Sodium in PDB 6o51: Structure of Hla-A2:01 with Peptide MM90

The structure of Structure of Hla-A2:01 with Peptide MM90, PDB code: 6o51 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)	31.47 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.260, 79.467, 57.251, 90.00, 115.96, 90.00
R / Rfree (%)	19.2 / 22.5

The binding sites of Sodium atom in the Structure of Hla-A2:01 with Peptide MM90 (pdb code 6o51). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Hla-A2:01 with Peptide MM90, PDB code: 6o51:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of Hla-A2:01 with Peptide MM90


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 MM90 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:42.4 occ:1.00 OG1 A:THR190 2.7 19.5 1.0 CB B:ASP98 3.1 42.1 1.0 NE1 A:TRP204 3.3 15.7 1.0 NH1 A:ARG202 3.4 21.2 1.0 O B:ASP98 3.4 39.9 1.0 CB A:THR190 3.5 18.8 1.0 CG2 A:THR190 3.6 19.3 1.0 CD A:ARG202 3.8 16.7 1.0 CE1 A:HIS192 3.9 40.7 1.0 CE2 A:TRP204 3.9 15.6 1.0 CZ2 A:TRP204 3.9 16.3 1.0 CA B:ASP98 4.1 41.7 1.0 C B:ASP98 4.2 39.9 1.0 CB A:ARG202 4.3 14.5 1.0 O A:HOH542 4.4 27.3 1.0 CG A:ARG202 4.4 15.7 1.0 CD1 A:TRP204 4.4 15.0 1.0 CZ A:ARG202 4.4 20.1 1.0 NE A:ARG202 4.6 18.0 1.0 ND1 A:HIS192 4.6 39.5 1.0 O A:HOH601 4.8 30.8 1.0 CA A:THR190 4.9 18.2 1.0 NE2 A:HIS192 4.9 39.8 1.0

Sodium binding site 2 out of 5 in the Structure of Hla-A2:01 with Peptide MM90


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 MM90 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:34.4 occ:1.00 O A:HOH681 2.6 33.2 1.0 OG1 A:THR214 2.7 19.0 1.0 OE1 A:GLU212 3.1 29.5 1.0 N A:THR214 3.5 14.6 1.0 C A:ILE213 3.5 14.0 1.0 CB A:THR214 3.7 17.0 1.0 CA A:ILE213 3.8 14.1 1.0 O A:GLN262 3.8 14.9 1.0 CG A:GLU212 3.9 20.0 1.0 CD A:GLU212 3.9 23.0 1.0 O A:ILE213 4.0 14.3 1.0 N A:ILE213 4.0 13.7 1.0 CA A:THR214 4.2 15.6 1.0 O A:HOH494 4.4 51.0 1.0 CB A:GLN262 4.4 17.4 1.0 C A:GLU212 4.4 13.6 1.0 C A:GLN262 4.5 15.1 1.0 O A:GLU212 4.7 13.1 1.0 CG2 A:THR214 5.0 18.1 1.0

