8 32.9 1.0
CE1 B:HIS2185 3.1 32.2 1.0
CG B:ASP2233 3.2 45.0 1.0
CD2 B:HIS2185 3.6 37.5 1.0
CB B:CYS2011 3.7 27.8 1.0
O1 B:PEP2268 3.9 29.6 1.0
CB B:ASP2233 4.0 40.5 1.0
OD1 B:ASP2233 4.1 46.0 1.0
NZ B:LYS2046 4.1 26.9 1.0
CG B:GLU2222 4.2 35.9 1.0
ND1 B:HIS2185 4.2 35.7 1.0
C1 B:PEP2268 4.3 30.1 1.0
CA B:CYS2011 4.4 25.1 1.0
CG B:HIS2185 4.5 28.9 1.0
NZ B:LYS2041 4.6 21.6 1.0
O2' B:PEP2268 4.7 22.4 1.0
O B:HOH3252 4.7 31.1 1.0
OG B:SER2232 4.7 44.0 1.0
C2 B:PEP2268 4.8 31.4 1.0
O B:HOH3335 4.8 57.3 1.0
CE B:LYS2046 4.8 31.1 1.0
CG2 B:THR2184 5.0 27.9 1.0

Reference:

X.Xu, J.Wang, F.Kona, P.Divvela, T.Stemmler, D.L.Gatti. Effects of the ARG106==>Gly Mutation on the Catalytic and Conformational Cycle of Aquifex Aeolicus KDO8P Synthase. To Be Published.
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