Sodium in PDB 6o5e: Crystal Structure of the Vitronectin Hemopexin-Like Domain

The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain, PDB code: 6o5e was solved by B.C.Lechtenberg, K.Shin, F.M.Marassi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.21 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.560, 97.360, 49.160, 90.00, 99.90, 90.00
R / Rfree (%)	17.9 / 21

The structure of Crystal Structure of the Vitronectin Hemopexin-Like Domain 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 (pdb code 6o5e). 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, PDB code: 6o5e:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:18.9 occ:1.00 O A:HOH689 2.1 33.6 1.0 O A:ASP255 2.3 21.6 1.0 O A:ASP207 2.3 24.0 1.0 O A:ASP162 2.3 19.9 1.0 O A:ASP347 2.3 25.0 1.0 C A:ASP255 3.4 23.8 1.0 O A:HOH671 3.4 51.5 1.0 C A:ASP347 3.5 24.9 1.0 C A:ASP207 3.5 22.5 1.0 C A:ASP162 3.5 23.1 1.0 HA A:ASP255 3.7 26.5 1.0 HA A:ASP207 3.8 29.4 1.0 HA A:ASP162 3.8 28.7 1.0 HA A:ALA348 3.9 23.0 1.0 HB2 A:ALA348 3.9 22.6 1.0 HA A:ASP347 4.0 31.0 1.0 HA A:ALA256 4.1 24.5 1.0 HB2 A:ALA163 4.1 23.4 1.0 CA A:ASP255 4.1 22.1 1.0 HA A:ALA208 4.2 26.7 1.0 CA A:ASP162 4.2 23.9 1.0 CA A:ASP207 4.2 24.6 1.0 HA A:ALA163 4.2 22.8 1.0 HB3 A:ASP162 4.2 25.6 1.0 HB2 A:ALA208 4.3 23.8 1.0 N A:ALA348 4.3 20.0 1.0 CA A:ASP347 4.3 25.8 1.0 HB2 A:ALA256 4.4 27.8 1.0 CA A:ALA348 4.4 19.3 1.0 HB3 A:ASP255 4.4 25.9 1.0 N A:ALA256 4.5 23.0 1.0 N A:ALA208 4.5 23.3 1.0 N A:ALA163 4.5 19.9 1.0 HB3 A:ASP347 4.6 40.1 1.0 CB A:ALA348 4.6 19.0 1.0 CA A:ALA256 4.7 20.4 1.0 HB3 A:ASP207 4.7 30.9 1.0 CA A:ALA163 4.7 19.2 1.0 CA A:ALA208 4.7 22.2 1.0 O A:ILE206 4.7 28.7 1.0 CB A:ASP162 4.8 21.5 1.0 CB A:ALA163 4.9 19.4 1.0 CB A:ASP255 4.9 21.6 1.0 O A:VAL254 4.9 29.1 1.0 CB A:ALA208 5.0 19.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:16.2 occ:1.00 O A:ALA209 2.2 18.0 1.0 O A:ALA257 2.3 22.1 1.0 O A:ALA349 2.3 18.5 1.0 O A:PHE164 2.3 21.5 1.0 O A:HOH621 2.3 64.4 1.0 CL A:CL502 2.7 19.0 1.0 H A:ALA209 3.2 25.2 1.0 H A:PHE164 3.3 22.3 1.0 H A:ALA257 3.3 26.1 1.0 C A:ALA209 3.4 19.0 1.0 C A:ALA257 3.4 22.5 1.0 C A:ALA349 3.4 20.4 1.0 