Sodium in PDB 7m8u: Crystal Structure of Hla-B*35:01 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904)

The structure of Crystal Structure of Hla-B*35:01 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904), PDB code: 7m8u was solved by S.Gras, A.T.Nguyen, C.Szeto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.06 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.238, 82.38, 111.011, 90, 90, 90
R / Rfree (%)	20.4 / 22.9

The binding sites of Sodium atom in the Crystal Structure of Hla-B*35:01 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904) (pdb code 7m8u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Hla-B*35:01 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904), PDB code: 7m8u:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Hla-B*35:01 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904)


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 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:53.3 occ:1.00 CE A:MET12 2.3 29.6 1.0 O A:HOH472 2.6 39.0 1.0 CD A:ARG21 3.3 22.6 1.0 O B:HOH133 3.4 49.9 1.0 O A:HOH601 3.4 32.9 1.0 SD A:MET12 3.8 29.5 1.0 NH1 A:ARG14 3.9 21.2 1.0 O B:HOH138 3.9 24.3 1.0 CB A:ARG21 3.9 18.4 1.0 NH1 A:ARG21 4.1 23.6 1.0 OD1 B:ASP34 4.2 25.5 1.0 CG A:ARG21 4.3 20.3 1.0 NE A:ARG21 4.4 22.9 1.0 OD2 A:ASP39 4.6 29.6 1.0 O B:HOH139 4.6 42.8 1.0 O A:HOH403 4.6 29.1 1.0 CZ A:ARG14 4.7 21.7 1.0 CZ A:ARG21 4.7 25.5 1.0 CD A:ARG14 4.8 21.4 1.0 CB A:MET12 4.9 19.9 1.0 CG A:MET12 4.9 24.9 1.0 O A:HOH599 4.9 30.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Hla-B*35:01 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904)


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 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:48.4 occ:1.00 O A:HOH468 2.2 43.1 1.0 O A:ARG145 2.6 31.5 1.0 C A:ARG145 3.5 29.2 1.0 CA A:ARG145 3.7 27.8 1.0 N A:ALA149 3.7 31.8 1.0 CB A:ARG145 3.8 31.5 1.0 CB A:ALA149 3.8 32.3 1.0 CB A:GLU148 4.0 29.3 1.0 CA A:ALA149 4.2 31.6 1.0 OE1 A:GLU148 4.3 33.4 1.0 C A:GLU148 4.4 35.2 1.0 CG A:ARG145 4.7 33.3 1.0 N A:LYS146 4.7 22.7 1.0 CA A:GLU148 4.7 28.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Hla-B*35:01 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Hla-B*35:01 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:63.4 occ:1.00 O A:HOH631 2.6 28.5 1.0 O C:MET7 3.0 38.0 1.0 CB C:MET7 3.1 47.7 1.0 NH1 A:ARG97 3.4 30.7 1.0 CA C:MET7 3.5 43.6 1.0 N C:MET7 3.6 44.1 1.0 C C:MET7 3.7 37.9 1.0 CZ2 A:TRP147 3.9 23.5 1.0 O A:HOH525 4.0 35.0 1.0 NH2 A:ARG97 4.0 33.3 1.0 CE2 A:TRP147 4.0 24.4 1.0 CZ A:ARG97 4.1 43.9 1.0 NE1 A:TRP147 4.1 25.6 1.0 CG C:MET7 4.2 54.0 1.0 O A:HOH614 4.4 53.3 1.0 O C:HOH201 4.5 37.4 1.0 CG1 A:VAL152 4.5 30.6 1.0 O C:MET5 4.6 32.7 1.0 C C:GLN6 4.6 46.5 1.0 CH2 A:TRP147 4.6 22.0 1.0 CD2 A:TRP147 4.7 22.5 1.0 CG2 A:VAL152 4.7 30.5 1.0 CD1 A:TRP147 4.9 27.1 1.0 N C:ALA8 5.0 30.4 1.0

A.T.Nguyen, C.Szeto, D.Jayasinghe, C.A.Lobos, H.Halim, D.S.M.Chatzileontiadou, E.J.Grant, S.Gras. Sars-Cov-2 Spike-Derived Peptides Presented By Hla Molecules Biophysica V. 1 2021.
DOI: 10.3390/BIOPHYSICA1020015