Sodium in PDB 2gt9: Human Class I Mhc Hla-A2 in Complex with the Decameric Melan-A/Mart- 1(26-35) Peptide

The structure of Human Class I Mhc Hla-A2 in Complex with the Decameric Melan-A/Mart- 1(26-35) Peptide, PDB code: 2gt9 was solved by O.Y.Borbulevych, B.M.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.340, 84.179, 84.061, 90.00, 90.08, 90.00
R / Rfree (%)	17.1 / 21.3

The binding sites of Sodium atom in the Human Class I Mhc Hla-A2 in Complex with the Decameric Melan-A/Mart- 1(26-35) Peptide (pdb code 2gt9). 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 Class I Mhc Hla-A2 in Complex with the Decameric Melan-A/Mart- 1(26-35) Peptide, PDB code: 2gt9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Class I Mhc Hla-A2 in Complex with the Decameric Melan-A/Mart- 1(26-35) Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Class I Mhc Hla-A2 in Complex with the Decameric Melan-A/Mart- 1(26-35) Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na806 b:31.3 occ:1.00 O B:LEU87 2.3 17.5 1.0 O B:HOH927 2.5 31.9 1.0 O B:HOH928 2.5 32.9 1.0 O B:HOH926 2.5 39.6 1.0 OD1 B:ASN83 2.6 20.8 1.0 O B:HIS84 2.7 14.8 1.0 CG B:ASN83 3.5 20.2 1.0 C B:LEU87 3.6 17.2 1.0 C B:HIS84 3.6 15.1 1.0 ND2 B:ASN83 3.8 25.1 1.0 N B:HIS84 4.0 15.0 1.0 N B:LEU87 4.2 15.1 1.0 CA B:VAL85 4.3 15.4 1.0 CA B:LEU87 4.3 16.3 1.0 CB B:LEU87 4.3 15.2 1.0 N B:VAL85 4.4 15.6 1.0 O B:VAL85 4.4 15.2 1.0 C B:VAL85 4.4 15.1 1.0 CA B:HIS84 4.5 15.6 1.0 N B:SER88 4.5 18.3 1.0 C B:SER88 4.5 20.6 1.0 CA B:SER88 4.6 20.5 1.0 O B:SER88 4.8 20.8 1.0 CB B:ASN83 4.8 16.4 1.0 N B:GLN89 4.8 20.9 1.0 C B:ASN83 5.0 15.4 1.0

Sodium binding site 2 out of 2 in the Human Class I Mhc Hla-A2 in Complex with the Decameric Melan-A/Mart- 1(26-35) Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Class I Mhc Hla-A2 in Complex with the Decameric Melan-A/Mart- 1(26-35) Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Na807 b:26.6 occ:1.00 O E:HOH929 2.5 29.3 1.0 O E:HIS84 2.5 16.3 1.0 OD1 E:ASN83 2.5 22.1 1.0 O E:HOH910 2.5 29.5 1.0 O E:LEU87 2.5 21.6 1.0 CG E:ASN83 3.3 18.5 1.0 C E:HIS84 3.5 15.7 1.0 ND2 E:ASN83 3.6 24.7 1.0 C E:LEU87 3.7 18.5 1.0 N E:HIS84 3.9 16.4 1.0 CA E:VAL85 4.2 14.9 1.0 N E:VAL85 4.2 14.2 1.0 N E:LEU87 4.3 16.1 1.0 CA E:LEU87 4.3 17.6 1.0 CB E:LEU87 4.3 16.4 1.0 O E:VAL85 4.3 15.0 1.0 C E:VAL85 4.4 14.9 1.0 CA E:HIS84 4.4 15.5 1.0 CB E:ASN83 4.7 16.1 1.0 N E:SER88 4.8 20.1 1.0 C E:ASN83 4.9 15.5 1.0 C E:SER88 4.9 21.3 1.0 N E:GLN89 5.0 20.7 1.0

O.Y.Borbulevych, F.K.Insaidoo, T.K.Baxter, D.J.Powell, L.A.Johnson, N.P.Restifo, B.M.Baker. Structures of Mart-1(26/27-35) Peptide/Hla-A2 Complexes Reveal A Remarkable Disconnect Between Antigen Structural Homology and T Cell Recognition J.Mol.Biol. V. 372 1123 2007.
ISSN: ISSN 0022-2836
PubMed: 17719062
DOI: 10.1016/J.JMB.2007.07.025