Sodium in PDB 7jyw: Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope

The structure of Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope, PDB code: 7jyw was solved by S.Gras, A.T.Nguyen, C.Szeto, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.16 / 2.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.295, 87.295, 312.441, 90, 90, 120
R / Rfree (%)	24.1 / 27.5

The structure of Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Nickel	(Ni)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope (pdb code 7jyw). 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 A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope, PDB code: 7jyw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope


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 A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:93.2 occ:1.00 OE2 A:GLU19 3.1 136.9 1.0 NH2 A:ARG79 3.1 135.1 1.0 CZ A:ARG79 3.9 148.7 1.0 NE A:ARG79 4.0 127.0 1.0 NE A:ARG75 4.0 125.8 1.0 CD A:PRO20 4.2 92.7 1.0 CD A:GLU19 4.3 142.9 1.0 CD A:ARG75 4.3 111.2 1.0 CA A:GLU19 4.7 99.3 1.0 CZ A:ARG75 4.8 138.3 1.0 CG A:GLU19 5.0 114.3 1.0 O A:GLY18 5.0 107.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Hla A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope


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 A*2402 in Complex with Tyqwiirnw, An 9-Mer Influenza Epitope within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:102.3 occ:1.00 N A:ALA135 3.1 97.9 1.0 CE A:LYS144 3.4 138.6 1.0 CA A:THR134 3.7 98.8 1.0 CD A:LYS144 3.7 127.3 1.0 O A:TRP133 3.9 105.2 1.0 C A:THR134 3.9 101.6 1.0 O A:ALA135 3.9 101.6 1.0 NZ A:LYS144 4.0 147.7 1.0 CA A:ALA135 4.1 97.8 1.0 CB A:ALA135 4.1 98.6 1.0 CG2 A:THR134 4.3 100.5 1.0 C A:ALA135 4.5 101.9 1.0 CB A:THR134 4.5 103.9 1.0 N A:THR134 4.6 99.7 1.0 NZ A:LYS127 4.6 144.4 1.0 C A:TRP133 4.6 104.9 1.0

A.T.Nguyen, C.Szeto, J.Rossjohn, S.Gras. Crystal Structure of Hla A*2402 in Complex with Iyfspirvtf, An 10-Mer Influenza B Epitope Nat Commun 2021.
ISSN: ESSN 2041-1723