H A:ALA349 3.5 22.9 1.0 C A:PHE164 3.5 20.1 1.0 HA A:MET350 3.7 24.6 1.0 HB2 A:PHE164 3.7 26.1 1.0 HA A:LEU258 3.8 27.9 1.0 HA A:PHE210 3.9 26.4 1.0 N A:ALA209 3.9 21.0 1.0 HB3 A:MET350 4.0 26.5 1.0 HB3 A:ALA209 4.0 20.8 1.0 N A:PHE164 4.0 18.8 1.0 N A:ALA257 4.0 21.7 1.0 HA A:THR165 4.0 24.2 1.0 HB3 A:PHE210 4.1 26.1 1.0 HB3 A:ALA257 4.1 26.5 1.0 HB3 A:ALA349 4.1 25.5 1.0 CA A:ALA209 4.2 16.8 1.0 N A:ALA349 4.2 19.1 1.0 CA A:PHE164 4.2 20.7 1.0 CA A:ALA257 4.2 19.9 1.0 HB3 A:LEU258 4.3 28.4 1.0 N A:MET350 4.3 18.4 1.0 CA A:ALA349 4.3 18.8 1.0 CA A:MET350 4.4 20.5 1.0 N A:LEU258 4.4 20.2 1.0 N A:PHE210 4.4 22.1 1.0 CB A:PHE164 4.4 21.7 1.0 CA A:LEU258 4.5 23.2 1.0 CA A:PHE210 4.5 22.0 1.0 N A:THR165 4.5 18.8 1.0 CA A:THR165 4.6 20.1 1.0 CB A:ALA209 4.6 17.3 1.0 CB A:MET350 4.7 22.1 1.0 HB3 A:PHE164 4.7 26.1 1.0 HB1 A:ALA208 4.7 23.8 1.0 CB A:ALA257 4.7 22.1 1.0 CB A:PHE210 4.8 21.7 1.0 CB A:ALA349 4.8 21.2 1.0 OD1 A:ASP166 4.8 26.0 1.0 C A:THR165 4.8 24.1 1.0 HB1 A:ALA163 4.8 23.4 1.0 CB A:LEU258 4.9 23.6 1.0 HB1 A:ALA256 4.9 27.8 1.0 HA A:ALA208 4.9 26.7 1.0 HA A:ALA163 5.0 22.8 1.0 O A:THR165 5.0 27.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:22.9 occ:1.00 O B:HOH664 2.1 33.2 1.0 O B:ASP207 2.2 24.1 1.0 O B:ASP255 2.2 26.4 1.0 O B:ASP162 2.2 26.6 1.0 O B:ASP347 2.4 25.4 1.0 C B:ASP162 3.2 27.6 1.0 C B:ASP255 3.3 26.8 1.0 C B:ASP207 3.3 24.4 1.0 HA B:ASP162 3.3 33.5 1.0 C B:ASP347 3.5 25.5 1.0 HA B:ASP255 3.5 29.4 1.0 HA B:ASP207 3.7 30.8 1.0 CA B:ASP162 3.8 28.1 1.0 HA B:ALA256 3.9 26.5 1.0 HA B:ASP347 3.9 31.9 1.0 CA B:ASP255 4.0 24.4 1.0 HA B:ALA348 4.0 28.0 1.0 HA B:ALA208 4.0 29.7 1.0 CA B:ASP207 4.1 25.6 1.0 HB3 B:ASP162 4.1 35.3 1.0 HB2 B:ALA348 4.2 27.9 1.0 HB2 B:ALA208 4.2 33.6 1.0 HA B:ALA163 4.2 33.6 1.0 N B:ALA256 4.3 22.6 1.0 HB2 B:ALA163 4.3 35.6 1.0 CA B:ASP347 4.3 26.8 1.0 N B:ALA208 4.3 26.9 1.0 N B:ALA163 4.3 28.3 1.0 HB2 B:ALA256 4.4 27.7 1.0 N B:ALA348 4.4 24.6 1.0 HB3 B:ASP255 4.4 30.9 1.0 O B:HOH637 4.4 50.9 1.0 HB3 B:ASP347 4.5 37.0 1.0 CA B:ALA256 4.5 22.1 1.0 CA B:ALA348 4.5 23.5 1.0 CA B:ALA208 4.5 24.7 1.0 CB B:ASP162 4.6 29.6 1.0 HB3 B:ASP207 4.6 33.8 1.0 CA B:ALA163 4.7 28.1 1.0 CB B:ASP255 4.8 25.7 1.0 O B:VAL254 4.8 27.4 1.0 CB B:ALA348 4.8 23.3 1.0 O B:PHE161 4.8 28.0 1.0 CB B:ALA208 4.9 28.0 1.0 O B:ILE206 4.9 28.8 1.0 CB B:ALA256 4.9 23.0 1.0 CB B:ASP207 5.0 28.1 1.0 CB B:ALA163 5.0 29.6 1.0 CB B:ASP347 5.0 30.