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

The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium-2, PDB code: 7txr 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)	37.24 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.835, 98.277, 49.433, 90, 99.82, 90
R / Rfree (%)	18.4 / 22.6

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

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium-2 (pdb code 7txr). 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-2, PDB code: 7txr:
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-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 Calcium-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:22.2 occ:1.00 O A:ALA257 2.2 23.1 1.0 O A:ALA209 2.2 21.2 1.0 O A:ALA349 2.3 22.4 1.0 O A:PHE164 2.3 21.8 1.0 O A:HOH627 2.3 50.7 1.0 CL A:CL502 2.8 24.4 1.0 C A:ALA209 3.4 25.0 1.0 C A:ALA349 3.4 23.5 1.0 C A:ALA257 3.4 27.1 1.0 C A:PHE164 3.5 25.5 1.0 N A:ALA209 4.0 25.0 1.0 N A:PHE164 4.0 23.7 1.0 N A:ALA257 4.1 28.4 1.0 N A:ALA349 4.2 20.9 1.0 CA A:ALA209 4.2 25.7 1.0 CA A:PHE164 4.2 21.6 1.0 CA A:MET350 4.2 28.2 1.0 CA A:ALA257 4.3 27.2 1.0 N A:MET350 4.3 23.9 1.0 CA A:ALA349 4.3 22.1 1.0 N A:PHE210 4.3 26.3 1.0 N A:LEU258 4.3 25.3 1.0 CA A:LEU258 4.4 28.7 1.0 CA A:PHE210 4.5 28.3 1.0 CB A:PHE164 4.5 22.1 1.0 N A:THR165 4.5 27.3 1.0 CB A:MET350 4.5 29.9 1.0 CA A:THR165 4.6 30.9 1.0 CB A:ALA209 4.6 25.2 1.0 CB A:ALA257 4.7 29.1 1.0 CB A:ALA349 4.7 21.7 1.0 C A:THR165 4.8 31.1 1.0 CB A:PHE210 4.8 28.8 1.0 OD1 A:ASP166 4.8 35.9 1.0 CB A:LEU258 4.8 29.9 1.0 O A:THR165 4.9 29.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain Binding Calcium-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 Calcium-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:34.6 occ:1.00 O B:ALA257 2.2 34.2 1.0 O B:ALA349 2.3 31.1 1.0 O B:ALA209 2.3 31.2 1.0 O B:PHE164 2.3 36.6 1.0 O4 B:SO4505 2.8 46.9 1.0 CL B:CL503 2.8 34.2 1.0 C B:ALA257 3.4 32.8 1.0 C B:ALA209 3.4 31.5 1.0 C B:ALA349 3.4 32.4 1.0 C B:PHE164 3.5 39.9 1.0 N B:ALA209 4.1 31.2 1.0 S B:SO4505 4.2 54.5 1.0 N B:ALA257 4.2 32.3 1.0 N B:PHE164 4.2 33.8 1.0 N B:ALA349 4.2 33.6 1.0 CA B:MET350 4.2 36.6 1.0 N B:LEU258 4.3 34.0 1.0 CA B:ALA209 4.3 30.9 1.0 N B:MET350 4.3 31.9 1.0 CA B:ALA257 4.3 32.6 1.0 N B:PHE210 4.3 31.5 1.0 CA B:ALA349 4.3 35.6 1.0 CA B:LEU258 4.3 34.3 1.0 CA B:PHE164 4.3 35.3 1.0 N B:THR165 4.4 42.0 1.0 CA B:PHE210 4.4 35.9 1.0 CA B:THR165 4.4 44.2 1.0 CB B:MET350 4.4 42.1 1.0 O1 B:SO4505 4.6 53.9 1.0 CB B:PHE164 4.6 37.2 1.0 CB B:PHE210 4.7 36.2 1.0 CB B:ALA209 4.7 32.8 1.0 CB B:LEU258 4.7 38.3 1.0 CB B:ALA349 4.7 35.0 1.0 CB B:ALA257 4.8 32.8 1.0 O2 B:SO4505 4.8 58.0 1.0 CB B:THR165 4.9 44.5 1.0

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