Chlorine 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:

Sodium

(Na)

4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Vitronectin Hemopexin-Like Domain, PDB code: 6o5e:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of the Vitronectin Hemopexin-Like Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl502 b:19.0 occ:1.00 H A:ALA349 2.6 22.9 1.0 H A:PHE164 2.7 22.3 1.0 NA A:NA503 2.7 16.2 1.0 H A:ALA209 2.7 25.2 1.0 H A:ALA257 2.7 26.1 1.0 HA A:ALA208 2.9 26.7 1.0 HA A:ALA163 2.9 22.8 1.0 HA A:ALA256 3.0 24.5 1.0 HA A:ALA348 3.1 23.0 1.0 HB1 A:ALA163 3.3 23.4 1.0 HB1 A:ALA208 3.4 23.8 1.0 HB1 A:ALA348 3.4 22.6 1.0 N A:ALA349 3.5 19.1 1.0 N A:ALA209 3.5 21.0 1.0 O A:ALA349 3.5 18.5 1.0 N A:PHE164 3.5 18.8 1.0 HB1 A:ALA256 3.5 27.8 1.0 N A:ALA257 3.5 21.7 1.0 CA A:ALA208 3.6 22.2 1.0 CA A:ALA163 3.7 19.2 1.0 O A:ALA257 3.7 22.1 1.0 O A:PHE164 3.8 21.5 1.0 O A:ALA209 3.8 18.0 1.0 CA A:ALA256 3.8 20.4 1.0 CA A:ALA348 3.8 19.3 1.0 CB A:ALA163 3.9 19.4 1.0 CB A:ALA208 3.9 19.8 1.0 HB2 A:ALA163 4.0 23.4 1.0 CB A:ALA348 4.0 19.0 1.0 HB2 A:ALA208 4.0 23.8 1.0 CB A:ALA256 4.0 23.1 1.0 C A:ALA208 4.1 20.9 1.0 C A:ALA163 4.1 19.2 1.0 C A:ALA348 4.2 22.9 1.0 C A:ALA256 4.2 19.8 1.0 HB2 A:ALA256 4.2 27.8 1.0 HB2 A:ALA348 4.3 22.6 1.0 HB2 A:PHE164 4.3 26.1 1.0 C A:ALA349 4.4 20.4 1.0 HB3 A:ALA209 4.4 20.8 1.0 CA A:ALA349 4.4 18.8 1.0 HB3 A:ALA349 4.5 25.5 1.0 HB3 A:ALA257 4.5 26.5 1.0 CA A:ALA209 4.5 16.8 1.0 CA A:PHE164 4.5 20.7 1.0 CA A:ALA257 4.5 19.9 1.0 C A:ALA257 4.6 22.5 1.0 C A:PHE164 4.6 20.1 1.0 C A:ALA209 4.6 19.0 1.0 O A:ASP162 4.6 19.9 1.0 O A:ASP207 4.7 24.0 1.0 HD2 A:PHE164 4.7 24.8 1.0 HB3 A:ALA163 4.8 23.4 1.0 O A:ASP255 4.8 21.6 1.0 HB3 A:ALA208 4.8 23.8 1.0 N A:ALA208 4.9 23.3 1.0 N A:ALA163 4.9 19.9 1.0 HB3 A:ALA348 4.9 22.6 1.0 CB A:PHE164 4.9 21.7 1.0 HB3 A:ALA256 4.9 27.8 1.0 CB A:ALA209 5.0 17.3 1.0 CB A:ALA349 5.0 21.2 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Vitronectin Hemopexin-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:22.9 occ:1.00 H B:ALA349 2.5 26.8 1.0 H B:PHE164 2.6 33.9 1.0 H B:ALA209 2.7 22.3 1.0 H B:ALA257 2.7 27.7 1.0 HA B:ALA163 2.8 33.6 1.0 NA B:NA503 2.8 22.2 1.0 HA B:ALA348 3.0 28.0 1.0 HA B:ALA208 3.0 29.7 1.0 HA B:ALA256 3.1 26.5 1.0 HB1 B:ALA348 3.2 27.9 1.0 HB1 B:ALA163 3.3 35.6 1.0 N B:ALA349 3.3 22.4 1.0 HB1 B:ALA256 3.4 27.7 1.0 N B:ALA209 3.4 18.5 1.0 N B:PHE164 3.5 28.4 1.0 N B:ALA257 3.5 23.0 1.0 HB1 B:ALA208 3.5 33.6 1.0 O B:ALA349 3.5 21.2 1.0 CA B:ALA163 3.6 28.1 1.0 O B:ALA257 3.6 22.8 1.0 O B:PHE164 3.6 28.1 1.0 CA B:ALA348 3.7 23.5 1.0 O B:ALA209 3.7 22.9 1.0 CA B:ALA208 3.8 24.7 1.0 CA B:ALA256 3.8 22.1 1.0 CB B:ALA163 3.8 29.6 1.0 CB B:ALA348 3.8 23.3 1.0 HB2 B:ALA163 3.9 35.6 1.0 CB B:ALA208 4.0 28.0 1.0 CB B:ALA256 4.0 23.0 1.0 C B:ALA348 4.0 23.0 1.0 C B:ALA163 4.1 29.0 1.0 C B:ALA208 4.1 24.6 1.0 HB2 B:ALA348 4.1 27.9 1.0 HB2 B:ALA208 4.1 33.6 1.0 C B:ALA256 4.2 22.7 1.0 HB3 B:ALA209 4.3 29.6 1.0 HB2 B:ALA256 4.3 27.7 1.0 HB3 B:ALA349 4.3 29.4 1.0 C B:ALA349 4.4 22.6 1.0 CA B:ALA349 4.4 23.4 1.0 HB2 B:PHE164 4.4 33.6 1.0 CA B:ALA209 4.5 21.7 1.0 C B:PHE164 4.5 29.3 1.0 C B:ALA257 4.5 23.0 1.0 HB3 B:ALA257 4.5 29.2 1.0 CA B:ALA257 4.5 23.4 1.0 CA B:PHE164 4.5 29.2 1.0 C B:ALA209 4.5 21.1 1.0 O B:ASP162 4.6 26.6 1.0 HB3 B:ALA348 4.7 27.9 1.0 HB3 B:ALA163 4.7 35.6 1.0 N B:ALA163 4.8 28.3 1.0 HB3 B:ALA256 4.9 27.7 1.0 CB B:ALA209 4.9 24.6 1.0 CB B:ALA349 4.9 24.5 1.0 HB3 B:ALA208 4.9 33.6 1.0 O B:ASP255 5.0 26.4 1.0 O B:ASP207 5.0 24.1 1.0 N B:ALA348 5.0 24.6 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