Sodium in PDB 6o4y: Structure of Hla-A2:01 with Peptide MM91

The structure of Structure of Hla-A2:01 with Peptide MM91, PDB code: 6o4y 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)	32.00 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.990, 80.861, 56.933, 90.00, 113.32, 90.00
R / Rfree (%)	17.9 / 20.5

The binding sites of Sodium atom in the Structure of Hla-A2:01 with Peptide MM91 (pdb code 6o4y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Hla-A2:01 with Peptide MM91, PDB code: 6o4y:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Hla-A2:01 with Peptide MM91


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 MM91 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:25.4 occ:1.00 O A:ASP37 2.7 16.3 1.0 NA A:NA303 2.8 21.9 1.0 N A:GLN43 2.8 16.3 1.0 CA A:GLN43 3.2 16.4 1.0 O A:ALA40 3.3 18.3 1.0 CB A:ALA40 3.4 20.3 1.0 C A:ALA40 3.6 19.5 1.0 OG A:SER42 3.6 19.0 1.0 NE2 A:GLN43 3.6 17.1 1.0 C A:ASP37 3.8 15.9 1.0 CA A:ALA40 3.8 19.9 1.0 N A:ARG44 3.9 16.2 1.0 N A:SER42 3.9 17.9 1.0 C A:SER42 4.0 16.9 1.0 N A:ALA40 4.0 20.6 1.0 C A:GLN43 4.0 15.9 1.0 CD A:GLN43 4.1 16.4 1.0 CE1 A:PHE36 4.2 15.2 1.0 N A:ASP37 4.2 14.4 1.0 N A:ALA41 4.3 19.7 1.0 CA A:SER42 4.3 17.9 1.0 OE1 A:GLU46 4.4 24.6 1.0 O A:ARG44 4.4 15.2 1.0 CB A:GLN43 4.4 16.3 1.0 CG A:GLN43 4.4 16.8 1.0 CZ A:PHE36 4.5 15.7 1.0 CD1 A:PHE36 4.5 14.7 1.0 C A:ALA41 4.5 18.9 1.0 CB A:SER42 4.5 19.1 1.0 O A:HOH539 4.6 24.7 1.0 CA A:ASP37 4.6 15.6 1.0 N A:SER38 4.8 15.7 1.0 OE1 A:GLN43 4.8 17.5 1.0 C A:SER38 4.8 17.6 1.0 O A:SER38 4.9 19.7 1.0 CA A:SER38 5.0 16.5 1.0

Sodium binding site 2 out of 4 in the Structure of Hla-A2:01 with Peptide MM91


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 MM91 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:21.9 occ:1.00 OE1 A:GLU46 2.6 24.6 1.0 NA A:NA302 2.8 25.4 1.0 O A:ARG44 2.8 15.2 1.0 N A:ASP37 3.2 14.4 1.0 OG A:SER42 3.5 19.0 1.0 CA A:PHE36 3.5 13.1 1.0 CD A:GLU46 3.6 21.1 1.0 O A:ASP37 3.8 16.3 1.0 CG A:GLU46 3.8 18.6 1.0 C A:PHE36 3.8 13.4 1.0 CD1 A:PHE36 3.9 14.7 1.0 C A:ARG44 4.0 15.1 1.0 NH1 A:ARG35 4.1 22.6 1.0 O A:ARG35 4.1 13.2 1.0 N A:ARG44 4.2 16.2 1.0 CB A:ALA40 4.2 20.3 1.0 CD A:ARG35 4.2 19.2 1.0 CG A:PHE36 4.2 14.5 1.0 CA A:ASP37 4.3 15.6 1.0 CB A:PHE36 4.4 14.0 1.0 CE1 A:PHE36 4.4 15.2 1.0 N A:PHE36 4.4 12.7 1.0 C A:ASP37 4.5 15.9 1.0 C A:ARG35 4.6 13.2 1.0 O A:HOH539 4.6 24.7 1.0 N A:GLN43 4.7 16.3 1.0 CB A:ASP37 4.7 17.3 1.0 OE2 A:GLU46 4.7 26.0 1.0 CA A:ARG44 4.7 16.4 1.0 CZ A:ARG35 4.8 22.1 1.0 NE A:ARG35 4.8 20.8 1.0 CB A:GLU46 4.8 16.4 1.0 CB A:SER42 4.8 19.1 1.0 N A:MET45 4.9 14.7 1.0 N A:GLU46 4.9 14.5 1.0 CA A:GLN43 5.0 16.4 1.0 C A:GLN43 5.0 15.9 1.0