Sodium binding site 3 out of 5 in the Structure of Hla-A2:01 with Peptide MM90


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 MM90 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:21.4 occ:1.00 NA A:NA308 2.6 24.2 1.0 OE1 A:GLU46 2.8 23.0 1.0 O A:ARG44 2.8 13.2 1.0 N A:ASP37 3.2 13.6 1.0 OG A:SER42 3.5 16.6 1.0 CA A:PHE36 3.5 12.2 1.0 CD A:GLU46 3.7 19.5 1.0 O A:ASP37 3.8 13.1 1.0 CD2 A:PHE36 3.8 13.2 1.0 CG A:GLU46 3.8 16.9 1.0 C A:PHE36 3.9 12.6 1.0 C A:ARG44 4.0 13.7 1.0 NH1 A:ARG35 4.1 20.3 1.0 CB A:ALA40 4.1 17.5 1.0 O A:ARG35 4.1 11.1 1.0 CG A:PHE36 4.1 12.8 1.0 N A:ARG44 4.2 14.6 1.0 CD A:ARG35 4.2 17.3 1.0 CA A:ASP37 4.3 13.7 1.0 CB A:PHE36 4.3 12.4 1.0 CE2 A:PHE36 4.4 13.4 1.0 C A:ASP37 4.4 14.5 1.0 N A:PHE36 4.5 11.4 1.0 C A:ARG35 4.6 12.2 1.0 N A:GLN43 4.6 14.1 1.0 CB A:ASP37 4.7 14.6 1.0 CA A:ARG44 4.8 14.7 1.0 CB A:GLU46 4.8 15.2 1.0 O A:HOH593 4.8 19.6 1.0 CZ A:ARG35 4.8 19.4 1.0 OE2 A:GLU46 4.8 24.4 1.0 NE A:ARG35 4.8 18.4 1.0 CB A:SER42 4.9 15.6 1.0 CD1 A:PHE36 4.9 13.7 1.0 N A:GLU46 4.9 13.0 1.0 CA A:GLN43 4.9 13.9 1.0 C A:GLN43 4.9 14.1 1.0 N A:MET45 5.0 13.1 1.0

Sodium binding site 4 out of 5 in the Structure of Hla-A2:01 with Peptide MM90


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 MM90 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:24.2 occ:1.00 O A:ASP37 2.6 13.1 1.0 NA A:NA307 2.6 21.4 1.0 N A:GLN43 2.9 14.1 1.0 O A:ALA40 3.3 16.3 1.0 CA A:GLN43 3.3 13.9 1.0 CB A:ALA40 3.4 17.5 1.0 C A:ALA40 3.5 16.5 1.0 NE2 A:GLN43 3.6 13.8 1.0 OG A:SER42 3.7 16.6 1.0 C A:ASP37 3.8 14.5 1.0 CA A:ALA40 3.8 16.6 1.0 N A:ALA40 4.0 16.8 1.0 N A:ARG44 4.0 14.6 1.0 N A:SER42 4.0 15.1 1.0 C A:SER42 4.1 14.9 1.0 C A:GLN43 4.1 14.1 1.0 CE2 A:PHE36 4.2 13.4 1.0 CD A:GLN43 4.2 13.7 1.0 N A:ASP37 4.2 13.6 1.0 N A:ALA41 4.3 16.4 1.0 OE1 A:GLU46 4.4 23.0 1.0 O A:ARG44 4.4 13.2 1.0 CZ A:PHE36 4.4 13.8 1.0 CA A:SER42 4.4 15.0 1.0 CD2 A:PHE36 4.5 13.2 1.0 CB A:GLN43 4.5 13.7 1.0 CG A:GLN43 4.5 14.1 1.0 C A:ALA41 4.5 15.6 1.0 CA A:ASP37 4.5 13.7 1.0 CB A:SER42 4.6 15.6 1.0 N A:SER38 4.7 14.6 1.0 O A:HOH593 4.7 19.6 1.0 C A:SER38 4.8 16.2 1.0 CA A:SER38 4.8 15.2 1.0 CE1 A:PHE36 4.9 13.5 1.0 OE1 A:GLN43 4.9 15.6 1.0 O A:SER38 4.9 16.2 1.0 CG A:PHE36 5.0 12.8 1.0

Sodium binding site 5 out of 5 in the Structure of Hla-A2:01 with Peptide MM90


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 MM90 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:49.3 occ:1.00 NH1 A:ARG111 3.7 28.4 1.0 OG A:SER2 4.1 32.4 1.0 CB A:SER2 4.1 27.4 1.0 O A:HOH591 4.3 37.2 1.0 NH2 A:ARG111 4.4 30.9 1.0 CD2 A:LEU110 4.5 18.4 1.0 CZ A:ARG111 4.5 29.2 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