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Cadmium in PDB 1xwa: Drospohila Thioredoxin, Oxidized, P41212

Protein crystallography data

The structure of Drospohila Thioredoxin, Oxidized, P41212, PDB code: 1xwa was solved by M.C.Wahl, A.Irmler, B.Hecker, R.H.Schirmer, K.Becker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.544, 92.544, 97.624, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 28.8

Other elements in 1xwa:

The structure of Drospohila Thioredoxin, Oxidized, P41212 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Drospohila Thioredoxin, Oxidized, P41212 (pdb code 1xwa). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Drospohila Thioredoxin, Oxidized, P41212, PDB code: 1xwa:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 1xwa

Go back to Cadmium Binding Sites List in 1xwa
Cadmium binding site 1 out of 3 in the Drospohila Thioredoxin, Oxidized, P41212


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Drospohila Thioredoxin, Oxidized, P41212 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd801

b:27.5
occ:1.00
O A:HOH905 2.1 20.3 1.0
OE1 A:GLU99 2.3 32.7 1.0
O A:HOH904 2.3 14.9 1.0
OE2 A:GLU99 2.6 29.2 1.0
CL A:CL901 2.7 26.5 1.0
CD A:GLU99 2.8 29.9 1.0
NZ A:LYS41 4.1 27.1 1.0
OE2 A:GLU44 4.1 27.2 1.0
O A:HOH903 4.2 25.1 1.0
OE1 A:GLN48 4.2 34.5 1.0
CG A:GLU99 4.3 28.4 1.0
O A:HOH982 4.5 42.3 1.0
NE2 A:GLN48 4.5 31.6 1.0
CD A:CD802 4.6 26.6 1.0
NZ A:LYS103 4.6 31.4 1.0
CD A:GLN48 4.8 33.8 1.0

Cadmium binding site 2 out of 3 in 1xwa

Go back to Cadmium Binding Sites List in 1xwa
Cadmium binding site 2 out of 3 in the Drospohila Thioredoxin, Oxidized, P41212


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Drospohila Thioredoxin, Oxidized, P41212 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd802

b:26.6
occ:1.00
O A:HOH903 2.2 25.1 1.0
O A:HOH902 2.3 17.8 1.0
OE1 A:GLU44 2.4 26.3 1.0
OE2 A:GLU44 2.5 27.2 1.0
CL A:CL901 2.6 26.5 1.0
CD A:GLU44 2.8 29.5 1.0
O A:HOH905 4.2 20.3 1.0
NZ A:LYS41 4.3 27.1 1.0
CG A:GLU44 4.3 31.1 1.0
CD A:CD801 4.6 27.5 1.0
O A:HOH933 4.6 36.8 1.0

Cadmium binding site 3 out of 3 in 1xwa

Go back to Cadmium Binding Sites List in 1xwa
Cadmium binding site 3 out of 3 in the Drospohila Thioredoxin, Oxidized, P41212


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Drospohila Thioredoxin, Oxidized, P41212 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd803

b:64.9
occ:1.00
O A:HOH907 2.2 27.8 1.0
O A:HOH906 2.5 37.7 1.0
O A:HOH908 2.6 59.9 1.0
OG1 A:THR30 2.9 37.0 1.0
OD2 A:ASP61 3.2 48.8 1.0
O A:HOH1008 3.7 71.0 1.0
OD2 A:ASP59 3.9 41.5 1.0
CG2 A:THR30 3.9 35.5 1.0
CG A:ASP61 3.9 48.5 1.0
CB A:THR30 3.9 33.4 1.0
CB A:ASP61 4.0 46.4 1.0
OD1 A:ASP59 4.1 36.0 1.0
N A:THR30 4.3 30.5 1.0
CG A:ASP59 4.4 36.6 1.0
OE2 A:GLU62 4.6 64.5 1.0
CD1 A:TRP31 4.7 35.1 1.0
CA A:THR30 4.8 31.1 1.0
O A:HOH949 4.9 70.5 1.0

Reference:

M.C.Wahl, A.Irmler, B.Hecker, R.H.Schirmer, K.Becker. Comparative Structural Analysis of Oxidized and Reduced Thioredoxin From Drosophila Melanogaster J.Mol.Biol. V. 345 1119 2005.
ISSN: ISSN 0022-2836
PubMed: 15644209
DOI: 10.1016/J.JMB.2004.11.004
Page generated: Sat Dec 12 08:15:33 2020

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