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Cadmium in PDB 5qrf: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z373768900

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z373768900, PDB code: 5qrf 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) 40.65 / 2.03
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 60.060, 60.060, 110.250, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 27.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z373768900 (pdb code 5qrf). 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 Z373768900, PDB code: 5qrf:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5qrf

Go back to Cadmium Binding Sites List in 5qrf
Cadmium binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:32.5
occ:0.50
O A:HOH457 2.0 28.9 0.5
SG A:CYS186 2.4 30.7 0.2
SG A:CYS186 2.5 28.8 0.2
OE1 A:GLU167 2.6 31.2 1.0
CB A:CYS186 3.2 33.4 0.2
CB A:CYS186 3.3 32.7 0.2
CD A:CD302 3.6 34.9 1.0
CD A:GLU167 3.8 38.0 1.0
O A:HOH440 4.3 33.2 1.0
OE2 A:GLU167 4.6 32.7 1.0
CA A:CYS186 4.7 33.1 0.2
CG A:GLU167 4.8 34.8 1.0
CA A:CYS186 4.8 32.4 0.2

Cadmium binding site 2 out of 5 in 5qrf

Go back to Cadmium Binding Sites List in 5qrf
Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:34.9
occ:1.00
O A:HOH463 2.3 21.2 1.0
OE2 A:GLU167 2.5 32.7 1.0
OE1 A:GLU167 2.6 31.2 1.0
CD A:GLU167 2.9 38.0 1.0
CD A:CD301 3.6 32.5 0.5
NE2 A:GLN191 3.8 56.0 1.0
CG A:GLU167 4.4 34.8 1.0
O A:HOH457 4.4 28.9 0.5
CG A:PRO188 4.5 40.3 1.0
CB A:PRO188 4.7 35.5 1.0
SG A:CYS186 4.7 28.8 0.2
CA A:PRO188 5.0 36.3 1.0
CB A:GLU167 5.0 32.9 1.0

Cadmium binding site 3 out of 5 in 5qrf

Go back to Cadmium Binding Sites List in 5qrf
Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:78.9
occ:1.00
O A:HOH454 2.5 42.6 1.0
SG A:CYS122 2.6 61.3 1.0
O A:HOH474 2.8 47.4 1.0
O A:HOH442 2.8 53.6 1.0
CB A:CYS122 3.3 50.3 1.0
CD A:CD305 3.8 75.5 1.0
O A:HOH475 4.0 62.4 1.0
O A:HOH415 4.7 47.8 1.0
CA A:CYS122 4.8 45.4 1.0
O A:GLN157 4.8 50.2 1.0

Cadmium binding site 4 out of 5 in 5qrf

Go back to Cadmium Binding Sites List in 5qrf
Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:43.1
occ:1.00
NE2 A:HIS100 2.2 60.8 1.0
O A:HOH462 2.2 33.7 1.0
O A:HOH461 2.3 28.4 1.0
O A:HOH464 2.5 26.9 1.0
CD2 A:HIS100 3.1 52.5 1.0
CE1 A:HIS100 3.2 62.5 1.0
O A:HOH450 3.2 45.6 1.0
CB A:PRO115 4.3 78.7 1.0
CG A:HIS100 4.3 54.8 1.0
ND1 A:HIS100 4.3 56.5 1.0
CG A:PRO115 4.7 76.1 1.0

Cadmium binding site 5 out of 5 in 5qrf

Go back to Cadmium Binding Sites List in 5qrf
Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:75.5
occ:1.00
SG A:CYS122 2.4 61.3 1.0
O A:HOH475 2.7 62.4 1.0
O A:HOH448 2.7 37.4 1.0
O A:HOH474 2.9 47.4 1.0
CB A:CYS122 3.5 50.3 1.0
CD A:CD303 3.8 78.9 1.0
CA A:CYS122 4.1 45.4 1.0
N A:VAL123 5.0 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: Sat Dec 12 08:27:16 2020

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