Sodium in PDB 6o4z: Structure of Hla-A2:01 with Peptide MM92

The structure of Structure of Hla-A2:01 with Peptide MM92, PDB code: 6o4z 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)	28.65 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.134, 79.689, 57.442, 90.00, 116.27, 90.00
R / Rfree (%)	17.5 / 19.3

The binding sites of Sodium atom in the Structure of Hla-A2:01 with Peptide MM92 (pdb code 6o4z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Hla-A2:01 with Peptide MM92, PDB code: 6o4z:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structure of Hla-A2:01 with Peptide MM92


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 MM92 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:23.2 occ:1.00 NA A:NA303 2.6 29.2 1.0 OE1 A:GLU46 2.7 25.2 1.0 O A:ARG44 2.9 14.0 1.0 N A:ASP37 3.2 13.4 1.0 OG A:SER42 3.5 18.8 1.0 CA A:PHE36 3.5 12.6 1.0 CD A:GLU46 3.6 21.5 1.0 O A:ASP37 3.8 14.6 1.0 CG A:GLU46 3.9 18.4 1.0 C A:PHE36 3.9 13.0 1.0 CD2 A:PHE36 4.0 14.2 1.0 C A:ARG44 4.0 14.2 1.0 CB A:ALA40 4.1 18.5 1.0 NH1 A:ARG35 4.1 20.2 1.0 O A:ARG35 4.1 11.8 1.0 CD A:ARG35 4.1 17.6 1.0 CG A:PHE36 4.2 13.3 1.0 N A:ARG44 4.2 14.8 1.0 CA A:ASP37 4.3 14.1 1.0 CB A:PHE36 4.4 12.9 1.0 C A:ASP37 4.4 14.5 1.0 N A:PHE36 4.5 12.2 1.0 CE2 A:PHE36 4.5 14.4 1.0 C A:ARG35 4.6 12.2 1.0 CB A:ASP37 4.7 15.3 1.0 OE2 A:GLU46 4.7 25.2 1.0 N A:GLN43 4.7 15.9 1.0 CZ A:ARG35 4.7 19.8 1.0 NE A:ARG35 4.7 19.1 1.0 CB A:GLU46 4.8 16.3 1.0 O A:HOH538 4.8 22.9 1.0 CA A:ARG44 4.8 15.7 1.0 CB A:SER42 4.8 17.5 1.0 CD1 A:PHE36 4.8 14.4 1.0 N A:GLU46 4.9 13.7 1.0 N A:MET45 5.0 13.9 1.0

Sodium binding site 2 out of 6 in the Structure of Hla-A2:01 with Peptide MM92


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 MM92 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:29.2 occ:1.00 NA A:NA302 2.6 23.2 1.0 O A:ASP37 2.7 14.6 1.0 N A:GLN43 2.9 15.9 1.0 CA A:GLN43 3.2 14.9 1.0 O A:ALA40 3.4 18.1 1.0 CB A:ALA40 3.4 18.5 1.0 OG A:SER42 3.6 18.8 1.0 C A:ALA40 3.7 18.0 1.0 NE2 A:GLN43 3.7 15.4 1.0 C A:ASP37 3.8 14.5 1.0 N A:ARG44 3.9 14.8 1.0 CA A:ALA40 3.9 18.6 1.0 C A:GLN43 4.0 14.4 1.0 N A:SER42 4.0 16.9 1.0 C A:SER42 4.0 16.4 1.0 N A:ALA40 4.1 18.7 1.0 N A:ASP37 4.2 13.4 1.0 CE2 A:PHE36 4.2 14.4 1.0 CD A:GLN43 4.2 15.0 1.0 OE1 A:GLU46 4.3 25.2 1.0 O A:ARG44 4.3 14.0 1.0 CZ A:PHE36 4.3 14.4 1.0 CA A:SER42 4.4 16.9 1.0 N A:ALA41 4.4 17.9 1.0 CB A:GLN43 4.5 15.1 1.0 CD2 A:PHE36 4.5 14.2 1.0 CG A:GLN43 4.5 15.1 1.0 CA A:ASP37 4.6 14.1 1.0 CB A:SER42 4.6 17.5 1.0 C A:ALA41 4.6 18.0 1.0 N A:SER38 4.7 14.7 1.0 CE1 A:PHE36 4.7 14.1 1.0 O A:HOH538 4.8 22.9 1.0 CA A:SER38 4.8 15.6 1.0 C A:SER38 4.8 17.0 1.0 CG A:PHE36 4.9 13.3 1.0 OE1 A:GLN43 4.9 16.6 1.0 O A:SER38 4.9 16.6 1.0 CD1 A:PHE36 5.0 14.4 1.0

