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Cadmium in PDB 1t99: R106G KDO8PS Without Substrates

Enzymatic activity of R106G KDO8PS Without Substrates

All present enzymatic activity of R106G KDO8PS Without Substrates:
2.5.1.55;

Protein crystallography data

The structure of R106G KDO8PS Without Substrates, PDB code: 1t99 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) 42.41 / 1.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.819, 84.819, 160.262, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 24.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the R106G KDO8PS Without Substrates (pdb code 1t99). 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 Without Substrates, PDB code: 1t99:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1t99

Go back to Cadmium Binding Sites List in 1t99
Cadmium binding site 1 out of 2 in the R106G KDO8PS Without Substrates


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of R106G KDO8PS Without Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1270

b:39.9
occ:0.50
OE1 A:GLU1222 2.3 45.9 1.0
OD2 A:ASP1233 2.3 55.9 1.0
OE2 A:GLU1222 2.4 45.0 1.0
SG A:CYS1011 2.4 46.5 1.0
NE2 A:HIS1185 2.5 41.9 1.0
CD A:GLU1222 2.6 45.5 1.0
O A:HOH3207 2.8 47.7 1.0
CE1 A:HIS1185 3.3 41.0 1.0
CG A:ASP1233 3.3 54.7 1.0
CB A:CYS1011 3.4 39.7 1.0
CD2 A:HIS1185 3.6 40.8 1.0
CB A:ASP1233 4.0 52.2 1.0
CG A:GLU1222 4.1 42.7 1.0
NZ A:LYS1046 4.1 37.5 1.0
OD1 A:ASP1233 4.1 56.0 1.0
CA A:CYS1011 4.3 37.0 1.0
O A:HOH3093 4.4 45.2 1.0
ND1 A:HIS1185 4.4 38.4 1.0
CG A:HIS1185 4.6 38.2 1.0
NZ A:LYS1041 4.8 30.4 1.0
CE A:LYS1046 4.9 38.3 1.0
CB A:GLU1222 5.0 35.5 1.0

Cadmium binding site 2 out of 2 in 1t99

Go back to Cadmium Binding Sites List in 1t99
Cadmium binding site 2 out of 2 in the R106G KDO8PS Without Substrates


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of R106G KDO8PS Without Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2270

b:42.9
occ:0.50
OD2 B:ASP2233 2.2 57.5 1.0
OE1 B:GLU2222 2.3 49.9 1.0
NE2 B:HIS2185 2.3 50.2 1.0
OE2 B:GLU2222 2.4 50.5 1.0
CD B:GLU2222 2.6 48.8 1.0
SG B:CYS2011 2.6 44.7 1.0
O B:HOH3146 2.9 45.1 1.0
CE1 B:HIS2185 3.1 48.1 1.0
CG B:ASP2233 3.2 58.8 1.0
CD2 B:HIS2185 3.4 48.6 1.0
CB B:CYS2011 3.5 41.7 1.0
CB B:ASP2233 4.0 56.2 1.0
CG B:GLU2222 4.1 48.0 1.0
OD1 B:ASP2233 4.1 60.3 1.0
NZ B:LYS2046 4.2 40.4 1.0
CA B:CYS2011 4.3 39.3 1.0
ND1 B:HIS2185 4.3 48.4 1.0
CG B:HIS2185 4.5 47.0 1.0
O B:HOH3188 4.7 52.2 1.0
NZ B:LYS2041 4.7 38.8 1.0
OG B:SER2232 4.7 64.1 1.0
CB B:GLU2222 5.0 40.2 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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