Sodium in PDB 8emk: Crystal Structure of Hla-B*35:01-NP3 Epitope From 1957 H2N2 Influenza Strain

The structure of Crystal Structure of Hla-B*35:01-NP3 Epitope From 1957 H2N2 Influenza Strain, PDB code: 8emk was solved by D.R.Littler, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.19 / 1.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.821, 81.523, 109.14, 90, 90, 90
R / Rfree (%)	17.8 / 20.6

The binding sites of Sodium atom in the Crystal Structure of Hla-B*35:01-NP3 Epitope From 1957 H2N2 Influenza Strain (pdb code 8emk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Hla-B*35:01-NP3 Epitope From 1957 H2N2 Influenza Strain, PDB code: 8emk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Hla-B*35:01-NP3 Epitope From 1957 H2N2 Influenza Strain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hla-B*35:01-NP3 Epitope From 1957 H2N2 Influenza Strain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:20.8 occ:1.00 OG A:SER38 2.6 6.5 1.0 OD1 A:ASP39 2.7 19.8 1.0 NH2 A:ARG75 3.1 17.6 1.0 NH2 A:ARG14 3.3 13.7 1.0 O A:SER38 3.4 11.5 1.0 CB A:SER38 3.5 7.9 1.0 C A:SER38 3.5 10.3 1.0 CG A:ASP39 3.7 17.5 1.0 O A:PRO20 3.7 10.2 1.0 N A:ASP39 3.7 7.3 1.0 CA A:ARG21 3.7 4.8 1.0 CA A:ASP39 4.0 8.8 1.0 CA A:SER38 4.1 6.8 1.0 C A:PRO20 4.3 7.7 1.0 N A:ARG21 4.3 5.8 1.0 CB A:ARG21 4.3 6.8 1.0 O A:HOH489 4.4 23.3 1.0 CB A:ASP39 4.4 12.0 1.0 O A:GLU19 4.4 9.0 1.0 CZ A:ARG75 4.4 19.2 1.0 OD2 A:ASP39 4.5 20.0 1.0 CG A:ARG21 4.5 12.1 1.0 CZ A:ARG14 4.5 13.2 1.0 N A:PHE22 4.6 5.6 1.0 C A:ARG21 4.7 6.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Hla-B*35:01-NP3 Epitope From 1957 H2N2 Influenza Strain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Hla-B*35:01-NP3 Epitope From 1957 H2N2 Influenza Strain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:24.9 occ:1.00 O B:LEU87 2.2 27.9 1.0 O B:HOH292 2.4 23.3 1.0 O B:HOH281 2.5 24.7 1.0 O B:HIS84 2.5 18.8 1.0 O B:HOH280 2.5 32.0 1.0 OD1 B:ASN83 2.5 21.3 1.0 CG B:ASN83 3.4 22.4 1.0 C B:LEU87 3.4 26.8 1.0 C B:HIS84 3.5 17.4 1.0 ND2 B:ASN83 3.7 27.2 1.0 N B:HIS84 4.1 14.7 1.0 N B:LEU87 4.2 21.2 1.0 CA B:LEU87 4.2 24.0 1.0 CA B:VAL85 4.2 18.5 1.0 N B:VAL85 4.2 16.3 1.0 O B:HOH311 4.2 35.8 1.0 O B:VAL85 4.3 23.6 1.0 C B:VAL85 4.3 21.9 1.0 CB B:LEU87 4.4 23.0 1.0 CA B:HIS84 4.5 12.4 1.0 N B:SER88 4.5 29.8 1.0 O B:HOH258 4.6 28.4 1.0 O B:SER88 4.6 35.0 1.0 C B:SER88 4.6 33.0 1.0 CA B:SER88 4.7 32.0 1.0 CB B:ASN83 4.7 15.8 1.0 O B:HOH305 4.9 38.1 1.0 C B:ASN83 4.9 17.0 1.0 N B:GLN89 5.0 28.2 1.0

S.M.Quinones-Parra, D.R.Littler, J.Rossjohn, K.Kedzierska. Molecular Determinants of Cross-Strain Influenza A Virus Recognition By T-Cell Receptors To Be Published.