Sodium binding site 3 out of 6 in the Structure of Hla-A2:01 with Peptide MM92


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 MM92 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:19.9 occ:1.00 OE1 A:GLN96 2.7 13.1 1.0 N A:GLY120 2.9 12.9 1.0 O A:THR94 3.1 11.8 1.0 N A:ASP119 3.2 12.1 1.0 O A:ALA117 3.3 10.5 1.0 C A:ALA117 3.5 10.2 1.0 CD A:GLN96 3.5 11.6 1.0 C A:TYR118 3.5 11.6 1.0 N A:GLN96 3.7 10.2 1.0 C A:THR94 3.7 11.0 1.0 CA A:GLY120 3.7 13.5 1.0 CA A:TYR118 3.7 10.7 1.0 CG A:GLN96 3.7 11.0 1.0 N A:TYR118 3.7 10.3 1.0 CG2 A:THR94 3.8 12.4 1.0 CA A:ASP119 3.8 13.4 1.0 C A:ASP119 3.8 13.6 1.0 CB A:ALA117 3.8 10.2 1.0 CA A:VAL95 4.0 10.6 0.5 C A:VAL95 4.0 10.5 1.0 CB A:THR94 4.0 12.2 1.0 CB A:GLN96 4.0 10.3 1.0 CA A:VAL95 4.0 10.8 0.5 NE2 B:HIS31 4.1 17.2 1.0 N A:VAL95 4.1 10.7 1.0 CA A:ALA117 4.3 10.1 1.0 O A:TYR118 4.3 11.4 1.0 CE1 B:HIS31 4.3 16.4 1.0 CA A:GLN96 4.4 10.1 1.0 CA A:THR94 4.5 11.7 1.0 C A:GLY120 4.7 14.0 1.0 O A:VAL95 4.7 10.9 1.0 NE2 A:GLN96 4.8 11.0 1.0 N A:LYS121 4.8 14.2 1.0 O A:ASP119 5.0 14.7 1.0

Sodium binding site 4 out of 6 in the Structure of Hla-A2:01 with Peptide MM92


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 MM92 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:21.4 occ:1.00 O A:HOH589 2.7 33.7 1.0 O A:TRP147 2.8 14.1 1.0 NE1 A:TRP133 2.9 13.7 1.0 N A:ALA153 3.0 14.4 1.0 N A:VAL152 3.4 15.3 1.0 CB A:ALA153 3.4 14.7 1.0 C A:TRP147 3.4 13.9 1.0 O A:HOH546 3.5 23.4 1.0 CA A:GLU148 3.6 16.0 1.0 N A:GLU148 3.7 14.3 1.0 CA A:ALA153 3.8 14.9 1.0 CE2 A:TRP133 3.8 13.2 1.0 O A:HOH490 3.8 35.5 1.0 C A:VAL152 3.9 15.1 1.0 C A:HIS151 3.9 17.2 1.0 CD1 A:TRP133 4.0 13.7 1.0 CA A:VAL152 4.0 15.3 1.0 CZ2 A:TRP133 4.0 13.2 1.0 CA A:HIS151 4.1 18.0 1.0 CB A:VAL152 4.2 15.5 1.0 O A:GLU148 4.4 17.2 1.0 C A:GLU148 4.4 16.8 1.0 N A:HIS151 4.5 17.9 1.0 O A:HOH459 4.5 36.9 1.0 CB A:TRP147 4.5 12.3 1.0 CA A:TRP147 4.5 13.2 1.0 CG A:GLU148 4.6 19.6 1.0 CB A:GLU148 4.7 17.1 1.0 O A:HIS151 4.8 16.1 1.0 N A:GLU154 4.9 17.1 1.0 C A:ALA153 4.9 16.0 1.0

Sodium binding site 5 out of 6 in the Structure of Hla-A2:01 with Peptide MM92


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Hla-A2:01 with Peptide MM92 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:40.7 occ:1.00 O A:HOH462 3.1 27.9 1.0 O A:HOH579 3.2 52.3 1.0 N A:PHE109 3.6 16.9 1.0 NH1 A:ARG169 3.8 22.4 1.0 O A:HOH506 3.9 40.6 1.0 CA A:ARG108 4.1 19.4 1.0 CB A:PHE109 4.2 16.6 1.0 NH2 A:ARG169 4.2 22.5 1.0 CB A:ARG108 4.2 22.1 1.0 C A:ARG108 4.4 17.4 1.0 CZ A:ARG169 4.5 21.6 1.0 CA A:PHE109 4.5 16.5 1.0 CG2 A:VAL165 4.6 16.6 1.0 CG A:ARG108 4.7 25.0 1.0 O A:GLU161 4.9 21.4 1.0

Sodium binding site 6 out of 6 in the Structure of Hla-A2:01 with Peptide MM92


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Hla-A2:01 with Peptide MM92 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:40.3 occ:1.00 NE2 B:HIS51 3.8 25.9 1.0 NH2 A:ARG21 3.9 20.1 1.0 NH1 A:ARG21 4.0 19.5 1.0 CE1 B:HIS51 4.4 24.5 1.0 CZ A:ARG21 4.4 18.8 1.0 O A:HOH591 4.5 36.6 1.0 CD2 B:HIS51 4.9 23.9 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