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Cadmium in PDB 7kgp: Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324

Protein crystallography data

The structure of Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324, PDB code: 7kgp was solved by C.Szeto, D.S.M.Chatzileontiadou, A.Riboldi-Tunnicliffe, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.192, 79.546, 111.578, 90, 90, 90
R / Rfree (%) 19.4 / 20.4

Other elements in 7kgp:

The structure of Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324 also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324 (pdb code 7kgp). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324, PDB code: 7kgp:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 7kgp

Go back to Cadmium Binding Sites List in 7kgp
Cadmium binding site 1 out of 2 in the Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:16.9
occ:1.00
ND1 A:HIS151 2.3 21.3 1.0
OE2 A:GLU154 2.4 16.5 1.0
OE1 A:GLU154 2.4 14.8 1.0
CD A:GLU154 2.7 15.4 1.0
CE1 A:HIS151 3.1 21.9 1.0
CG A:HIS151 3.4 20.7 1.0
CB A:HIS151 3.9 19.0 1.0
O A:HOH887 4.1 30.9 1.0
NE2 A:HIS151 4.2 23.6 1.0
CG A:GLU154 4.3 16.1 1.0
CD2 A:HIS151 4.4 22.6 1.0
O A:HOH649 4.6 27.1 1.0
O A:HOH747 4.8 34.8 1.0
CA A:HIS151 4.8 19.1 1.0

Cadmium binding site 2 out of 2 in 7kgp

Go back to Cadmium Binding Sites List in 7kgp
Cadmium binding site 2 out of 2 in the Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Hla-A*0201 in Complex with Sars-Cov-2 N316-324 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:45.2
occ:1.00
NE2 A:HIS145 2.2 27.9 1.0
CE1 A:HIS145 2.9 28.4 1.0
CD2 A:HIS145 3.3 27.0 1.0
ND1 A:HIS145 4.1 28.2 1.0
CG A:HIS145 4.2 25.8 1.0
NE2 A:GLN141 4.4 23.0 1.0
CG A:GLN141 5.0 19.4 1.0

Reference:

C.Szeto, D.S.M.Chatzileontiadou, A.T.Nguyen, H.Sloane, C.A.Lobos, D.Jayasinghe, H.Halim, C.Smith, A.Riboldi-Tunnicliffe, E.J.Grant, S.Gras. The Presentation of Sars-Cov-2 Peptides By the Common Hla-A*02:01 Molecule To Be Published.
Page generated: Sun Jan 24 09:57:39 2021

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