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Cadmium in PDB 3boh: Carbonic Anhydrase From Marine Diatom Thalassiosira Weissflogii- Cadmium Bound Domain 1 with Acetate (CDCA1-R1)

Enzymatic activity of Carbonic Anhydrase From Marine Diatom Thalassiosira Weissflogii- Cadmium Bound Domain 1 with Acetate (CDCA1-R1)

All present enzymatic activity of Carbonic Anhydrase From Marine Diatom Thalassiosira Weissflogii- Cadmium Bound Domain 1 with Acetate (CDCA1-R1):
4.2.1.1;

Protein crystallography data

The structure of Carbonic Anhydrase From Marine Diatom Thalassiosira Weissflogii- Cadmium Bound Domain 1 with Acetate (CDCA1-R1), PDB code: 3boh was solved by Y.Xu, L.Feng, P.D.Jeffrey, Y.Shi, F.M.M.Morel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.54 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.390, 43.540, 76.770, 90.00, 92.40, 90.00
R / Rfree (%) 18.6 / 22.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Carbonic Anhydrase From Marine Diatom Thalassiosira Weissflogii- Cadmium Bound Domain 1 with Acetate (CDCA1-R1) (pdb code 3boh). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Carbonic Anhydrase From Marine Diatom Thalassiosira Weissflogii- Cadmium Bound Domain 1 with Acetate (CDCA1-R1), PDB code: 3boh:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3boh

Go back to Cadmium Binding Sites List in 3boh
Cadmium binding site 1 out of 2 in the Carbonic Anhydrase From Marine Diatom Thalassiosira Weissflogii- Cadmium Bound Domain 1 with Acetate (CDCA1-R1)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Carbonic Anhydrase From Marine Diatom Thalassiosira Weissflogii- Cadmium Bound Domain 1 with Acetate (CDCA1-R1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:14.0
occ:1.00
OXT A:ACT1002 2.3 15.9 1.0
NE2 A:HIS105 2.4 13.1 1.0
SG A:CYS53 2.5 14.3 1.0
O A:HOH1003 2.5 15.7 1.0
SG A:CYS115 2.5 13.7 1.0
CD2 A:HIS105 3.2 12.1 1.0
C A:ACT1002 3.3 24.5 1.0
CE1 A:HIS105 3.4 17.1 1.0
CB A:CYS115 3.4 14.7 1.0
CB A:CYS53 3.4 15.9 1.0
CA A:CYS115 3.5 10.2 1.0
O A:ACT1002 3.6 20.7 1.0
N A:GLY116 3.7 15.8 1.0
C A:CYS115 3.9 11.5 1.0
N A:PHE117 4.2 10.9 1.0
N A:GLY71 4.2 13.8 1.0
CA A:GLY71 4.2 10.8 1.0
OD2 A:ASP55 4.3 13.9 1.0
CG A:HIS105 4.4 12.4 1.0
CB A:ASP55 4.4 17.9 1.0
ND1 A:HIS105 4.4 17.2 1.0
O A:HOH1029 4.5 16.1 1.0
CB A:PHE117 4.5 13.6 1.0
CH3 A:ACT1002 4.6 19.0 1.0
CA A:GLY116 4.8 17.6 1.0
N A:CYS115 4.9 14.6 1.0
CA A:CYS53 4.9 13.0 1.0
CG A:ASP55 4.9 18.6 1.0
O A:CYS115 4.9 14.2 1.0
C A:GLY116 5.0 15.7 1.0
CA A:PHE117 5.0 12.6 1.0

Cadmium binding site 2 out of 2 in 3boh

Go back to Cadmium Binding Sites List in 3boh
Cadmium binding site 2 out of 2 in the Carbonic Anhydrase From Marine Diatom Thalassiosira Weissflogii- Cadmium Bound Domain 1 with Acetate (CDCA1-R1)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Carbonic Anhydrase From Marine Diatom Thalassiosira Weissflogii- Cadmium Bound Domain 1 with Acetate (CDCA1-R1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1001

b:14.7
occ:1.00
NE2 B:HIS105 2.3 14.2 1.0
OXT B:ACT1002 2.4 12.0 1.0
O B:HOH1004 2.4 12.0 1.0
SG B:CYS53 2.5 14.0 1.0
SG B:CYS115 2.5 16.0 1.0
CE1 B:HIS105 3.2 14.2 1.0
C B:ACT1002 3.3 16.3 1.0
CD2 B:HIS105 3.3 13.7 1.0
CB B:CYS115 3.4 13.1 1.0
CA B:CYS115 3.5 10.6 1.0
CB B:CYS53 3.5 16.0 1.0
O B:ACT1002 3.6 20.4 1.0
N B:GLY116 3.7 18.6 1.0
C B:CYS115 3.8 12.8 1.0
N B:PHE117 4.2 12.9 1.0
CA B:GLY71 4.2 11.2 1.0
N B:GLY71 4.2 11.2 1.0
OD2 B:ASP55 4.3 15.8 1.0
ND1 B:HIS105 4.4 15.5 1.0
CB B:ASP55 4.4 20.9 1.0
CG B:HIS105 4.4 19.3 1.0
CB B:PHE117 4.5 12.9 1.0
CH3 B:ACT1002 4.6 19.3 1.0
O B:HOH1030 4.6 15.5 1.0
O B:CYS115 4.7 15.0 1.0
CA B:GLY116 4.8 19.5 1.0
N B:CYS115 4.9 16.4 1.0
CA B:CYS53 4.9 16.1 1.0
CG B:ASP55 4.9 22.6 1.0

Reference:

Y.Xu, L.Feng, P.D.Jeffrey, Y.Shi, F.M.Morel. Structure and Metal Exchange in the Cadmium Carbonic Anhydrase of Marine Diatoms. Nature V. 452 56 2008.
ISSN: ISSN 0028-0836
PubMed: 18322527
DOI: 10.1038/NATURE06636
Page generated: Wed Oct 28 10:01:01 2020
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