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Cadmium in PDB 5qrm: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1899842917

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1899842917, PDB code: 5qrm 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) 52.79 / 1.55
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 60.089, 60.089, 109.982, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 24

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1899842917 (pdb code 5qrm). 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 Z1899842917, PDB code: 5qrm:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5qrm

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Cadmium binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:17.3
occ:0.50
OE1 A:GLU167 2.4 17.2 1.0
O A:HOH453 2.5 21.1 0.5
SG A:CYS186 2.5 19.3 0.2
SG A:CYS186 2.6 15.5 0.2
CB A:CYS186 3.3 20.1 0.2
CB A:CYS186 3.4 16.8 0.2
CD A:GLU167 3.6 15.5 1.0
CD A:CD302 3.7 18.3 1.0
O A:HOH441 4.3 20.8 1.0
OE2 A:GLU167 4.3 14.3 1.0
CG A:GLU167 4.7 16.6 1.0
CA A:CYS186 4.8 18.4 0.2
CA A:CYS186 4.8 16.9 0.2

Cadmium binding site 2 out of 5 in 5qrm

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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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:18.3
occ:1.00
OE2 A:GLU167 2.2 14.3 1.0
O A:HOH461 2.5 10.1 1.0
OE1 A:GLU167 2.7 17.2 1.0
CD A:GLU167 2.7 15.5 1.0
CD A:CD301 3.7 17.3 0.5
NE2 A:GLN191 3.9 25.3 1.0
CG A:GLU167 4.2 16.6 1.0
CG A:PRO188 4.4 20.5 1.0
CB A:PRO188 4.6 19.3 1.0
SG A:CYS186 4.9 15.5 0.2
CB A:GLU167 4.9 14.7 1.0

Cadmium binding site 3 out of 5 in 5qrm

Go back to Cadmium Binding Sites List in 5qrm
Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:48.8
occ:1.00
O A:HOH455 2.4 30.5 1.0
SG A:CYS122 2.6 40.8 1.0
O A:HOH467 2.7 32.9 1.0
O A:HOH446 2.7 41.1 1.0
CB A:CYS122 3.4 34.6 1.0
CD A:CD305 3.8 47.9 1.0
O A:HOH468 4.1 35.8 1.0
O A:HOH430 4.5 36.9 1.0
O A:GLN157 4.8 36.9 1.0
CA A:CYS122 4.9 30.2 1.0

Cadmium binding site 4 out of 5 in 5qrm

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Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:25.9
occ:1.00
NE2 A:HIS100 2.2 25.4 1.0
O A:HOH458 2.4 19.7 1.0
O A:HOH456 2.5 17.4 1.0
O A:HOH457 2.5 15.4 1.0
CE1 A:HIS100 3.2 30.1 1.0
CD2 A:HIS100 3.2 26.6 1.0
CG A:PRO115 4.2 49.0 1.0
ND1 A:HIS100 4.3 29.1 1.0
CG A:HIS100 4.3 28.0 1.0
CB A:PRO115 4.4 47.5 1.0

Cadmium binding site 5 out of 5 in 5qrm

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Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:47.9
occ:1.00
O A:HOH468 2.5 35.8 1.0
SG A:CYS122 2.5 40.8 1.0
O A:HOH449 2.5 28.4 1.0
O A:HOH467 2.9 32.9 1.0
CB A:CYS122 3.5 34.6 1.0
CD A:CD303 3.8 48.8 1.0
CA A:CYS122 4.1 30.2 1.0
N A:VAL123 5.0 25.2 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 08:27:23 2020

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