Sodium in PDB 7lfi: Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide Refined at 1.70 Angstroms Resolution

All present enzymatic activity of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide Refined at 1.70 Angstroms Resolution:
7.1.1.2;

The structure of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide Refined at 1.70 Angstroms Resolution, PDB code: 7lfi was solved by D.R.Tomchick, J.Deisenhofer, S.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.53 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.567, 68.646, 54.973, 101.99, 95.1, 113.5
R / Rfree (%)	22.3 / 25.9

The binding sites of Sodium atom in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide Refined at 1.70 Angstroms Resolution (pdb code 7lfi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide Refined at 1.70 Angstroms Resolution, PDB code: 7lfi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide Refined at 1.70 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide Refined at 1.70 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2002 b:28.1 occ:1.00 H A:GLY120 2.1 19.0 1.0 OE1 A:GLN96 2.2 10.4 1.0 N A:GLY120 2.9 15.7 1.0 HG3 A:GLN96 3.0 22.3 1.0 HA2 A:GLY120 3.1 19.8 1.0 CD A:GLN96 3.1 11.5 1.0 HG22 A:ILE94 3.2 25.1 1.0 HB2 A:GLN96 3.2 14.5 1.0 HB1 A:ALA117 3.4 27.3 1.0 O A:ALA117 3.4 15.1 1.0 CG A:GLN96 3.4 18.4 1.0 H A:ASP119 3.4 22.2 1.0 H A:GLN96 3.4 16.8 1.0 HB A:ILE94 3.4 20.5 1.0 HB3 A:ALA117 3.5 27.3 1.0 CA A:GLY120 3.5 16.3 1.0 N A:ASP119 3.6 18.4 1.0 C A:ALA117 3.6 16.9 1.0 O A:ILE94 3.7 17.0 1.0 CB A:GLN96 3.8 11.9 1.0 HA A:TYR118 3.8 19.4 1.0 N A:GLN96 3.8 13.8 1.0 CB A:ALA117 3.8 22.6 1.0 NE2 B:HIS31 3.9 27.6 1.0 CG2 A:ILE94 3.9 20.8 1.0 C A:TYR118 3.9 20.6 1.0 HA A:ASP119 3.9 23.4 1.0 C A:ASP119 4.0 24.3 1.0 HA A:LEU95 4.0 19.4 1.0 HG21 A:ILE94 4.0 25.1 1.0 N A:TYR118 4.0 15.9 1.0 C A:ILE94 4.1 20.6 1.0 HE1 B:HIS31 4.1 24.5 1.0 CA A:ASP119 4.1 19.4 1.0 CB A:ILE94 4.1 16.9 1.0 CA A:TYR118 4.1 16.0 1.0 HA3 A:GLY120 4.2 19.8 1.0 HB3 B:TRP60 4.3 21.8 1.0 HG2 A:GLN96 4.3 22.3 1.0 NE2 A:GLN96 4.3 13.0 1.0 CE1 B:HIS31 4.3 20.3 1.0 C A:LEU95 4.4 14.7 1.0 CA A:ALA117 4.4 14.0 1.0 CA A:GLN96 4.4 15.0 1.0 N A:LEU95 4.4 21.6 1.0 H A:SER121 4.4 21.4 1.0 CA A:LEU95 4.5 16.1 1.0 C A:GLY120 4.5 15.5 1.0 H A:TYR118 4.5 19.3 1.0 HE22 A:GLN96 4.6 15.8 1.0 HB3 A:GLN96 4.6 14.5 1.0 O A:TYR118 4.7 14.7 1.0 HB2 A:ALA117 4.7 27.3 1.0 HG23 A:ILE94 4.7 25.1 1.0 CA A:ILE94 4.8 14.3 1.0 N A:SER121 4.8 17.7 1.0 H A:ALA117 4.9 18.7 1.0 HE21 A:GLN96 5.0 15.8 1.0

Sodium binding site 2 out of 2 in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide Refined at 1.70 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide Refined at 1.70 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:42.9 occ:1.00 OH E:TYR26 2.3 27.4 1.0 HE2 E:TYR26 2.8 33.2 1.0 O D:THR233 3.0 24.2 1.0 CZ E:TYR26 3.2 20.8 1.0 CE2 E:TYR26 3.3 27.6 1.0 HG21 E:THR28 3.7 26.6 1.0 HB3 D:GLU232 4.0 35.6 1.0 OE1 D:GLU232 4.1 41.3 1.0 HA D:ARG234 4.1 31.4 1.0 C D:THR233 4.2 21.7 1.0 O E:HOH236 4.3 34.4 1.0 HD3 D:PRO235 4.4 28.4 1.0 CE1 E:TYR26 4.5 22.8 1.0 HG22 E:THR28 4.6 26.6 1.0 CG2 E:THR28 4.6 22.0 1.0 CD2 E:TYR26 4.7 22.1 1.0 HB D:THR233 4.7 32.2 1.0 CB D:GLU232 4.8 29.5 1.0 HE1 E:TYR26 4.8 27.6 1.0 HB2 D:GLU232 4.8 35.6 1.0 CA D:ARG234 5.0 26.0 1.0

A.Strand, S.T.Shen, D.R.Tomchick, J.Wang, C.R.Wang, J.Deisenhofer. Structure and Dynamics of Major Histocompatibility Class Ib Molecule H2-M3 Complexed with Mitochondrial-Derived Peptides. J.Biomol.Struct.Dyn. 1 2021.
ISSN: ESSN 1538-0254
PubMed: 34176438
DOI: 10.1080/07391102.2021.1942214