Sodium in PDB 7u68: Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Sodium-2

The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Sodium-2, PDB code: 7u68 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)	35.52 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.582, 124.905, 40.778, 90, 119.5, 90
R / Rfree (%)	18.4 / 24.7

The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Sodium-2 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Sodium-2 (pdb code 7u68). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Sodium-2, PDB code: 7u68:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Sodium-2


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 Sodium-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:24.4 occ:1.00 O A:ASP255 2.1 21.3 1.0 O A:ASP347 2.1 22.2 1.0 O A:ASP207 2.2 23.4 1.0 O A:ASP162 2.2 26.0 1.0 C A:ASP347 3.2 24.3 1.0 C A:ASP255 3.3 22.1 1.0 C A:ASP207 3.3 25.3 1.0 C A:ASP162 3.4 26.0 1.0 N A:ALA348 4.1 22.5 1.0 CA A:ASP255 4.1 23.7 1.0 CA A:ASP207 4.1 28.2 1.0 CA A:ALA348 4.2 22.1 1.0 N A:ALA256 4.2 19.7 1.0 CA A:ASP162 4.2 29.0 1.0 CA A:ASP347 4.2 27.5 1.0 N A:ALA208 4.2 22.9 1.0 CB A:ALA348 4.4 21.1 1.0 N A:ALA163 4.4 25.7 1.0 CA A:ALA256 4.4 18.9 1.0 CA A:ALA208 4.4 21.1 1.0 CA A:ALA163 4.5 22.8 1.0 CL A:CL503 4.7 22.7 1.0 CB A:ALA163 4.7 21.2 1.0 CB A:ALA208 4.8 20.8 1.0 CB A:ALA256 4.8 19.5 1.0 CB A:ASP162 4.9 32.3 1.0 O A:VAL254 5.0 22.6 1.0 CB A:ASP347 5.0 31.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Sodium-2


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 Sodium-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:21.0 occ:1.00 O A:ALA209 2.3 19.8 1.0 O A:PHE164 2.3 20.1 1.0 O A:ALA257 2.4 20.4 1.0 O A:ALA349 2.4 20.7 1.0 O2 A:SO4504 2.5 28.5 1.0 CL A:CL503 3.1 22.7 1.0 C A:ALA209 3.4 22.3 1.0 C A:ALA349 3.5 23.8 1.0 C A:PHE164 3.5 25.8 1.0 C A:ALA257 3.5 19.5 1.0 S A:SO4504 4.0 28.6 1.0 CA A:MET350 4.2 28.5 1.0 N A:ALA209 4.2 19.9 1.0 CA A:THR165 4.3 30.5 1.0 N A:MET350 4.3 24.8 1.0 N A:PHE210 4.3 22.5 1.0 CA A:ALA209 4.3 21.5 1.0 N A:ALA257 4.3 18.8 1.0 N A:ALA349 4.3 22.5 1.0 CA A:PHE210 4.3 22.4 1.0 N A:THR165 4.3 29.6 1.0 CA A:LEU258 4.4 23.2 1.0 N A:LEU258 4.4 21.3 1.0 N A:PHE164 4.4 22.3 1.0 CA A:ALA349 4.4 22.7 1.0 O1 A:SO4504 4.4 29.9 1.0 CA A:ALA257 4.5 19.2 1.0 CA A:PHE164 4.5 26.6 1.0 CB A:PHE210 4.6 22.4 1.0 O4 A:SO4504 4.6 26.8 1.0 CB A:MET350 4.6 32.6 1.0 CB A:ALA209 4.7 23.0 1.0 CB A:THR165 4.7 29.4 1.0 CB A:ALA349 4.8 21.1 1.0 CB A:LEU258 4.8 23.2 1.0 CB A:PHE164 4.8 28.1 1.0 O3 A:SO4504 4.9 28.0 1.0 CB A:ALA257 5.0 19.6 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Sodium-2


