Sodium in PDB 6iwg: Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein

The structure of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein, PDB code: 6iwg was solved by Y.Yamamoto, D.Morita, M.Sugita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.70 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.823, 81.756, 106.635, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.5

The binding sites of Sodium atom in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein (pdb code 6iwg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein, PDB code: 6iwg:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:31.5 occ:1.00 O A:LEU266 2.2 22.5 1.0 OE1 A:GLN262 2.4 28.4 1.0 O A:HIS263 2.5 18.5 1.0 O A:HOH563 2.5 36.5 1.0 O A:HOH472 2.5 38.9 1.0 CD A:GLN262 3.0 38.0 1.0 NE2 A:GLN262 3.3 37.3 1.0 C A:LEU266 3.4 25.5 1.0 C A:HIS263 3.6 16.1 1.0 O A:HOH591 3.9 43.5 1.0 N A:HIS263 4.1 18.3 1.0 CG A:GLN262 4.1 30.8 1.0 CA A:LEU266 4.1 23.9 1.0 N A:LEU266 4.1 19.5 1.0 CB A:LEU266 4.2 22.6 1.0 O A:PRO267 4.2 25.0 1.0 CA A:GLU264 4.3 15.7 1.0 O A:GLU264 4.3 21.1 1.0 C A:PRO267 4.3 24.4 1.0 N A:GLU264 4.3 17.3 1.0 C A:GLU264 4.4 18.4 1.0 N A:PRO267 4.5 23.4 1.0 CA A:HIS263 4.5 17.8 1.0 CA A:PRO267 4.6 22.4 1.0 N A:GLU268 4.7 24.5 1.0 C A:GLU268 4.9 23.3 1.0 O A:GLU268 5.0 28.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:33.9 occ:1.00 OE2 A:GLU264 2.0 41.8 1.0 CD A:GLU264 2.8 30.5 1.0 O1 A:EDO310 2.8 47.8 1.0 O A:HOH564 2.8 39.1 1.0 OE1 A:GLU264 2.9 46.8 1.0 O2 A:EDO310 3.0 35.5 1.0 C1 A:EDO310 3.8 35.7 1.0 C2 A:EDO310 3.9 29.7 1.0 CG A:GLU264 4.2 20.9 1.0 CA A:GLY1 4.5 36.6 1.0 O A:HOH403 4.7 33.9 1.0 CE1 A:HIS3 5.0 25.7 1.0 O A:SER2 5.0 28.3 0.5 O A:SER2 5.0 27.6 0.5

Sodium binding site 3 out of 4 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:27.6 occ:1.00 O1 A:EDO313 2.0 47.1 1.0 OD2 A:ASP183 2.0 46.5 1.0 CG A:ASP183 2.8 38.0 1.0 O2 A:EDO313 2.9 40.8 1.0 OD1 A:ASP183 3.0 41.4 1.0 C1 A:EDO313 3.2 25.7 1.0 C2 A:EDO313 3.8 29.5 1.0 CB A:HIS181 4.1 34.6 1.0 O A:THR178 4.2 22.9 1.0 CB A:ASP183 4.2 20.1 1.0 O A:HIS181 4.3 31.3 1.0 O A:HOH419 4.7 47.8 1.0 CA A:THR178 4.7 28.1 1.0 ND1 A:HIS181 4.9 64.8 1.0 CB A:TYR209 4.9 15.2 1.0 C A:THR178 4.9 23.2 1.0 CG A:HIS181 5.0 55.8 1.0 C A:HIS181 5.0 29.8 1.0 CB A:THR178 5.0 29.7 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with N-Myristoylated 4-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:22.8 occ:1.00 O B:LEU87 2.3 20.8 1.0 O B:HOH209 2.4 18.2 1.0 O B:HOH287 2.4 25.9 1.0 O B:HIS84 2.5 15.6 1.0 O B:HOH255 2.5 24.0 1.0 O B:HOH278 2.6 27.1 1.0 C B:LEU87 3.4 25.8 1.0 C B:HIS84 3.5 15.6 1.0 N B:HIS84 3.9 16.5 1.0 N B:LEU87 4.0 22.8 1.0 CA B:LEU87 4.0 19.7 1.0 N B:GLY89 4.0 26.9 1.0 CB B:LEU87 4.1 15.2 1.0 O B:VAL85 4.2 21.7 1.0 CA B:VAL85 4.2 17.3 1.0 N B:VAL85 4.3 16.2 1.0 C B:VAL85 4.3 20.7 1.0 CA B:HIS84 4.4 15.2 1.0 N B:SER88 4.5 25.0 1.0 ND2 B:ASN83 4.5 31.1 1.0 CA B:SER88 4.6 30.5 1.0 O B:HOH288 4.6 41.7 1.0 O B:GLY89 4.7 23.4 1.0 CA B:GLY89 4.8 24.3 1.0 C B:SER88 4.8 35.7 1.0 C B:ASN83 4.9 18.9 1.0 C B:GLY89 4.9 24.0 1.0 N B:THR86 5.0 16.1 1.0

Y.Yamamoto, D.Morita, Y.Shima, A.Midorikawa, T.Mizutani, J.Suzuki, N.Mori, T.Shiina, H.Inoko, Y.Tanaka, B.Mikami, M.Sugita. Identification and Structure of An Mhc Class I-Encoded Protein with the Potential to Presentn-Myristoylated 4-Mer Peptides to T Cells. J Immunol. V. 202 3349 2019.
ISSN: ESSN 1550-6606
PubMed: 31043477
DOI: 10.4049/JIMMUNOL.1900087