Sodium in PDB 6tdr: Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Devoid of Peptide (Annealed)

The structure of Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Devoid of Peptide (Annealed), PDB code: 6tdr was solved by R.Anjanappa, M.Garcia Alai, S.Springer, R.Meijers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.89 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.728, 82.735, 83.891, 90.00, 90.06, 90.00
R / Rfree (%)	17.7 / 23

The binding sites of Sodium atom in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Devoid of Peptide (Annealed) (pdb code 6tdr). 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 the Disulfide Engineered Hla-A0201 Molecule Devoid of Peptide (Annealed), PDB code: 6tdr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Devoid of Peptide (Annealed)


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 the Disulfide Engineered Hla-A0201 Molecule Devoid of Peptide (Annealed) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:31.9 occ:1.00 O B:HIS85 2.2 20.9 1.0 O B:LEU88 2.3 28.9 1.0 O B:HOH352 2.3 38.6 1.0 O B:HOH454 2.4 33.1 1.0 O B:HOH320 2.6 30.6 1.0 OD1 B:ASN84 2.7 20.7 1.0 C B:HIS85 3.2 19.3 1.0 C B:LEU88 3.4 22.4 1.0 CG B:ASN84 3.8 20.4 1.0 N B:LEU88 3.8 19.9 1.0 N B:HIS85 3.9 17.6 1.0 CA B:VAL86 3.9 20.4 1.0 N B:VAL86 3.9 18.0 1.0 CA B:LEU88 3.9 20.8 1.0 O B:VAL86 4.0 20.7 1.0 C B:VAL86 4.0 18.7 1.0 CB B:LEU88 4.0 20.9 1.0 CA B:HIS85 4.2 17.8 1.0 ND2 B:ASN84 4.2 25.6 1.0 N B:SER89 4.5 27.8 1.0 N B:THR87 4.7 18.4 1.0 O B:HOH418 4.7 46.6 1.0 O B:HOH425 4.7 34.4 1.0 C B:SER89 4.7 29.2 1.0 CA B:SER89 4.8 26.3 1.0 C B:ASN84 4.9 18.4 1.0 N B:GLN90 4.9 27.5 0.4 N B:GLN90 4.9 25.2 0.6 C B:THR87 4.9 20.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Devoid of Peptide (Annealed)


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 the Disulfide Engineered Hla-A0201 Molecule Devoid of Peptide (Annealed) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:36.2 occ:1.00 O C:HOH635 2.3 30.6 1.0 OG C:SER11 2.8 22.0 1.0 O C:ARG21 3.2 22.1 1.0 CB C:SER11 3.3 20.1 1.0 CB C:PRO20 3.5 22.1 1.0 CB C:PHE22 3.6 18.4 1.0 CA C:SER11 3.8 15.6 1.0 CD1 C:PHE22 3.9 21.5 1.0 C C:ARG21 3.9 22.5 1.0 O C:SER71 4.0 21.9 1.0 CA C:PHE22 4.1 16.0 1.0 CG C:PHE22 4.2 21.4 1.0 CB C:HIS74 4.2 21.2 1.0 N C:ARG75 4.2 23.1 1.0 O C:PRO20 4.2 23.2 1.0 N C:PHE22 4.2 18.4 1.0 C C:PRO20 4.3 21.6 1.0 CG C:PRO20 4.4 24.2 1.0 CD1 C:LEU78 4.4 23.2 1.0 O C:HOH426 4.4 44.6 1.0 C C:HIS74 4.4 21.6 1.0 CA C:ARG75 4.5 24.1 1.0 C C:SER11 4.5 16.5 1.0 N C:VAL12 4.5 17.0 1.0 CA C:PRO20 4.6 21.9 1.0 N C:ARG21 4.7 22.5 1.0 CB C:ARG75 4.8 23.5 1.0 O C:HIS74 4.8 21.5 1.0 C C:SER71 4.9 21.9 1.0 CA C:HIS74 4.9 22.5 1.0 CA C:SER71 4.9 22.3 1.0 CA C:ARG21 5.0 23.7 1.0 N C:SER11 5.0 14.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule Devoid of Peptide (Annealed)


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 the Disulfide Engineered Hla-A0201 Molecule Devoid of Peptide (Annealed) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:24.2 occ:1.00 O D:LEU88 2.3 24.7 1.0 O D:HOH374 2.3 28.4 1.0 O D:HIS85 2.4 17.3 1.0 O D:HOH421 2.4 25.9 1.0 OD1 D:ASN84 2.6 22.3 1.0 O D:HOH428 2.7 30.6 1.0 C D:HIS85 3.3 15.1 1.0 CG D:ASN84 3.4 24.5 1.0 C D:LEU88 3.5 18.5 1.0 ND2 D:ASN84 3.7 29.5 1.0 N D:HIS85 3.9 17.5 1.0 CA D:VAL86 4.0 16.5 1.0 N D:VAL86 4.0 17.9 1.0 N D:LEU88 4.0 16.3 1.0 C D:VAL86 4.1 15.1 1.0 O D:VAL86 4.1 17.6 1.0 CA D:LEU88 4.1 17.5 1.0 CA D:HIS85 4.2 14.9 1.0 CB D:LEU88 4.2 18.2 1.0 N D:SER89 4.5 23.6 1.0 C D:SER89 4.6 25.6 1.0 CB D:ASN84 4.7 23.4 1.0 CA D:SER89 4.8 25.2 1.0 O D:SER89 4.8 25.2 1.0 N D:THR87 4.8 15.5 1.0 C D:ASN84 4.8 19.0 1.0 N D:GLN90 4.9 22.5 1.0

R.Anjanappa, M.Garcia-Alai, J.D.Kopicki, J.Lockhauserbaumer, M.Aboelmagd, J.Hinrichs, I.M.Nemtanu, C.Uetrecht, M.Zacharias, S.Springer, R.Meijers. Structures of Peptide-Free and Partially Loaded Mhc Class I Molecules Reveal Mechanisms of Peptide Selection. Nat Commun V. 11 1314 2020.
ISSN: ESSN 2041-1723
PubMed: 32161266
DOI: 10.1038/S41467-020-14862-4