Sodium in PDB 7tlt: Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02

The structure of Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02, PDB code: 7tlt was solved by L.D.Murdolo, C.Szeto, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.29 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.812, 64.467, 76.422, 106.53, 92.43, 97.51
R / Rfree (%)	19.2 / 23.8

The structure of Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02 (pdb code 7tlt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02, PDB code: 7tlt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:49.8 occ:1.00 O B:SER11 3.5 36.1 1.0 OE1 A:GLN242 3.6 38.9 1.0 NH2 A:ARG234 3.8 32.5 1.0 CZ3 A:TRP204 3.8 37.3 1.0 OG B:SER11 4.0 39.6 1.0 CH2 A:TRP204 4.1 38.1 1.0 CD A:GLN242 4.2 44.2 1.0 NE2 A:GLN242 4.2 36.3 1.0 CD2 A:LEU206 4.4 43.8 1.0 C B:SER11 4.5 37.4 1.0 N B:SER11 4.5 34.5 1.0 CB B:TYR10 4.6 34.3 1.0 CE3 A:TRP204 4.7 36.2 1.0 OXT B:MET99 4.7 51.0 1.0 O B:HIS13 4.7 44.9 1.0 C B:HIS13 4.8 44.4 1.0 CA B:SER11 5.0 33.6 1.0 O B:ARG97 5.0 49.2 1.0

Sodium binding site 2 out of 2 in the Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:57.3 occ:1.00 NH2 C:ARG108 3.1 43.2 1.0 NE C:ARG108 3.6 40.6 1.0 CB A:SER2 3.6 46.1 1.0 CZ C:ARG108 3.8 50.8 1.0 CD2 C:LEU110 4.0 50.1 1.0 N A:SER2 4.2 44.1 1.0 N A:GLY1 4.6 51.4 1.0 CA A:SER2 4.6 43.3 1.0 OG A:SER2 4.6 58.5 1.0 OE1 A:GLU212 4.9 76.4 1.0 CD C:ARG108 4.9 46.6 1.0

L.D.Murdolo, C.Szeto, S.Gras. Sars-Cov-2 Spike-Derived Peptide S489-497 (Yfplqsygf) Presented By Hla-A*29:02 To Be Published.