Sodium in PDB 7rj9: Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium

The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium, PDB code: 7rj9 was solved by A.E.Aleshin, F.M.Marassi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.69 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.832, 125.575, 40.883, 90, 119.25, 90
R / Rfree (%)	17.1 / 21

The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium (pdb code 7rj9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium, PDB code: 7rj9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium


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 Vitronectin Hemopexin-Like Domain Binding Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:11.9 occ:1.00 O A:ALA209 2.3 12.5 1.0 O A:PHE164 2.3 17.4 1.0 O A:ALA349 2.3 15.4 1.0 O A:ALA257 2.3 13.9 1.0 CL A:CL502 2.8 13.9 1.0 C A:ALA349 3.4 15.7 1.0 C A:ALA209 3.5 13.7 1.0 C A:PHE164 3.5 16.9 1.0 C A:ALA257 3.5 12.8 1.0 N A:PHE164 4.1 15.0 1.0 N A:ALA209 4.1 12.9 1.0 N A:ALA257 4.2 12.2 1.0 N A:ALA349 4.2 13.2 1.0 CA A:PHE164 4.3 17.1 1.0 OD1 A:ASP166 4.3 25.5 1.0 CA A:ALA209 4.3 13.5 1.0 N A:MET350 4.3 16.1 1.0 CA A:ALA349 4.3 14.3 1.0 CA A:MET350 4.4 17.8 1.0 CA A:ALA257 4.4 12.2 1.0 N A:LEU258 4.4 13.3 1.0 N A:PHE210 4.4 12.9 1.0 CA A:LEU258 4.5 13.9 1.0 N A:THR165 4.5 18.5 1.0 CA A:PHE210 4.5 15.0 1.0 CB A:PHE164 4.5 16.7 1.0 C A:THR165 4.6 21.9 1.0 CA A:THR165 4.6 19.2 1.0 CB A:ALA209 4.7 14.4 1.0 CB A:ALA349 4.7 14.6 1.0 O A:THR165 4.8 25.2 1.0 CB A:LEU258 4.8 14.8 1.0 CB A:PHE210 4.8 14.4 1.0 CG A:ASP166 4.9 21.7 1.0 CB A:ALA257 4.9 12.6 1.0 OD2 A:ASP166 5.0 22.8 1.0 N A:ASP166 5.0 20.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium


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 Vitronectin Hemopexin-Like Domain Binding Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:11.3 occ:1.00 O B:ALA209 2.3 11.1 1.0 O B:ALA349 2.3 12.7 1.0 O B:PHE164 2.3 12.9 1.0 O B:ALA257 2.4 11.1 1.0 O2 B:SO4504 2.6 27.4 0.8 CL B:CL502 2.9 12.9 1.0 C B:ALA349 3.4 14.2 1.0 C B:ALA209 3.5 11.1 1.0 C B:PHE164 3.5 13.4 1.0 C B:ALA257 3.6 12.7 1.0 S B:SO4504 4.0 26.8 0.8 N B:PHE164 4.2 11.8 1.0 N B:ALA209 4.2 10.1 1.0 CA B:MET350 4.2 17.8 1.0 N B:MET350 4.3 15.7 1.0 N B:ALA349 4.3 11.0 1.0 N B:ALA257 4.3 12.2 1.0 CA B:ALA209 4.3 11.7 1.0 CA B:PHE164 4.4 13.6 1.0 N B:PHE210 4.4 10.4 1.0 CA B:ALA349 4.4 12.9 1.0 CA B:PHE210 4.4 11.0 1.0 CA B:LEU258 4.4 14.3 1.0 N B:THR165 4.5 15.0 1.0 CA B:ALA257 4.5 11.2 1.0 N B:LEU258 4.5 11.6 1.0 CA B:THR165 4.5 15.0 1.0 O3 B:SO4504 4.6 27.4 0.8 CB B:THR165 4.6 16.3 1.0 CB B:ALA209 4.7 13.5 1.0 CB B:MET350 4.7 19.7 1.0 CB B:PHE210 4.7 11.2 1.0 O1 B:SO4504 4.7 34.2 0.8 CB B:LEU258 4.7 16.5 1.0 O4 B:SO4504 4.7 24.8 0.8 CB B:PHE164 4.8 14.1 1.0 CB B:ALA349 4.9 12.7 1.0 CB B:ALA257 4.9 12.2 1.0

A.E.Aleshin, F.M.Marassi. Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium To Be Published.