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Cadmium in PDB 5qrj: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z416341642

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z416341642, PDB code: 5qrj 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) 60.10 / 1.81
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 60.104, 60.104, 109.812, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 27.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z416341642 (pdb code 5qrj). 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 Z416341642, PDB code: 5qrj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5qrj

Go back to Cadmium Binding Sites List in 5qrj
Cadmium binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z416341642


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 Z416341642 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:25.2
occ:0.50
O A:HOH462 2.4 20.3 0.5
SG A:CYS186 2.5 23.8 0.2
SG A:CYS186 2.5 21.3 0.2
OE1 A:GLU167 2.5 23.8 1.0
CB A:CYS186 3.3 27.5 0.2
CB A:CYS186 3.3 24.9 0.2
CD A:CD302 3.6 26.2 1.0
CD A:GLU167 3.7 25.0 1.0
O A:HOH444 4.2 23.7 1.0
OE2 A:GLU167 4.5 24.0 1.0
CG A:GLU167 4.7 25.3 1.0
CA A:CYS186 4.7 26.3 0.2
CA A:CYS186 4.8 24.6 0.2

Cadmium binding site 2 out of 5 in 5qrj

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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 Z416341642


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 Z416341642 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:26.2
occ:1.00
O A:HOH461 2.4 18.8 1.0
OE2 A:GLU167 2.4 24.0 1.0
OE1 A:GLU167 2.6 23.8 1.0
CD A:GLU167 2.8 25.0 1.0
CD A:CD301 3.6 25.2 0.5
NE2 A:GLN191 3.9 43.5 1.0
CG A:GLU167 4.3 25.3 1.0
CG A:PRO188 4.4 31.6 1.0
CB A:PRO188 4.6 28.5 1.0
SG A:CYS186 4.8 21.3 0.2
CB A:GLU167 4.9 25.9 1.0
CA A:PRO188 5.0 28.3 1.0

Cadmium binding site 3 out of 5 in 5qrj

Go back to Cadmium Binding Sites List in 5qrj
Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z416341642


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 Z416341642 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:69.5
occ:1.00
O A:HOH458 2.4 38.8 1.0
SG A:CYS122 2.7 52.3 1.0
O A:HOH445 2.8 48.8 1.0
O A:HOH473 2.8 41.8 1.0
CB A:CYS122 3.3 42.0 1.0
CD A:CD305 3.7 66.0 1.0
O A:HOH474 4.2 48.4 1.0
O A:HOH424 4.8 41.0 1.0
O A:GLN157 4.8 46.4 1.0
CA A:CYS122 4.8 39.0 1.0

Cadmium binding site 4 out of 5 in 5qrj

Go back to Cadmium Binding Sites List in 5qrj
Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z416341642


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 Z416341642 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:35.5
occ:1.00
NE2 A:HIS100 2.2 49.6 1.0
O A:HOH463 2.2 27.1 1.0
O A:HOH460 2.3 23.7 1.0
O A:HOH464 2.5 20.7 1.0
CE1 A:HIS100 3.2 55.7 1.0
CD2 A:HIS100 3.2 45.0 1.0
O A:HOH446 3.6 36.2 1.0
ND1 A:HIS100 4.3 47.6 1.0
CG A:HIS100 4.3 46.0 1.0
CB A:PRO115 4.4 64.1 1.0
CG A:PRO115 4.7 66.0 1.0

Cadmium binding site 5 out of 5 in 5qrj

Go back to Cadmium Binding Sites List in 5qrj
Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z416341642


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 Z416341642 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:66.0
occ:1.00
SG A:CYS122 2.5 52.3 1.0
O A:HOH452 2.6 31.6 1.0
O A:HOH474 2.6 48.4 1.0
O A:HOH473 2.9 41.8 1.0
CB A:CYS122 3.5 42.0 1.0
CD A:CD303 3.7 69.5 1.0
CA A:CYS122 4.1 39.0 1.0
N A:VAL123 5.0 33.0 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: Sat Dec 12 08:27:21 2020

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