Sodium in PDB 5wlg: Crystal Structure of H-2DB with the GAP501 Peptide (Sql)

The structure of Crystal Structure of H-2DB with the GAP501 Peptide (Sql), PDB code: 5wlg was solved by S.Gras, C.Farenc, T.Josephs, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.05 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	115.735, 70.210, 116.488, 90.00, 108.28, 90.00
R / Rfree (%)	21.8 / 24.9

The structure of Crystal Structure of H-2DB with the GAP501 Peptide (Sql) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of H-2DB with the GAP501 Peptide (Sql) (pdb code 5wlg). 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 H-2DB with the GAP501 Peptide (Sql), PDB code: 5wlg:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of H-2DB with the GAP501 Peptide (Sql)


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 H-2DB with the GAP501 Peptide (Sql) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:45.4 occ:1.00 CL A:CL302 2.2 67.5 1.0 O A:HOH454 3.1 30.2 1.0 OD1 A:ASN30 3.3 63.0 1.0 O A:HOH548 3.6 53.0 1.0 CB A:TYR27 3.6 24.0 1.0 CG A:ARG6 3.7 22.2 1.0 O A:HOH600 3.7 55.2 1.0 CG A:TYR27 3.8 25.2 1.0 CA A:ASN30 3.8 32.7 1.0 CB A:ARG6 3.9 20.0 1.0 CG A:ASN30 4.2 63.1 1.0 CD1 A:TYR27 4.2 26.4 1.0 CD2 A:TYR27 4.3 25.9 1.0 O B:HOH148 4.3 49.9 1.0 N A:ASN30 4.3 32.8 1.0 CB A:ASN30 4.3 35.8 1.0 CE1 A:PHE8 4.4 20.9 1.0 CZ A:PHE8 4.4 20.0 1.0 C A:ASN30 4.8 35.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of H-2DB with the GAP501 Peptide (Sql)


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 H-2DB with the GAP501 Peptide (Sql) within 5.0Å range: probe atom residue distance (Å) B Occ G:Na101 b:66.2 occ:1.00 OG G:SER52 2.7 94.0 1.0 O G:ASP53 3.2 74.0 1.0 O F:HOH330 3.2 50.9 1.0 CB G:SER52 3.5 86.8 1.0 OG G:SER55 4.2 66.0 1.0 C G:ASP53 4.3 75.0 1.0 N G:ASP53 4.3 79.7 1.0 NH1 F:ARG35 4.5 87.8 1.0 C G:SER52 4.6 85.6 1.0 OE1 F:GLU32 4.6 67.6 1.0 CA G:SER52 4.7 83.5 1.0 CE1 G:TYR63 4.7 47.6 1.0 NH2 F:ARG35 4.8 50.0 1.0 N G:LEU65 4.8 40.5 1.0 CB G:LEU65 4.9 40.9 1.0 CA G:ASP53 4.9 78.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of H-2DB with the GAP501 Peptide (Sql)


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 H-2DB with the GAP501 Peptide (Sql) within 5.0Å range: probe atom residue distance (Å) B Occ I:Na201 b:61.1 occ:1.00 CB I:PHE134 3.5 53.6 1.0 CB I:ALA173 3.6 72.8 1.0 O I:CYS132 3.8 68.8 1.0 N I:PHE134 4.1 53.5 1.0 O I:ALA171 4.2 62.4 1.0 CA I:PHE134 4.4 52.1 1.0 CB I:ALA185 4.4 95.0 1.0 CG I:PHE134 4.6 54.9 1.0 N I:ALA173 4.6 70.2 1.0 C I:CYS132 4.6 69.0 1.0 CA I:ALA173 4.7 72.3 1.0 C I:ALA171 4.7 62.8 1.0 CB I:ALA171 4.7 57.7 1.0 C I:VAL172 4.8 69.3 1.0 CD2 I:PHE134 4.9 57.0 1.0 CB I:CYS132 4.9 71.2 1.0 C I:LEU133 4.9 59.5 1.0

N.Van Braeckel-Budimir, S.Gras, K.Ladell, T.M.Josephs, L.Pewe, S.L.Urban, K.L.Miners, C.Farenc, D.A.Price, J.Rossjohn, J.T.Harty. A T Cell Receptor Locus Harbors A Malaria-Specific Immune Response Gene. Immunity V. 47 835 2017.
ISSN: ISSN 1074-7613
PubMed: 29150238
DOI: 10.1016/J.IMMUNI.2017.10.013