Sodium in PDB 4lcy: Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution

The structure of Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution, PDB code: 4lcy was solved by J.X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.20 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.950, 89.730, 94.620, 90.00, 98.45, 90.00
R / Rfree (%)	17.2 / 20.1

The binding sites of Sodium atom in the Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution (pdb code 4lcy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution, PDB code: 4lcy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution


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 Hla-B46 at 1.6 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:22.2 occ:1.00 O A:HOH424 2.5 17.4 1.0 OG1 A:THR187 2.8 13.5 1.0 O F:HOH708 2.8 34.2 1.0 O A:PRO185 3.1 12.7 1.0 CD1 A:LEU270 3.5 19.1 1.0 N A:THR187 3.5 10.9 1.0 CG2 A:THR187 3.6 11.9 1.0 CB A:THR187 3.6 12.1 1.0 CG F:PRO267 3.9 22.0 1.0 O A:HOH449 3.9 19.0 1.0 CA A:LYS186 4.0 11.2 1.0 C A:PRO185 4.1 10.9 1.0 CD F:PRO267 4.1 21.2 1.0 CA A:THR187 4.1 11.6 1.0 C A:LYS186 4.2 11.7 1.0 O A:HOH452 4.2 14.7 1.0 O A:HOH764 4.4 40.2 1.0 N A:LYS186 4.5 11.5 1.0 CB F:PRO267 4.6 21.9 1.0 O F:HOH428 4.6 22.4 1.0 CG A:LEU270 4.8 17.6 1.0 O A:HOH592 4.9 31.3 1.0 O A:THR187 4.9 15.2 1.0 C A:THR187 5.0 12.6 1.0 O F:HOH565 5.0 25.7 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution


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 Hla-B46 at 1.6 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:26.2 occ:1.00 O A:ALA158 2.8 11.9 1.0 O C:HOH106 3.0 18.9 1.0 N A:LEU163 3.1 12.2 1.0 CG A:LEU163 3.5 14.4 1.0 C A:ALA158 3.6 10.4 1.0 CD1 A:LEU163 3.7 15.0 1.0 CB A:LEU163 3.7 13.3 1.0 CA A:GLY162 3.7 12.3 1.0 CA A:TYR159 3.8 9.0 1.0 C A:GLY162 3.9 12.1 1.0 N A:TYR159 4.0 9.2 1.0 O A:HOH561 4.0 21.8 1.0 CA A:LEU163 4.0 11.5 1.0 O A:TYR159 4.2 9.5 1.0 N A:GLY162 4.3 12.0 1.0 O A:HOH618 4.3 37.4 1.0 O A:HOH713 4.4 45.2 1.0 C A:TYR159 4.4 9.0 1.0 CA A:ALA158 4.7 10.2 1.0 CB A:ALA158 4.7 10.8 1.0 CD2 A:LEU163 4.8 15.6 1.0 CB A:TYR159 4.9 8.3 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution


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 Hla-B46 at 1.6 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:31.1 occ:1.00 O A:HOH604 2.2 25.7 1.0 O B:HOH302 2.6 37.1 1.0 O B:ASP59 2.9 13.2 1.0 O A:HOH560 2.9 33.3 1.0 C B:ASP59 3.7 12.5 1.0 NH1 B:ARG3 3.7 34.1 1.0 CB B:ASP59 3.7 15.6 1.0 CA B:ASP59 3.8 14.6 1.0 O A:HOH576 3.8 27.1 1.0 NH2 B:ARG3 4.1 26.3 1.0 CD1 B:TRP60 4.1 9.8 1.0 O A:HOH705 4.1 44.4 1.0 CZ B:ARG3 4.1 29.5 1.0 O A:GLY120 4.2 14.1 1.0 O B:HOH357 4.6 36.4 1.0 O B:HOH337 4.7 44.6 1.0 CG B:ASP59 4.7 17.2 1.0 N B:TRP60 4.9 10.7 1.0 NE1 B:TRP60 5.0 9.9 1.0 CG B:TRP60 5.0 9.4 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution


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 Hla-B46 at 1.6 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:20.7 occ:1.00 O F:HOH515 2.4 25.3 1.0 O F:SER88 2.7 11.0 1.0 NE2 F:HIS93 2.8 9.1 1.0 N F:GLY91 3.1 13.6 1.0 CA F:GLY91 3.3 12.7 1.0 C F:SER88 3.5 12.0 1.0 O F:GLY91 3.7 12.5 1.0 CE1 F:HIS93 3.7 8.3 1.0 CD2 F:HIS93 3.7 8.8 1.0 OG F:SER88 3.8 12.7 1.0 N F:SER88 3.8 10.2 1.0 C F:GLY91 3.8 11.4 1.0 CB F:GLN87 3.9 8.9 1.0 CA F:SER88 4.1 11.3 1.0 O F:HOH452 4.2 19.3 1.0 N F:ALA90 4.2 14.2 1.0 O F:HOH606 4.2 37.3 1.0 C F:ALA90 4.3 14.7 1.0 C F:GLN87 4.3 8.9 1.0 C F:GLU89 4.5 15.8 1.0 N F:GLU89 4.5 14.1 1.0 CB F:SER88 4.6 12.6 1.0 CA F:GLN87 4.6 8.7 1.0 CD F:ARG82 4.7 10.7 1.0 CG F:GLN87 4.7 9.4 1.0 CA F:ALA90 4.8 14.5 1.0 CA F:GLU89 4.8 16.1 1.0 ND1 F:HIS93 4.9 8.2 1.0 CG F:HIS93 4.9 8.0 1.0 O F:HOH648 4.9 31.2 1.0 O F:GLN87 5.0 9.3 1.0 N F:SER92 5.0 10.8 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Na302 b:22.4 occ:1.00 OD2 F:ASP119 2.7 10.4 1.0 O H:HOH276 2.9 30.4 1.0 NE2 F:GLN87 3.0 12.3 1.0 O F:HOH578 3.3 31.3 1.0 CE2 F:TYR118 3.5 6.5 1.0 CG F:ASP119 3.6 8.7 1.0 CD2 F:TYR118 3.8 6.3 1.0 CB F:ASP119 3.8 8.4 1.0 O H:HOH385 4.1 30.1 1.0 CD F:GLN87 4.2 10.1 1.0 CZ F:TYR118 4.3 6.2 1.0 ND1 F:HIS93 4.4 8.2 1.0 OE1 F:GLN87 4.6 9.6 1.0 CE1 F:HIS93 4.6 8.3 1.0 N H:MET0 4.7 37.8 1.0 CG F:TYR118 4.8 6.2 1.0 OH F:TYR118 4.8 7.0 1.0 O F:HOH606 4.8 37.3 1.0 OD1 F:ASP119 4.8 8.3 1.0 O F:HOH522 4.9 28.5 1.0 O F:HOH639 4.9 39.3 1.0 CE H:MET0 4.9 28.3 1.0 CA H:MET0 5.0 34.6 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Hla-B46 at 1.6 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ H:Na101 b:30.6 occ:1.00 N H:LYS58 3.1 14.4 1.0 CB H:LYS58 3.6 20.7 1.0 CB H:SER57 3.7 12.7 1.0 CA H:SER57 3.7 11.8 1.0 O H:HOH266 3.8 22.3 1.0 C H:SER57 3.9 12.7 1.0 CA H:LYS58 3.9 17.4 1.0 O H:HOH242 4.0 30.2 1.0 OG H:SER57 4.2 14.8 1.0 O F:HOH749 4.8 34.6 1.0

J.X.Liu, J.X.Liu. N/A N/A.