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 Vitronectin Hemopexin-Like Domain Binding Sodium-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:15.0 occ:1.00 O B:ALA209 2.2 15.1 1.0 O B:PHE164 2.2 20.1 1.0 O B:ALA257 2.3 16.7 1.0 O B:ALA349 2.4 18.4 1.0 O1 B:SO4504 2.4 23.7 1.0 CL B:CL503 3.0 18.4 1.0 C B:ALA209 3.4 15.0 1.0 C B:PHE164 3.5 19.4 1.0 C B:ALA257 3.5 16.7 1.0 C B:ALA349 3.5 17.5 1.0 S B:SO4504 3.8 22.6 1.0 CA B:LEU258 4.2 18.2 1.0 N B:ALA209 4.3 15.5 1.0 N B:PHE210 4.3 15.3 1.0 CA B:THR165 4.3 19.9 1.0 CA B:MET350 4.3 21.6 1.0 CA B:PHE210 4.3 16.9 1.0 N B:MET350 4.3 18.4 1.0 N B:LEU258 4.3 16.6 1.0 N B:ALA257 4.3 16.8 1.0 CA B:ALA209 4.3 15.5 1.0 N B:THR165 4.3 18.8 1.0 N B:PHE164 4.3 17.5 1.0 N B:ALA349 4.3 15.7 1.0 O4 B:SO4504 4.4 27.4 1.0 CA B:ALA257 4.4 17.2 1.0 CA B:PHE164 4.4 18.5 1.0 CA B:ALA349 4.4 17.4 1.0 O3 B:SO4504 4.5 24.7 1.0 CB B:PHE210 4.5 16.5 1.0 CB B:THR165 4.6 18.0 1.0 CB B:LEU258 4.6 17.5 1.0 CB B:ALA209 4.7 16.3 1.0 O2 B:SO4504 4.7 28.1 1.0 CB B:MET350 4.8 23.6 1.0 CB B:PHE164 4.9 18.2 1.0 CB B:ALA349 4.9 16.7 1.0 CB B:ALA257 4.9 17.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Sodium-2


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 the Vitronectin Hemopexin-Like Domain Binding Sodium-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:21.2 occ:1.00 O B:ASP255 2.0 17.5 1.0 O B:ASP207 2.2 19.5 1.0 O B:ASP347 2.2 21.5 1.0 O B:ASP162 2.2 18.4 1.0 O B:HOH690 2.3 23.9 1.0 C B:ASP255 3.1 17.8 1.0 C B:ASP347 3.3 20.1 1.0 C B:ASP162 3.3 20.4 1.0 C B:ASP207 3.3 18.2 1.0 CA B:ASP255 3.9 17.5 1.0 CA B:ASP162 3.9 21.3 1.0 N B:ALA256 4.0 16.6 1.0 CA B:ASP207 4.1 18.6 1.0 N B:ALA348 4.1 21.1 1.0 CA B:ASP347 4.2 21.2 1.0 N B:ALA208 4.3 17.3 1.0 CA B:ALA256 4.3 16.4 1.0 N B:ALA163 4.3 20.3 1.0 CA B:ALA348 4.4 19.2 1.0 O B:HOH656 4.4 29.1 1.0 CA B:ALA208 4.4 16.4 1.0 CA B:ALA163 4.7 19.3 1.0 O B:HOH669 4.7 59.4 1.0 CB B:ALA256 4.7 16.5 1.0 CB B:ALA348 4.7 20.3 1.0 CB B:ALA208 4.8 17.0 1.0 CB B:ASP162 4.8 22.1 1.0 O B:VAL254 4.8 18.7 1.0 CB B:ASP255 4.8 18.2 1.0 O B:PHE161 4.9 21.1 1.0 CL B:CL503 4.9 18.4 1.0 N B:ASP255 5.0 17.2 1.0 CB B:ALA163 5.0 20.3 1.0 CB B:ASP207 5.0 18.2 1.0

Y.Tian, K.Shin, A.E.Aleshin, F.Marassi. Structural Basis For Calcium-Induced Thermostability of Human Vitronectin To Be Published.