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Cadmium in PDB 1cdp: Restrained Least Squares Refinement of Native (Calcium) and Cadmium- Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6-Angstroms Resolution

Protein crystallography data

The structure of Restrained Least Squares Refinement of Native (Calcium) and Cadmium- Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6-Angstroms Resolution, PDB code: 1cdp was solved by A.L.Swain, R.H.Kretsinger, E.L.Amma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 28.440, 60.460, 54.120, 90.00, 94.80, 90.00
R / Rfree (%) n/a / n/a

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Restrained Least Squares Refinement of Native (Calcium) and Cadmium- Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6-Angstroms Resolution (pdb code 1cdp). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Restrained Least Squares Refinement of Native (Calcium) and Cadmium- Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6-Angstroms Resolution, PDB code: 1cdp:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1cdp

Go back to Cadmium Binding Sites List in 1cdp
Cadmium binding site 1 out of 2 in the Restrained Least Squares Refinement of Native (Calcium) and Cadmium- Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6-Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Restrained Least Squares Refinement of Native (Calcium) and Cadmium- Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6-Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd109

b:12.0
occ:1.00
OD1 A:ASP94 2.2 12.6 1.0
OE1 A:GLU101 2.3 18.2 1.0
OD2 A:ASP90 2.3 7.0 1.0
O A:LYS96 2.3 10.7 1.0
O A:HOH116 2.4 10.0 1.0
OD1 A:ASP92 2.4 13.6 1.0
OE2 A:GLU101 2.7 21.6 1.0
CD A:GLU101 2.9 17.8 1.0
CG A:ASP94 3.1 13.5 1.0
CG A:ASP90 3.2 6.2 1.0
CG A:ASP92 3.3 17.5 1.0
C A:LYS96 3.5 10.1 1.0
OD2 A:ASP94 3.5 14.3 1.0
OD2 A:ASP92 3.6 19.1 1.0
CB A:ASP90 4.0 9.1 1.0
CA A:ASP90 4.0 11.3 1.0
OD1 A:ASP90 4.1 11.8 1.0
N A:ASP94 4.1 13.5 1.0
N A:LYS96 4.2 11.1 1.0
O A:HOH149 4.2 23.8 1.0
CA A:ILE97 4.2 8.0 1.0
N A:ASP92 4.3 15.2 1.0
N A:ILE97 4.3 9.1 1.0
CB A:ASP94 4.4 13.2 1.0
CG A:GLU101 4.4 14.8 1.0
CA A:LYS96 4.4 11.0 1.0
N A:GLY93 4.4 13.1 1.0
N A:GLY98 4.5 8.7 1.0
C A:ASP90 4.5 13.4 1.0
CB A:ASP92 4.6 13.7 1.0
CG A:LYS96 4.6 15.5 1.0
N A:SER91 4.6 14.3 1.0
CA A:ASP94 4.7 12.1 1.0
CA A:ASP92 4.7 14.8 1.0
N A:GLY95 4.8 11.4 1.0
C A:ILE97 4.8 9.1 1.0
C A:ASP92 4.8 14.0 1.0
C A:ASP94 4.9 11.9 1.0

Cadmium binding site 2 out of 2 in 1cdp

Go back to Cadmium Binding Sites List in 1cdp
Cadmium binding site 2 out of 2 in the Restrained Least Squares Refinement of Native (Calcium) and Cadmium- Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6-Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Restrained Least Squares Refinement of Native (Calcium) and Cadmium- Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6-Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd110

b:8.6
occ:1.00
OD1 A:ASP51 2.1 9.7 1.0
O A:PHE57 2.3 9.9 1.0
OE1 A:GLU59 2.3 11.0 1.0
OD1 A:ASP53 2.4 8.7 1.0
OE2 A:GLU62 2.4 7.2 1.0
OG A:SER55 2.6 9.6 1.0
OE1 A:GLU62 2.8 10.4 1.0
CD A:GLU62 2.9 8.9 1.0
CG A:ASP53 3.2 9.7 1.0
CG A:ASP51 3.2 5.2 1.0
CD A:GLU59 3.2 12.7 1.0
OE2 A:GLU59 3.5 9.4 1.0
C A:PHE57 3.5 7.6 1.0
OD2 A:ASP53 3.5 11.5 1.0
CB A:SER55 3.6 10.8 1.0
N A:SER55 3.9 8.7 1.0
CA A:ASP51 4.0 8.1 1.0
OD2 A:ASP51 4.1 10.6 1.0
CB A:ASP51 4.1 6.6 1.0
N A:GLU59 4.2 8.0 1.0
N A:ASP53 4.2 8.4 1.0
C A:ASP51 4.3 9.2 1.0
CG A:GLU62 4.3 9.6 1.0
CA A:SER55 4.3 8.4 1.0
CA A:ILE58 4.3 7.8 1.0
O A:HOH120 4.3 14.5 1.0
N A:PHE57 4.4 7.0 1.0
N A:ILE58 4.4 7.1 1.0
N A:GLN52 4.5 10.2 1.0
N A:LYS54 4.5 11.2 1.0
CB A:ASP53 4.5 9.5 1.0
CA A:PHE57 4.5 6.2 1.0
CA A:ASP53 4.6 9.7 1.0
C A:ASP53 4.6 9.7 1.0
CG A:GLU59 4.6 10.4 1.0
C A:ILE58 4.8 9.1 1.0
N A:GLY56 4.8 6.2 1.0
O A:ASP51 4.8 9.2 1.0
O A:HOH166 4.9 36.9 1.0
CB A:GLU59 4.9 10.9 1.0
C A:SER55 4.9 7.7 1.0

Reference:

A.L.Swain, R.H.Kretsinger, E.L.Amma. Restrained Least Squares Refinement of Native (Calcium) and Cadmium-Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6-A Resolution. J.Biol.Chem. V. 264 16620 1989.
ISSN: ISSN 0021-9258
PubMed: 2777802
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