Sodium binding site 3 out of 4 in the Structure of Hla-A2:01 with Peptide MM91


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Hla-A2:01 with Peptide MM91 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:23.7 occ:1.00 OE1 A:GLN96 2.6 14.6 1.0 N A:GLY120 2.9 17.1 1.0 O A:THR94 3.1 15.5 1.0 N A:ASP119 3.2 15.8 1.0 O A:ALA117 3.3 13.0 1.0 C A:ALA117 3.5 13.0 1.0 CD A:GLN96 3.5 13.9 1.0 C A:TYR118 3.6 13.8 1.0 N A:GLN96 3.7 12.6 1.0 C A:THR94 3.7 16.0 1.0 N A:TYR118 3.7 12.9 1.0 CB A:ALA117 3.7 13.4 1.0 CA A:GLY120 3.7 17.4 1.0 CA A:TYR118 3.7 13.3 1.0 CG A:GLN96 3.8 13.0 1.0 CG2 A:THR94 3.8 17.6 1.0 CA A:ASP119 3.9 16.7 1.0 C A:ASP119 3.9 17.0 1.0 C A:VAL95 4.0 13.4 1.0 CB A:GLN96 4.0 12.6 1.0 CA A:VAL95 4.0 14.4 1.0 CB A:THR94 4.1 17.4 1.0 NE2 B:HIS31 4.1 19.2 1.0 N A:VAL95 4.1 14.9 1.0 CA A:ALA117 4.2 13.1 1.0 CE1 B:HIS31 4.3 18.7 1.0 O A:TYR118 4.3 14.3 1.0 CA A:GLN96 4.5 12.3 1.0 CA A:THR94 4.5 16.1 1.0 C A:GLY120 4.7 17.6 1.0 N A:LYS121 4.7 17.4 1.0 O A:VAL95 4.8 13.7 1.0 NE2 A:GLN96 4.8 14.4 1.0

Sodium binding site 4 out of 4 in the Structure of Hla-A2:01 with Peptide MM91


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Hla-A2:01 with Peptide MM91 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:20.2 occ:1.00 OD2 A:ASP77 2.7 13.4 1.0 NH2 A:ARG97 2.8 12.9 1.0 O C:VAL7 2.8 13.4 1.0 O3 C:GOL101 3.4 13.8 1.0 CG2 A:THR73 3.5 12.8 1.0 CG A:ASP77 3.6 12.5 1.0 CE2 A:TYR116 3.6 13.2 1.0 CZ A:ARG97 3.7 13.1 1.0 NH1 A:ARG97 3.7 14.2 1.0 CZ2 A:TRP147 3.7 12.9 1.0 N C:VAL9 3.7 13.8 1.0 CG1 C:VAL9 3.8 13.4 1.0 OD1 A:ASP77 3.8 13.0 1.0 CA C:GLY8 3.8 13.5 1.0 C C:VAL7 3.8 14.3 1.0 C C:GLY8 3.9 13.4 1.0 CH2 A:TRP147 4.3 13.3 1.0 N C:GLY8 4.3 14.3 1.0 OH A:TYR116 4.3 14.7 1.0 CZ A:TYR116 4.3 13.8 1.0 CD2 A:TYR116 4.4 13.0 1.0 C3 C:GOL101 4.6 14.6 1.0 CA C:VAL9 4.6 13.5 1.0 CB C:VAL9 4.7 13.3 1.0 O C:GLY8 4.8 13.9 1.0 CE2 A:TRP147 4.8 13.8 1.0 NE A:ARG97 4.9 12.8 1.0 CB A:THR73 4.9 12.8 1.0 CB A:ASP77 5.0 12.4 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