Sodium in PDB 2gtz: Human Class I Mhc Hla-A2 in Complex with the Nonameric Melan-A/Mart- 1(27-35) Peptide Having A28L Substitution

The structure of Human Class I Mhc Hla-A2 in Complex with the Nonameric Melan-A/Mart- 1(27-35) Peptide Having A28L Substitution, PDB code: 2gtz 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 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.400, 84.310, 84.140, 90.00, 90.13, 90.00
R / Rfree (%)	17.2 / 21.7

The binding sites of Sodium atom in the Human Class I Mhc Hla-A2 in Complex with the Nonameric Melan-A/Mart- 1(27-35) Peptide Having A28L Substitution (pdb code 2gtz). 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 Nonameric Melan-A/Mart- 1(27-35) Peptide Having A28L Substitution, PDB code: 2gtz:
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 Nonameric Melan-A/Mart- 1(27-35) Peptide Having A28L Substitution


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 Nonameric Melan-A/Mart- 1(27-35) Peptide Having A28L Substitution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na5001 b:29.9 occ:1.00 O B:HOH5079 2.2 31.5 1.0 O B:HOH5072 2.2 30.9 1.0 O B:LEU87 2.4 21.4 1.0 O B:HOH5088 2.4 35.5 1.0 OD1 B:ASN83 2.7 20.1 1.0 O B:HIS84 2.7 16.4 1.0 CG B:ASN83 3.6 21.1 1.0 C B:LEU87 3.6 19.8 1.0 C B:HIS84 3.7 17.1 1.0 ND2 B:ASN83 3.9 26.4 1.0 N B:HIS84 4.1 16.9 1.0 CA B:VAL85 4.2 17.3 1.0 N B:LEU87 4.3 17.2 1.0 CA B:LEU87 4.3 17.8 1.0 N B:VAL85 4.3 17.5 1.0 CB B:LEU87 4.4 16.3 1.0 O B:VAL85 4.4 17.6 1.0 C B:VAL85 4.4 16.6 1.0 CA B:HIS84 4.6 17.4 1.0 C B:SER88 4.6 22.4 1.0 N B:SER88 4.6 20.0 1.0 CA B:SER88 4.7 22.4 1.0 O B:SER88 4.8 23.4 1.0 N B:GLN89 4.9 22.8 1.0 CB B:ASN83 4.9 18.2 1.0

Sodium binding site 2 out of 2 in the Human Class I Mhc Hla-A2 in Complex with the Nonameric Melan-A/Mart- 1(27-35) Peptide Having A28L Substitution


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 Nonameric Melan-A/Mart- 1(27-35) Peptide Having A28L Substitution within 5.0Å range: probe atom residue distance (Å) B Occ E:Na5002 b:40.2 occ:1.00 O E:HOH5119 2.2 39.2 1.0 O E:HOH5102 2.7 40.7 1.0 O E:LEU87 2.7 20.8 1.0 O E:HIS84 2.8 17.0 1.0 OD1 E:ASN83 2.8 19.2 1.0 CG E:ASN83 3.7 20.2 1.0 C E:HIS84 3.7 17.3 1.0 C E:LEU87 3.9 20.7 1.0 O E:HOH5127 3.9 38.1 1.0 ND2 E:ASN83 3.9 25.7 1.0 CA E:VAL85 4.2 16.3 1.0 N E:HIS84 4.2 17.1 1.0 O E:VAL85 4.3 17.0 1.0 N E:VAL85 4.4 15.8 1.0 C E:VAL85 4.4 16.4 1.0 N E:LEU87 4.5 18.6 1.0 CA E:LEU87 4.5 19.5 1.0 CB E:LEU87 4.6 19.1 1.0 CA E:HIS84 4.7 17.1 1.0 N E:SER88 4.9 22.1 1.0 C E:SER88 5.0 23.6 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