Sodium in PDB 6o53: Structure of Hla-A2:01 with Peptide MM96

The structure of Structure of Hla-A2:01 with Peptide MM96, PDB code: 6o53 was solved by G.Ying, A.Bitra, D.M.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.49 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.247, 79.638, 57.227, 90.00, 116.12, 90.00
R / Rfree (%)	18.9 / 21

The binding sites of Sodium atom in the Structure of Hla-A2:01 with Peptide MM96 (pdb code 6o53). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Hla-A2:01 with Peptide MM96, PDB code: 6o53:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Hla-A2:01 with Peptide MM96


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Hla-A2:01 with Peptide MM96 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:29.5 occ:1.00 O A:THR200 2.9 15.8 1.0 OG1 A:THR190 3.0 19.7 1.0 CD2 A:HIS192 3.2 35.9 1.0 O A:THR190 3.2 18.0 1.0 CG A:HIS192 3.4 33.3 1.0 C A:THR190 3.4 19.2 1.0 N A:HIS192 3.5 24.1 1.0 N A:HIS191 3.6 20.3 1.0 NE2 A:HIS192 3.6 37.2 1.0 N A:ARG202 3.6 13.4 1.0 NH1 A:ARG202 3.6 21.5 1.0 C A:THR200 3.7 15.4 1.0 CB A:ARG202 3.8 14.4 1.0 C A:HIS191 3.8 23.4 1.0 CA A:HIS191 3.8 21.6 1.0 ND1 A:HIS192 3.8 36.6 1.0 CB A:THR190 3.9 18.9 1.0 CB A:HIS192 3.9 29.6 1.0 CE1 A:HIS192 3.9 36.6 1.0 CG2 A:THR200 4.0 18.2 1.0 C A:LEU201 4.2 13.6 1.0 CB A:THR200 4.2 17.8 1.0 CA A:THR190 4.2 18.3 1.0 CA A:LEU201 4.3 14.0 1.0 CA A:ARG202 4.3 13.8 1.0 CA A:HIS192 4.3 26.5 1.0 N A:LEU201 4.4 14.1 1.0 NA A:NA606 4.5 53.1 1.0 O A:HIS191 4.5 24.8 1.0 CA A:THR200 4.6 16.7 1.0 CZ A:ARG202 4.6 20.1 1.0 N A:THR190 5.0 17.4 1.0

Sodium binding site 2 out of 2 in the Structure of Hla-A2:01 with Peptide MM96


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Hla-A2:01 with Peptide MM96 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:53.1 occ:1.00 NE2 A:HIS192 3.1 37.2 1.0 OG1 A:THR190 3.1 19.7 1.0 O B:ASP98 3.2 46.7 1.0 CB B:ASP98 3.4 44.4 1.0 NH1 A:ARG202 3.5 21.5 1.0 NE1 A:TRP204 3.6 16.1 1.0 CB A:THR190 3.8 18.9 1.0 CG2 A:THR190 3.8 19.4 1.0 CE1 A:HIS192 4.0 36.6 1.0 CD2 A:HIS192 4.0 35.9 1.0 CZ2 A:TRP204 4.1 16.6 1.0 C B:ASP98 4.1 44.1 1.0 CD A:ARG202 4.2 16.8 1.0 CE2 A:TRP204 4.2 16.5 1.0 CA B:ASP98 4.3 44.2 1.0 NA A:NA605 4.5 29.5 1.0 CZ A:ARG202 4.6 20.1 1.0 O A:HOH885 4.7 30.6 1.0 CB A:ARG202 4.7 14.4 1.0 NE A:ARG202 4.8 18.3 1.0 CD1 A:TRP204 4.8 15.8 1.0 CG A:ARG202 4.9 15.5 1.0

M.Mishto, A.Mansurkhodzhaev, G.Ying, A.Bitra, R.A.Cordfunke, S.Henze, D.Paul, J.Sidney, H.Urlaub, J.Neefjes, A.Sette, D.M.Zajonc, J.Liepe. Anin Silico-in Vitropipeline Identifying An Hla-A*02:01+Kras G12V+Spliced Epitope Candidate For A Broad Tumor-Immune Response in Cancer Patients. Front Immunol V. 10 2572 2019.
ISSN: ESSN 1664-3224
PubMed: 31803176
DOI: 10.3389/FIMMU.2019.02572