Atomistry » Cadmium » PDB 5qrf-5vp3 » 5qrg
Atomistry »
  Cadmium »
    PDB 5qrf-5vp3 »
      5qrg »

Cadmium in PDB 5qrg: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340, PDB code: 5qrg 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) 59.74 / 1.95
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 59.740, 59.740, 110.350, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 28.1

Other elements in 5qrg:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340 (pdb code 5qrg). 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 Z275151340, PDB code: 5qrg:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5qrg

Go back to Cadmium Binding Sites List in 5qrg
Cadmium binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340


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 Z275151340 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:29.0
occ:0.50
O A:HOH455 2.1 23.7 0.5
SG A:CYS186 2.4 20.1 0.2
SG A:CYS186 2.5 31.2 0.2
OE1 A:GLU167 2.6 29.1 1.0
CB A:CYS186 3.3 31.7 0.2
CB A:CYS186 3.3 25.8 0.2
CD A:CD302 3.7 30.7 1.0
CD A:GLU167 3.8 33.1 1.0
O A:HOH439 4.3 25.3 1.0
OE2 A:GLU167 4.5 29.0 1.0
CG A:GLU167 4.7 32.2 1.0
CA A:CYS186 4.7 31.8 0.2
CA A:CYS186 4.8 27.8 0.2
O A:HOH459 5.0 18.0 1.0

Cadmium binding site 2 out of 5 in 5qrg

Go back to Cadmium Binding Sites List in 5qrg
Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340


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 Z275151340 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:30.7
occ:1.00
O A:HOH459 2.3 18.0 1.0
OE2 A:GLU167 2.4 29.0 1.0
OE1 A:GLU167 2.7 29.1 1.0
CD A:GLU167 2.9 33.1 1.0
CD A:CD301 3.7 29.0 0.5
NE2 A:GLN191 3.8 52.5 1.0
CG A:GLU167 4.4 32.2 1.0
CG A:PRO188 4.4 38.7 1.0
O A:HOH455 4.5 23.7 0.5
CB A:PRO188 4.6 33.8 1.0
CA A:PRO188 4.8 32.8 1.0
SG A:CYS186 4.8 20.1 0.2
CB A:GLU167 5.0 32.1 1.0

Cadmium binding site 3 out of 5 in 5qrg

Go back to Cadmium Binding Sites List in 5qrg
Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340


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 Z275151340 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:61.7
occ:1.00
O A:HOH449 2.5 32.8 1.0
O A:HOH469 2.6 41.9 1.0
SG A:CYS122 2.7 53.7 1.0
O A:HOH457 3.0 50.2 1.0
CB A:CYS122 3.3 42.6 1.0
CD A:CD305 3.7 60.5 1.0
O A:HOH470 3.9 52.9 1.0
O A:HOH418 4.7 40.0 1.0
CA A:CYS122 4.8 40.2 1.0
O A:GLN157 4.9 54.1 1.0

Cadmium binding site 4 out of 5 in 5qrg

Go back to Cadmium Binding Sites List in 5qrg
Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340


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 Z275151340 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:42.5
occ:1.00
O A:HOH456 2.1 34.8 1.0
NE2 A:HIS100 2.2 51.6 1.0
O A:HOH461 2.3 26.4 1.0
O A:HOH460 2.5 30.5 1.0
O A:HOH446 3.1 36.1 1.0
CD2 A:HIS100 3.1 46.5 1.0
CE1 A:HIS100 3.3 49.9 1.0
CG A:HIS100 4.3 47.6 1.0
ND1 A:HIS100 4.4 47.8 1.0
CB A:PRO115 4.6 68.4 1.0
CG A:PRO115 4.7 72.0 1.0

Cadmium binding site 5 out of 5 in 5qrg

Go back to Cadmium Binding Sites List in 5qrg
Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340


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 Z275151340 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:60.5
occ:1.00
O A:HOH447 2.5 30.0 1.0
O A:HOH470 2.6 52.9 1.0
O A:HOH469 2.6 41.9 1.0
SG A:CYS122 2.7 53.7 1.0
CB A:CYS122 3.5 42.6 1.0
CD A:CD303 3.7 61.7 1.0
CA A:CYS122 4.1 40.2 1.0
N A:VAL123 5.0 36.7 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 08:27:19 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy