Sodium in PDB 8qyi: Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions

The structure of Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions, PDB code: 8qyi was solved by F.Fata, A.Costanzo, I.Freda, E.Gugole, G.Bulfaro, L.Barbizzi, M.Di Renzo, C.Savino, B.Vallone, L.C.Montemiglio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.01 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	249.373, 109.269, 160.658, 90, 129.6, 90
R / Rfree (%)	17.3 / 22.2

The structure of Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Sodium atom in the Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions (pdb code 8qyi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions, PDB code: 8qyi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na525 b:50.5 occ:1.00 O A:HOH682 2.7 29.5 1.0 O A:HOH660 2.8 33.6 1.0 N A:VAL297 3.2 31.1 1.0 CG A:PHE296 3.6 31.7 1.0 CD2 A:PHE296 3.6 32.1 1.0 CA A:PHE296 3.6 30.6 1.0 CZ A:PHE84 3.7 35.1 1.0 CD1 A:PHE296 3.8 30.6 1.0 CE2 A:PHE84 3.8 32.2 1.0 CB A:ARG82 3.8 35.3 1.0 CE2 A:PHE296 3.9 31.7 1.0 CB A:VAL297 3.9 33.5 1.0 C A:PHE296 3.9 32.3 1.0 CG2 A:VAL297 3.9 33.6 1.0 CE1 A:PHE296 4.0 30.1 1.0 CZ A:PHE296 4.0 32.0 1.0 CA A:VAL297 4.1 33.1 1.0 CB A:PHE296 4.2 31.5 1.0 CG A:PRO88 4.2 42.1 1.0 CA A:ARG82 4.3 36.3 1.0 O A:SER295 4.5 32.5 1.0 O A:PRO81 4.6 34.7 1.0 CE1 A:PHE84 4.7 36.9 1.0 N A:PHE296 4.7 30.7 1.0 CD2 A:PHE84 4.9 32.9 1.0 O A:VAL297 4.9 31.9 1.0 N A:MET83 5.0 36.2 1.0 O A:ALA75 5.0 44.2 1.0 CB A:ALA75 5.0 42.8 1.0

Sodium binding site 2 out of 6 in the Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na525 b:43.8 occ:1.00 O B:HOH665 2.6 32.4 1.0 O B:HOH687 2.9 35.5 1.0 N B:VAL297 3.2 33.1 1.0 CG B:PHE296 3.7 29.3 1.0 CD2 B:PHE296 3.7 30.6 1.0 CZ B:PHE84 3.7 41.6 1.0 CB B:ARG82 3.8 36.2 1.0 CA B:PHE296 3.8 29.1 1.0 CD1 B:PHE296 3.8 28.8 1.0 CB B:VAL297 3.8 35.1 1.0 CE2 B:PHE296 3.8 31.6 1.0 CE2 B:PHE84 3.9 38.8 1.0 CE1 B:PHE296 3.9 29.8 1.0 CZ B:PHE296 4.0 31.8 1.0 CG2 B:VAL297 4.0 35.0 1.0 C B:PHE296 4.0 31.1 1.0 CG B:PRO88 4.1 46.7 1.0 CA B:VAL297 4.1 33.3 1.0 CA B:ARG82 4.2 34.1 1.0 CB B:PHE296 4.3 30.1 1.0 O B:PRO81 4.4 37.4 1.0 CB B:ALA75 4.7 37.8 1.0 O B:ALA75 4.7 39.5 1.0 CE1 B:PHE84 4.8 42.6 1.0 O B:VAL297 4.8 30.3 1.0 O B:SER295 4.9 30.8 1.0 N B:PHE296 4.9 27.9 1.0 CD2 B:PHE84 5.0 38.9 1.0

Sodium binding site 3 out of 6 in the Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ C:Na527 b:44.8 occ:1.00 O C:HOH701 2.8 34.6 1.0 O C:HOH717 3.0 32.2 1.0 N C:VAL297 3.0 37.6 1.0 CD2 C:PHE296 3.5 35.1 1.0 CG C:PHE296 3.6 35.1 1.0 CA C:PHE296 3.6 31.7 1.0 CE2 C:PHE296 3.6 35.7 1.0 CD1 C:PHE296 3.7 34.0 1.0 C C:PHE296 3.8 36.5 1.0 CZ C:PHE84 3.8 39.8 1.0 CE2 C:PHE84 3.8 38.5 1.0 CZ C:PHE296 3.8 37.3 1.0 CB C:VAL297 3.9 38.2 1.0 CE1 C:PHE296 3.9 36.3 1.0 CA C:VAL297 4.0 36.0 1.0 CB C:ARG82 4.1 36.3 1.0 CG2 C:VAL297 4.2 41.5 1.0 CB C:PHE296 4.2 33.8 1.0 CA C:ARG82 4.4 36.2 1.0 CG C:PRO88 4.5 44.5 1.0 O C:PRO81 4.5 37.6 1.0 O C:SER295 4.6 32.5 1.0 O C:VAL297 4.6 36.6 1.0 CB C:ALA75 4.7 39.5 1.0 N C:PHE296 4.8 32.2 1.0 O C:ALA75 4.8 42.4 1.0 CE1 C:PHE84 4.9 39.6 1.0 C C:VAL297 4.9 35.9 1.0 CD2 C:PHE84 4.9 39.2 1.0

