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Cadmium in PDB 5qru: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991, PDB code: 5qru was solved by J.A.Newman, A.E.Gavard, A.Fernandez-Cid, L.Sherestha, N.A.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.80 / 1.76
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 60.080, 60.080, 110.130, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991 (pdb code 5qru). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991, PDB code: 5qru:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5qru

Go back to Cadmium Binding Sites List in 5qru
Cadmium binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:29.9
occ:0.50
O A:HOH455 2.2 28.4 0.5
SG A:CYS186 2.5 24.6 0.2
SG A:CYS186 2.5 28.9 0.2
OE1 A:GLU167 2.6 29.6 1.0
CB A:CYS186 3.3 33.5 0.2
CB A:CYS186 3.3 28.7 0.2
CD A:CD302 3.6 31.4 1.0
CD A:GLU167 3.7 28.2 1.0
O A:HOH441 4.2 30.2 1.0
OE2 A:GLU167 4.4 26.0 1.0
CG A:GLU167 4.7 29.9 1.0
CA A:CYS186 4.8 31.0 0.2
CA A:CYS186 4.8 27.8 0.2

Cadmium binding site 2 out of 5 in 5qru

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Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:31.4
occ:1.00
OE2 A:GLU167 2.3 26.0 1.0
O A:HOH461 2.4 23.5 1.0
OE1 A:GLU167 2.7 29.6 1.0
CD A:GLU167 2.8 28.2 1.0
CD A:CD301 3.6 29.9 0.5
NE2 A:GLN191 4.0 48.3 1.0
CG A:PRO188 4.3 38.1 1.0
CG A:GLU167 4.3 29.9 1.0
O A:HOH455 4.5 28.4 0.5
CB A:PRO188 4.6 32.0 1.0
SG A:CYS186 4.8 24.6 0.2
CB A:GLU167 4.9 28.9 1.0
CA A:PRO188 5.0 30.2 1.0

Cadmium binding site 3 out of 5 in 5qru

Go back to Cadmium Binding Sites List in 5qru
Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:67.2
occ:1.00
O A:HOH454 2.4 41.0 1.0
O A:HOH470 2.6 44.9 1.0
SG A:CYS122 2.7 52.3 1.0
O A:HOH450 2.8 53.9 1.0
CB A:CYS122 3.3 45.3 1.0
CD A:CD305 3.8 66.2 1.0
O A:HOH471 4.0 53.2 1.0
O A:HOH417 4.7 44.7 1.0
CA A:CYS122 4.8 41.3 1.0
O A:GLN157 4.8 46.6 1.0

Cadmium binding site 4 out of 5 in 5qru

Go back to Cadmium Binding Sites List in 5qru
Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:39.0
occ:1.00
O A:HOH460 2.2 31.3 1.0
NE2 A:HIS100 2.2 49.1 1.0
O A:HOH458 2.4 27.5 1.0
O A:HOH459 2.5 27.1 1.0
CD2 A:HIS100 3.2 41.7 1.0
CE1 A:HIS100 3.3 51.0 1.0
CG A:PRO115 4.3 61.8 0.6
CG A:HIS100 4.4 43.5 1.0
ND1 A:HIS100 4.4 44.8 1.0
CB A:PRO115 4.5 60.2 0.6

Cadmium binding site 5 out of 5 in 5qru

Go back to Cadmium Binding Sites List in 5qru
Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:66.2
occ:1.00
SG A:CYS122 2.4 52.3 1.0
O A:HOH449 2.6 36.9 1.0
O A:HOH471 2.6 53.2 1.0
O A:HOH470 2.8 44.9 1.0
CB A:CYS122 3.4 45.3 1.0
CD A:CD303 3.8 67.2 1.0
CA A:CYS122 4.1 41.3 1.0

Reference:

J.A.Newman, A.E.Gavard, A.Fernandez-Cid, L.Sherestha, N.A.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi. Pandda Analysis Group Deposition To Be Published.
Page generated: Thu Jul 10 14:37:03 2025

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