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Cadmium in PDB 1pw3: Crystal Structure of JTOR68S

Protein crystallography data

The structure of Crystal Structure of JTOR68S, PDB code: 1pw3 was solved by C.Dealwis, V.Gupta, M.Wilkerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.90
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 72.247, 72.247, 94.256, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 23.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of JTOR68S (pdb code 1pw3). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of JTOR68S, PDB code: 1pw3:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 1pw3

Go back to Cadmium Binding Sites List in 1pw3
Cadmium binding site 1 out of 4 in the Crystal Structure of JTOR68S


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of JTOR68S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:36.9
occ:1.00
N B:ALA43 3.7 15.1 1.0
CA B:ALA43 3.7 15.6 1.0
C B:SER42 3.9 15.0 1.0
CB B:ALA43 4.1 16.0 1.0
O B:SER42 4.1 14.3 1.0
CA B:SER42 4.7 15.4 1.0

Cadmium binding site 2 out of 4 in 1pw3

Go back to Cadmium Binding Sites List in 1pw3
Cadmium binding site 2 out of 4 in the Crystal Structure of JTOR68S


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of JTOR68S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:38.6
occ:1.00
NH2 B:ARG54 4.2 17.6 1.0
O B:HOH211 4.4 27.7 1.0

Cadmium binding site 3 out of 4 in 1pw3

Go back to Cadmium Binding Sites List in 1pw3
Cadmium binding site 3 out of 4 in the Crystal Structure of JTOR68S


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of JTOR68S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd203

b:39.6
occ:1.00
CB B:GLU83 2.2 15.3 1.0
O B:GLU83 2.3 14.9 1.0
O B:THR80 2.6 16.1 1.0
CA B:GLU83 2.7 15.5 1.0
N B:GLU83 2.8 15.5 1.0
C B:GLU83 2.8 15.6 1.0
CG B:GLU83 3.3 16.6 1.0
O B:GLU81 3.6 17.5 1.0
C B:GLU81 3.7 17.2 1.0
C B:THR80 3.8 16.6 1.0
C B:ASP82 3.9 15.9 1.0
CA B:GLU81 4.0 17.7 1.0
CD B:GLU83 4.1 17.9 1.0
N B:ASP82 4.1 16.7 1.0
N B:ALA84 4.1 15.5 1.0
O B:HOH238 4.2 34.6 1.0
NH1 B:ARG39 4.3 18.0 1.0
N B:GLU81 4.4 16.9 1.0
OE1 B:GLU83 4.4 20.8 1.0
CA B:ASP82 4.6 16.1 1.0
O B:ASP82 4.7 16.0 1.0
OE2 B:GLU83 4.8 17.6 1.0
CA B:THR80 5.0 16.7 1.0

Cadmium binding site 4 out of 4 in 1pw3

Go back to Cadmium Binding Sites List in 1pw3
Cadmium binding site 4 out of 4 in the Crystal Structure of JTOR68S


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of JTOR68S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd204

b:35.0
occ:1.00
N B:HIS8 2.3 10.9 1.0
CA B:PRO7 2.9 12.8 1.0
CD2 B:HIS8 3.0 13.0 1.0
C B:PRO7 3.0 12.1 1.0
CG B:HIS8 3.4 12.5 1.0
CA B:HIS8 3.4 11.2 1.0
O B:GLN6 3.4 12.8 1.0
CB B:HIS8 3.5 11.3 1.0
N B:PRO7 3.9 13.1 1.0
CB B:PRO7 4.0 12.7 1.0
NE2 B:HIS8 4.0 12.4 1.0
C B:GLN6 4.1 13.7 1.0
O B:PRO7 4.1 11.6 1.0
ND1 B:HIS8 4.5 14.8 1.0
C B:HIS8 4.6 11.1 1.0
CE1 B:HIS8 4.8 13.3 1.0
N B:SER9 4.8 11.4 1.0
O B:HOH214 4.9 28.1 1.0

Reference:

J.S.Wall, V.Gupta, M.Wilkerson, M.Schell, R.Loris, P.Adams, A.Solomon, F.Stevens, C.Dealwis. Structural Basis of Light Chain Amyloidogenicity: Comparison of the Thermodynamic Properties, Fibrillogenic Potential and Tertiary Structural Features of Four VLAMBDA6 Proteins. J.Mol.Recog. V. 17 323 2004.
ISSN: ISSN 0952-3499
PubMed: 15227639
DOI: 10.1002/JMR.681
Page generated: Fri Aug 28 12:19:57 2020
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