Sodium binding site 4 out of 6 in the Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ D:Na516 b:50.7 occ:1.00 O D:HOH669 2.5 39.8 1.0 O D:HOH623 3.0 45.6 1.0 N D:VAL297 3.1 46.5 1.0 CB D:ARG82 3.6 51.0 1.0 CA D:PHE296 3.7 41.5 1.0 CB D:VAL297 3.7 47.0 1.0 CZ D:PHE84 3.7 44.5 1.0 CG D:PHE296 3.7 38.6 1.0 CE2 D:PHE84 3.7 45.2 1.0 CD1 D:PHE296 3.8 40.1 1.0 CD2 D:PHE296 3.9 40.2 1.0 CG2 D:VAL297 3.9 48.0 1.0 C D:PHE296 3.9 45.3 1.0 CA D:VAL297 4.0 45.6 1.0 CE2 D:PHE296 4.1 40.5 1.0 CA D:ARG82 4.1 49.9 1.0 CE1 D:PHE296 4.1 41.7 1.0 CZ D:PHE296 4.2 42.6 1.0 CB D:PHE296 4.3 39.9 1.0 O D:PRO81 4.4 49.5 1.0 O D:SER295 4.6 39.7 1.0 CE1 D:PHE84 4.8 46.6 1.0 O D:VAL297 4.8 44.0 1.0 N D:PHE296 4.8 40.3 1.0 CD2 D:PHE84 4.8 46.0 1.0 O D:ALA75 4.9 50.6 1.0 N D:MET83 4.9 45.9 1.0 C D:VAL297 4.9 45.1 1.0 CG1 D:VAL297 4.9 48.5 1.0 CG D:PRO88 5.0 52.6 1.0 CG D:ARG82 5.0 52.5 1.0

Sodium binding site 5 out of 6 in the Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ E:Na513 b:61.8 occ:1.00 O E:HOH630 2.8 54.8 1.0 O E:HOH638 2.9 54.7 1.0 N E:VAL297 3.3 52.2 1.0 CZ E:PHE84 3.7 53.4 1.0 CB E:VAL297 3.7 54.5 1.0 CG E:PHE296 3.8 48.2 1.0 CB E:ARG82 3.8 55.8 1.0 CD2 E:PHE296 3.8 48.0 1.0 CD1 E:PHE296 3.8 48.0 1.0 CE2 E:PHE296 3.9 48.0 1.0 CA E:PHE296 3.9 50.9 1.0 CE1 E:PHE296 3.9 48.5 1.0 CG2 E:VAL297 3.9 53.8 1.0 CZ E:PHE296 4.0 49.2 1.0 CE2 E:PHE84 4.0 52.9 1.0 CG E:PRO88 4.1 55.6 1.0 C E:PHE296 4.1 52.1 1.0 CA E:VAL297 4.1 53.7 1.0 CA E:ARG82 4.3 56.5 1.0 CB E:PHE296 4.4 48.6 1.0 O E:PRO81 4.5 57.0 1.0 CB E:ALA75 4.6 60.2 1.0 CE1 E:PHE84 4.6 54.5 1.0 O E:SER295 4.8 56.5 1.0 O E:ALA75 4.9 60.0 1.0 CG1 E:VAL297 5.0 57.3 1.0 O E:VAL297 5.0 53.9 1.0

Sodium binding site 6 out of 6 in the Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Olep in Complex with Lithocholic Acid in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ F:Na514 b:55.7 occ:1.00 O F:HOH617 2.6 50.6 1.0 O F:HOH641 2.9 48.3 1.0 N F:VAL297 3.1 44.1 1.0 CG F:PHE296 3.6 48.4 1.0 CD1 F:PHE296 3.6 47.0 1.0 CD2 F:PHE296 3.6 50.7 1.0 CB F:VAL297 3.7 45.7 1.0 CA F:PHE296 3.7 45.8 1.0 CZ F:PHE84 3.7 51.6 1.0 CE1 F:PHE296 3.8 49.6 1.0 CE2 F:PHE296 3.8 49.4 1.0 CZ F:PHE296 3.8 47.7 1.0 CG2 F:VAL297 3.9 49.0 1.0 CB F:ARG82 3.9 47.0 1.0 C F:PHE296 3.9 44.2 1.0 CA F:VAL297 4.1 43.7 1.0 CE2 F:PHE84 4.1 53.4 1.0 CB F:PHE296 4.2 46.9 1.0 CG F:PRO88 4.3 52.3 1.0 CA F:ARG82 4.3 47.5 1.0 O F:PRO81 4.3 46.8 1.0 CE1 F:PHE84 4.6 55.4 1.0 O F:ALA75 4.6 52.6 1.0 CB F:ALA75 4.6 51.1 1.0 O F:SER295 4.7 46.3 1.0 O F:VAL297 4.8 44.6 1.0 N F:PHE296 4.9 46.1 1.0 C F:VAL297 5.0 44.6 1.0

F.Fata, A.Costanzo, I.Freda, E.Gugole, G.Bulfaro, L.Barbizzi, M.Di Renzo, C.Savino, B.Vallone, L.C.Montemiglio. Olep in Complex with Lithocolic Acid in High Salt Crystallization Conditions To Be Published.