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:22.2 occ:1.00 O B:ALA257 2.2 22.8 1.0 O B:ALA349 2.2 21.2 1.0 O B:ALA209 2.3 22.9 1.0 O B:PHE164 2.3 28.1 1.0 CL B:CL502 2.8 22.9 1.0 O2 B:SO4504 2.8 46.9 1.0 C B:ALA349 3.3 22.6 1.0 C B:ALA257 3.4 23.0 1.0 H B:ALA349 3.4 26.8 1.0 H B:ALA209 3.4 22.3 1.0 H B:ALA257 3.4 27.7 1.0 C B:ALA209 3.5 21.1 1.0 H B:PHE164 3.5 33.9 1.0 C B:PHE164 3.5 29.3 1.0 HA B:MET350 3.6 25.0 1.0 HA B:LEU258 3.6 34.9 1.0 HA B:THR165 3.8 36.9 1.0 HA B:PHE210 3.9 27.7 1.0 HB3 B:PHE210 3.9 27.8 1.0 HB3 B:LEU258 4.0 32.2 1.0 HB B:THR165 4.0 37.8 1.0 HB3 B:ALA349 4.1 29.4 1.0 N B:ALA349 4.1 22.4 1.0 N B:ALA209 4.1 18.5 1.0 N B:ALA257 4.2 23.0 1.0 HB3 B:ALA209 4.2 29.6 1.0 N B:PHE164 4.2 28.4 1.0 HB2 B:MET350 4.2 29.2 1.0 N B:MET350 4.2 21.2 1.0 CA B:ALA349 4.2 23.4 1.0 S B:SO4504 4.3 35.1 1.0 HB2 B:PHE164 4.3 33.6 1.0 N B:LEU258 4.3 26.4 1.0 CA B:MET350 4.3 20.8 1.0 HB3 B:ALA257 4.3 29.2 1.0 CA B:ALA257 4.3 23.4 1.0 CA B:LEU258 4.3 29.0 1.0 CA B:ALA209 4.3 21.7 1.0 CA B:PHE164 4.4 29.2 1.0 N B:PHE210 4.4 21.6 1.0 CA B:THR165 4.4 30.9 1.0 CA B:PHE210 4.4 23.1 1.0 N B:THR165 4.5 30.8 1.0 CB B:PHE210 4.6 23.1 1.0 CB B:LEU258 4.6 26.8 1.0 CB B:ALA349 4.7 24.5 1.0 CB B:THR165 4.7 31.6 1.0 CB B:PHE164 4.7 28.1 1.0 CB B:ALA209 4.8 24.6 1.0 CB B:MET350 4.8 24.3 1.0 O3 B:SO4504 4.8 44.0 1.0 CB B:ALA257 4.8 24.3 1.0 HB3 B:PHE164 4.8 33.6 1.0 HG3 B:MET350 4.9 38.1 1.0 HB1 B:ALA163 4.9 35.6 1.0 HB2 B:PHE210 4.9 27.8 1.0 HB2 B:LEU258 4.9 32.2 1.0 O4 B:SO4504 4.9 41.3 1.0 HB1 B:ALA256 4.9 27.7 1.0 HB1 B:ALA348 4.9 27.9 1.0 HB1 B:ALA208 5.0 33.6 1.0

K.Shin, B.C.Lechtenberg, L.M.Fujimoto, Y.Yao, S.S.Bartra, G.V.Plano, F.M.Marassi. Structure of Human Vitronectin C-Terminal Domain and Interaction Withyersinia Pestisouter Membrane Protein Ail. Sci Adv V. 5 X5068 2019.
ISSN: ESSN 2375-2548
PubMed: 31535027
DOI: 10.1126/SCIADV.AAX5068