Sodium in PDB 6ss7: Human Leukocyte Antigen Class I A02 Carrying Llwagpmav

The structure of Human Leukocyte Antigen Class I A02 Carrying Llwagpmav, PDB code: 6ss7 was solved by P.J.Rizkallah, A.Bovay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.62 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.560, 169.250, 49.070, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 30.4

The binding sites of Sodium atom in the Human Leukocyte Antigen Class I A02 Carrying Llwagpmav (pdb code 6ss7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Leukocyte Antigen Class I A02 Carrying Llwagpmav, PDB code: 6ss7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Leukocyte Antigen Class I A02 Carrying Llwagpmav


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Leukocyte Antigen Class I A02 Carrying Llwagpmav within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:31.2 occ:1.00 O A:HOH442 2.4 26.7 1.0 O A:TRP147 2.6 34.2 1.0 N A:ALA153 3.0 29.6 1.0 NE1 A:TRP133 3.0 30.2 1.0 CB A:ALA153 3.4 29.9 1.0 C A:TRP147 3.5 32.4 1.0 N A:VAL152 3.5 33.2 1.0 CA A:GLU148 3.7 36.6 1.0 CA A:ALA153 3.8 29.1 1.0 N A:GLU148 3.9 33.6 1.0 C A:VAL152 3.9 29.9 1.0 CE2 A:TRP133 4.0 28.2 1.0 C A:HIS151 4.0 37.3 1.0 CD1 A:TRP133 4.0 31.0 1.0 CA A:VAL152 4.0 30.6 1.0 CA A:HIS151 4.1 39.9 1.0 CB A:VAL152 4.2 29.0 1.0 CZ2 A:TRP133 4.2 27.1 1.0 OE2 A:GLU154 4.4 39.3 1.0 N A:HIS151 4.5 39.1 1.0 CG A:GLU148 4.5 38.9 1.0 O A:GLU148 4.5 38.9 1.0 CB A:TRP147 4.6 29.1 1.0 C A:GLU148 4.6 37.5 1.0 CA A:TRP147 4.6 30.3 1.0 CB A:GLU148 4.7 38.1 1.0 O A:HIS151 4.8 38.1 1.0 C A:ALA153 4.9 29.9 1.0 N A:GLU154 5.0 32.3 1.0

Sodium binding site 2 out of 2 in the Human Leukocyte Antigen Class I A02 Carrying Llwagpmav


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Leukocyte Antigen Class I A02 Carrying Llwagpmav within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:28.4 occ:1.00 O D:TRP147 2.6 27.4 1.0 O D:HOH450 2.7 25.1 1.0 NE1 D:TRP133 3.0 24.8 1.0 N D:ALA153 3.3 31.8 1.0 C D:TRP147 3.4 27.7 1.0 CB D:ALA153 3.6 34.2 1.0 CA D:GLU148 3.6 32.6 1.0 N D:VAL152 3.6 29.7 1.0 N D:GLU148 3.8 29.9 1.0 CD1 D:TRP133 3.9 25.3 1.0 CA D:ALA153 4.0 33.0 1.0 CA D:HIS151 4.0 32.5 1.0 CE2 D:TRP133 4.0 23.0 1.0 C D:HIS151 4.0 31.4 1.0 C D:VAL152 4.2 30.1 1.0 CA D:VAL152 4.2 29.2 1.0 OE2 D:GLU154 4.3 47.2 1.0 CG D:GLU148 4.3 34.8 1.0 O D:GLU148 4.4 35.6 1.0 CB D:VAL152 4.4 28.2 1.0 CZ2 D:TRP133 4.4 22.7 1.0 N D:HIS151 4.4 31.6 1.0 C D:GLU148 4.4 34.1 1.0 CB D:GLU148 4.5 34.0 1.0 CB D:TRP147 4.6 25.5 1.0 CA D:TRP147 4.6 26.3 1.0 O D:HIS151 4.9 32.4 1.0

A.Bovay, V.Zoete, P.J.Rizkallah, K.Beck, P.Delbreil, D.E.Speiser, D.K.Cole, S.A.Fuertes Marraco. Identification of A Superagonist Variant of the Immunodominant Yellow Fever Virus Epitope NS4B214-222BY Combinatorial Peptide Library Screening. Mol.Immunol. V. 125 43 2020.
ISSN: ISSN 0161-5890
PubMed: 32645549
DOI: 10.1016/J.MOLIMM.2020.06.025