Nickel in PDB 7kgo: Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359

The structure of Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359, PDB code: 7kgo 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)	47.51 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.794, 78.254, 111.511, 90, 90, 90
R / Rfree (%)	18.3 / 22.9

The structure of Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359 also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Cadmium	(Cd)	1 atom

The binding sites of Nickel atom in the Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359 (pdb code 7kgo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359, PDB code: 7kgo:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:55.4 occ:1.00 N A:GLY16 3.2 33.0 1.0 CA A:GLY16 3.6 35.9 1.0 C A:ARG14 3.7 35.5 1.0 CB A:ARG14 3.8 29.6 1.0 CA A:ARG14 3.8 34.6 1.0 N A:ARG17 3.9 33.2 1.0 N A:PRO15 4.0 40.2 1.0 O A:ARG14 4.1 38.9 1.0 CD A:PRO15 4.2 43.9 1.0 C A:GLY16 4.2 37.6 1.0 C A:PRO15 4.4 34.5 1.0 CG A:ARG14 4.6 38.0 1.0 CG A:PRO15 4.7 42.7 1.0 O A:ARG17 4.7 32.8 1.0 CA A:PRO15 4.8 44.8 1.0 CD A:ARG14 4.9 51.0 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:70.1 occ:1.00 O A:HOH451 3.3 28.9 1.0 O A:HOH511 3.5 41.9 1.0 OE2 A:GLU154 3.5 43.8 1.0 CD A:GLU154 3.9 46.0 1.0 CA A:HIS151 4.0 35.9 1.0 N A:GLU154 4.1 31.1 1.0 CB A:ALA153 4.1 28.9 1.0 CG A:GLU154 4.1 55.0 1.0 C A:HIS151 4.2 38.5 1.0 N A:ALA153 4.2 32.4 1.0 O A:GLU148 4.2 40.1 1.0 N A:VAL152 4.5 38.2 1.0 CA A:ALA153 4.5 29.8 1.0 O A:HIS151 4.6 33.2 1.0 N A:HIS151 4.7 31.5 1.0 C A:ALA153 4.7 39.8 1.0 CA A:GLU148 4.7 42.5 1.0 OE1 A:GLU154 4.8 71.5 1.0 O A:TRP147 4.8 34.9 1.0 CA A:GLU154 4.9 35.8 1.0 CB A:GLU154 4.9 46.1 1.0 C A:GLU148 5.0 37.4 1.0 CB A:HIS151 5.0 37.4 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Hla-A*0201IN Complex with Sars-Cov-2 N351-359 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:49.3 occ:1.00 N B:GLY43 3.3 47.0 1.0 CB B:ALA79 3.7 29.6 1.0 O B:GLU77 3.7 36.8 1.0 N B:ASN42 3.8 44.7 1.0 C B:GLU77 4.1 39.5 1.0 CA B:GLY43 4.1 46.4 1.0 CA B:ASN42 4.1 49.3 1.0 C B:TYR78 4.1 35.7 1.0 C B:ASN42 4.1 47.7 1.0 N B:ALA79 4.2 36.1 1.0 CB B:GLU77 4.2 41.0 1.0 CB B:LEU40 4.2 36.2 1.0 CA B:TYR78 4.3 36.8 1.0 N B:TYR78 4.4 39.5 1.0 O B:LEU40 4.4 38.4 1.0 O B:TYR78 4.4 33.1 1.0 CA B:ALA79 4.6 36.6 1.0 C B:LEU40 4.6 45.2 1.0 C B:LYS41 4.7 42.0 1.0 CA B:GLU77 4.8 44.1 1.0 CD1 B:LEU40 4.9 36.8 1.0 N B:LYS41 5.0 36.8 1.0

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.