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Cadmium in PDB 5qs4: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z30820160

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z30820160, PDB code: 5qs4 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 / 1.65
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 59.990, 59.990, 110.220, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 24.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z30820160 (pdb code 5qs4). 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 Z30820160, PDB code: 5qs4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5qs4

Go back to Cadmium Binding Sites List in 5qs4
Cadmium binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z30820160


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 Z30820160 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:28.2
occ:0.50
O A:HOH458 2.3 27.2 0.5
OE1 A:GLU167 2.4 27.0 1.0
SG A:CYS186 2.5 28.6 0.2
SG A:CYS186 2.5 23.1 0.2
CB A:CYS186 3.3 35.9 0.2
CB A:CYS186 3.4 28.0 0.2
CD A:CD302 3.6 30.6 1.0
CD A:GLU167 3.7 25.0 1.0
O A:HOH445 4.2 29.8 1.0
OE2 A:GLU167 4.4 24.1 1.0
CG A:GLU167 4.7 27.9 1.0
CA A:CYS186 4.7 30.7 0.2
CA A:CYS186 4.8 26.8 0.2

Cadmium binding site 2 out of 5 in 5qs4

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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 Z30820160


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 Z30820160 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:30.6
occ:1.00
OE2 A:GLU167 2.2 24.1 1.0
O A:HOH461 2.4 25.2 1.0
OE1 A:GLU167 2.7 27.0 1.0
CD A:GLU167 2.7 25.0 1.0
CD A:CD301 3.6 28.2 0.5
NE2 A:GLN191 3.9 48.0 1.0
CG A:GLU167 4.2 27.9 1.0
CG A:PRO188 4.3 37.0 1.0
CB A:PRO188 4.7 32.4 1.0
CB A:GLU167 4.9 26.3 1.0
SG A:CYS186 4.9 23.1 0.2
CA A:PRO188 5.0 28.4 1.0

Cadmium binding site 3 out of 5 in 5qs4

Go back to Cadmium Binding Sites List in 5qs4
Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z30820160


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 Z30820160 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:68.2
occ:1.00
O A:HOH455 2.4 41.3 1.0
SG A:CYS122 2.6 58.3 1.0
O A:HOH470 2.9 51.2 1.0
O A:HOH444 2.9 52.3 1.0
CB A:CYS122 3.4 48.2 1.0
CD A:CD305 3.8 67.9 1.0
O A:HOH471 4.1 51.3 1.0
O A:HOH429 4.6 46.8 1.0
O A:GLN157 4.8 47.4 1.0
CA A:CYS122 4.9 40.7 1.0

Cadmium binding site 4 out of 5 in 5qs4

Go back to Cadmium Binding Sites List in 5qs4
Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z30820160


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 Z30820160 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:39.0
occ:1.00
NE2 A:HIS100 2.2 43.5 1.0
O A:HOH463 2.3 32.1 1.0
O A:HOH457 2.4 27.7 1.0
O A:HOH460 2.4 25.4 1.0
CE1 A:HIS100 3.2 55.1 1.0
CD2 A:HIS100 3.2 43.8 1.0
O A:HOH440 3.6 36.5 1.0
CG A:PRO115 4.0 63.8 1.0
ND1 A:HIS100 4.3 50.1 1.0
CB A:PRO115 4.3 57.7 1.0
CG A:HIS100 4.3 47.6 1.0

Cadmium binding site 5 out of 5 in 5qs4

Go back to Cadmium Binding Sites List in 5qs4
Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z30820160


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 Z30820160 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:67.9
occ:1.00
O A:HOH448 2.6 39.2 1.0
SG A:CYS122 2.6 58.3 1.0
O A:HOH471 2.6 51.3 1.0
O A:HOH470 2.9 51.2 1.0
CB A:CYS122 3.6 48.2 1.0
CD A:CD303 3.8 68.2 1.0
CA A:CYS122 4.2 40.7 1.0
N A:VAL123 5.0 34.1 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 08:27:35 2020

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