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Cadmium in PDB 5qs3: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198195770

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198195770, PDB code: 5qs3 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) 52.75 / 1.71
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 59.962, 59.962, 110.408, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198195770 (pdb code 5qs3). 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 Z198195770, PDB code: 5qs3:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5qs3

Go back to Cadmium Binding Sites List in 5qs3
Cadmium binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:26.2
occ:0.50
O A:HOH455 2.2 22.2 0.5
SG A:CYS186 2.4 28.3 0.2
OE1 A:GLU167 2.5 25.2 1.0
SG A:CYS186 2.5 19.0 0.2
CB A:CYS186 3.3 31.1 0.2
CB A:CYS186 3.4 25.0 0.2
CD A:CD302 3.6 29.2 1.0
CD A:GLU167 3.7 26.0 1.0
O A:HOH447 4.2 27.8 1.0
OE2 A:GLU167 4.4 24.8 1.0
CA A:CYS186 4.7 29.1 0.2
CG A:GLU167 4.7 25.5 1.0
CA A:CYS186 4.8 25.0 0.2

Cadmium binding site 2 out of 5 in 5qs3

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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 Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:29.2
occ:1.00
OE2 A:GLU167 2.3 24.8 1.0
O A:HOH457 2.4 23.3 1.0
OE1 A:GLU167 2.7 25.2 1.0
CD A:GLU167 2.8 26.0 1.0
CD A:CD301 3.6 26.2 0.5
NE2 A:GLN191 3.9 40.5 1.0
CG A:PRO188 4.2 35.6 1.0
CG A:GLU167 4.3 25.5 1.0
CB A:PRO188 4.6 31.9 1.0
CA A:PRO188 4.9 29.7 1.0
CB A:GLU167 4.9 24.3 1.0
SG A:CYS186 5.0 19.0 0.2

Cadmium binding site 3 out of 5 in 5qs3

Go back to Cadmium Binding Sites List in 5qs3
Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:66.4
occ:1.00
O A:HOH452 2.5 38.0 1.0
SG A:CYS122 2.8 55.1 1.0
O A:HOH469 2.8 49.4 1.0
O A:HOH454 2.9 49.5 1.0
CB A:CYS122 3.3 41.8 1.0
CD A:CD305 3.8 67.6 1.0
O A:HOH470 3.9 53.2 1.0
O A:HOH410 4.8 43.3 1.0
CA A:CYS122 4.8 37.4 1.0
O A:GLN157 4.8 50.1 1.0

Cadmium binding site 4 out of 5 in 5qs3

Go back to Cadmium Binding Sites List in 5qs3
Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:41.8
occ:1.00
O A:HOH460 2.2 36.8 1.0
O A:HOH458 2.2 30.6 1.0
NE2 A:HIS100 2.2 49.7 1.0
CD2 A:HIS100 3.1 42.7 1.0
CE1 A:HIS100 3.3 52.8 1.0
CG A:HIS100 4.3 41.1 1.0
ND1 A:HIS100 4.4 43.8 1.0
CB A:PRO115 4.4 70.0 1.0
CG A:PRO115 4.4 73.1 1.0

Cadmium binding site 5 out of 5 in 5qs3

Go back to Cadmium Binding Sites List in 5qs3
Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:67.6
occ:1.00
SG A:CYS122 2.2 55.1 1.0
O A:HOH443 2.6 36.5 1.0
O A:HOH470 2.7 53.2 1.0
O A:HOH469 2.7 49.4 1.0
CB A:CYS122 3.4 41.8 1.0
CD A:CD303 3.8 66.4 1.0
CA A:CYS122 4.1 37.4 1.0
N A:VAL123 4.9 33.9 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 08:27:33 2020

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