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Cadmium in PDB 5qsl: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153, PDB code: 5qsl 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) 52.63 / 2.20
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 59.902, 59.902, 109.696, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 30.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153 (pdb code 5qsl). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153, PDB code: 5qsl:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 5qsl

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Cadmium binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:34.7
occ:0.50
O A:HOH410 1.6 1.1 0.3
OE1 A:GLU167 2.4 31.6 1.0
SG A:CYS186 2.7 26.4 0.5
SG A:CYS186 2.8 22.1 0.5
CB A:CYS186 3.1 31.4 0.5
CB A:CYS186 3.1 28.6 0.5
CD A:GLU167 3.5 36.0 1.0
CD A:CD302 3.6 34.5 1.0
O A:HOH431 4.3 24.8 1.0
OE2 A:GLU167 4.3 31.4 1.0
CG A:GLU167 4.5 31.8 1.0
CA A:CYS186 4.6 31.1 0.5
CA A:CYS186 4.6 29.3 0.5
O A:HOH455 5.0 45.0 1.0

Cadmium binding site 2 out of 6 in 5qsl

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Cadmium binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:34.5
occ:1.00
OE2 A:GLU167 2.4 31.4 1.0
OE1 A:GLU167 2.6 31.6 1.0
CD A:GLU167 2.8 36.0 1.0
CD A:CD301 3.6 34.7 0.5
NE2 A:GLN191 3.8 31.5 1.0
O A:HOH410 4.3 1.1 0.3
CG A:GLU167 4.3 31.8 1.0
CB A:PRO188 4.5 35.0 1.0
CG A:PRO188 4.5 34.4 1.0
CA A:PRO188 4.8 36.4 1.0
CB A:GLU167 4.9 32.0 1.0

Cadmium binding site 3 out of 6 in 5qsl

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Cadmium binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:70.8
occ:1.00
O A:HOH471 2.5 40.6 1.0
O A:HOH445 2.6 33.5 1.0
SG A:CYS122 2.8 53.4 1.0
CB A:CYS122 3.3 46.1 1.0
O A:HOH451 3.6 40.1 1.0
CD A:CD305 4.0 64.7 1.0
O A:HOH409 4.5 61.9 1.0
CA A:CYS122 4.8 45.1 1.0
O A:GLN157 5.0 43.5 1.0

Cadmium binding site 4 out of 6 in 5qsl

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Cadmium binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:44.1
occ:1.00
O A:HOH453 2.0 18.0 1.0
NE2 A:HIS100 2.4 63.2 1.0
CD2 A:HIS100 3.0 63.0 1.0
O A:HOH434 3.3 40.5 1.0
CE1 A:HIS100 3.6 65.2 1.0
CG A:HIS100 4.3 53.4 1.0
ND1 A:HIS100 4.5 52.2 1.0
CB A:PRO115 4.9 58.9 1.0

Cadmium binding site 5 out of 6 in 5qsl

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Cadmium binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:64.7
occ:1.00
SG A:CYS122 2.5 53.4 1.0
O A:HOH447 2.6 30.7 1.0
O A:HOH471 2.9 40.6 1.0
CB A:CYS122 3.3 46.1 1.0
CD A:CD303 4.0 70.8 1.0
CA A:CYS122 4.0 45.1 1.0
N A:VAL123 4.9 41.9 1.0

Cadmium binding site 6 out of 6 in 5qsl

Go back to Cadmium Binding Sites List in 5qsl
Cadmium binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:0.1
occ:1.00
ND1 A:HIS135 2.7 44.2 1.0
CG A:HIS135 3.5 42.2 1.0
CB A:HIS135 3.6 40.5 1.0
CE A:LYS138 3.6 73.0 1.0
O A:HOH456 3.6 51.0 1.0
CE1 A:HIS135 3.7 43.0 1.0
NZ A:LYS138 4.0 71.7 1.0
OD1 A:ASN131 4.1 38.1 1.0
CA A:HIS135 4.3 40.8 1.0
CD A:LYS138 4.6 69.3 1.0
CD2 A:HIS135 4.7 48.5 1.0
NE2 A:HIS135 4.8 44.1 1.0
ND2 A:ASN131 4.8 35.0 1.0
CG A:ASN131 4.8 41.1 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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