Sodium in PDB 3qfd: Human Class I Mhc Hla-A2 in Complex with Mart-1(27-35) Nonameric Peptide

The structure of Human Class I Mhc Hla-A2 in Complex with Mart-1(27-35) Nonameric Peptide, PDB code: 3qfd 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 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.254, 84.118, 83.964, 90.00, 90.05, 90.00
R / Rfree (%)	17 / 21.1

The binding sites of Sodium atom in the Human Class I Mhc Hla-A2 in Complex with Mart-1(27-35) Nonameric Peptide (pdb code 3qfd). 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 Mart-1(27-35) Nonameric Peptide, PDB code: 3qfd:
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 Mart-1(27-35) Nonameric 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 Mart-1(27-35) Nonameric Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:30.1 occ:1.00 O B:HOH804 2.3 25.9 1.0 O B:HOH402 2.3 24.1 1.0 O B:HOH401 2.4 26.7 1.0 O B:LEU87 2.4 29.6 1.0 O B:HIS84 2.6 20.3 1.0 OD1 B:ASN83 2.6 26.2 1.0 CG B:ASN83 3.5 27.2 1.0 C B:LEU87 3.6 27.1 1.0 C B:HIS84 3.6 20.3 1.0 ND2 B:ASN83 3.8 31.2 1.0 N B:HIS84 4.0 19.8 1.0 CA B:VAL85 4.1 21.1 1.0 N B:LEU87 4.2 21.1 1.0 N B:VAL85 4.3 21.0 1.0 CA B:LEU87 4.3 22.7 1.0 C B:VAL85 4.3 19.6 1.0 CB B:LEU87 4.4 20.6 1.0 O B:VAL85 4.4 23.0 1.0 CA B:HIS84 4.5 19.6 1.0 N B:SER88 4.6 28.8 1.0 C B:SER88 4.6 34.9 1.0 CA B:SER88 4.6 32.9 1.0 N B:GLN89 4.8 34.2 1.0 CB B:ASN83 4.9 24.0 1.0 O B:SER88 4.9 37.9 1.0

Sodium binding site 2 out of 2 in the Human Class I Mhc Hla-A2 in Complex with Mart-1(27-35) Nonameric 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 Mart-1(27-35) Nonameric Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Na100 b:33.8 occ:0.67 O E:HOH734 2.0 29.3 1.0 O E:HOH559 2.2 34.4 1.0 O E:HOH543 2.5 36.7 1.0 O E:LEU87 2.7 27.3 1.0 O E:HIS84 2.8 19.0 1.0 OD1 E:ASN83 2.9 25.4 1.0 CG E:ASN83 3.7 25.8 1.0 C E:HIS84 3.7 19.4 1.0 ND2 E:ASN83 3.9 31.3 1.0 C E:LEU87 3.9 25.1 1.0 CA E:VAL85 4.2 19.9 1.0 N E:HIS84 4.2 18.2 1.0 O E:VAL85 4.3 20.8 1.0 N E:VAL85 4.4 17.9 1.0 C E:VAL85 4.4 20.4 1.0 N E:LEU87 4.5 20.3 1.0 CA E:LEU87 4.6 22.5 1.0 CB E:LEU87 4.6 20.4 1.0 CA E:HIS84 4.7 18.8 1.0 N E:SER88 4.9 28.4 1.0 C E:SER88 4.9 32.3 1.0

F.K.Insaidoo, O.Y.Borbulevych, M.Hossain, S.M.Santhanagopolan, T.K.Baxter, B.M.Baker. Loss of T Cell Antigen Recognition Arising From Changes in Peptide and Major Histocompatibility Complex Protein Flexibility: Implications For Vaccine Design. J.Biol.Chem. V. 286 40163 2011.
ISSN: ISSN 0021-9258
PubMed: 21937447
DOI: 10.1074/JBC.M111.283564