Sodium in PDB 7vf4: Crystal Structure of VPS75 From Candida Albicans

The structure of Crystal Structure of VPS75 From Candida Albicans, PDB code: 7vf4 was solved by W.Wang, X.Chen, Z.Yang, X.Chen, C.Li, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.75 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.61, 137.17, 226.52, 90, 90, 90
R / Rfree (%)	24.5 / 29.2

The structure of Crystal Structure of VPS75 From Candida Albicans also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of VPS75 From Candida Albicans (pdb code 7vf4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of VPS75 From Candida Albicans, PDB code: 7vf4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Crystal Structure of VPS75 From Candida Albicans


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 VPS75 From Candida Albicans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:74.8 occ:1.00 O B:SER225 2.5 90.6 1.0 O B:ILE222 3.5 90.5 1.0 C B:SER225 3.7 94.9 1.0 C B:PRO226 3.9 88.2 1.0 CA B:PRO226 4.4 91.3 1.0 N B:PRO226 4.5 97.6 1.0 C B:ILE222 4.7 90.9 1.0 N B:SER225 4.7 89.4 1.0 CA B:SER225 4.8 87.5 1.0 O B:ALA223 4.9 90.5 1.0 O B:PRO226 4.9 82.8 1.0

Sodium binding site 2 out of 8 in the Crystal Structure of VPS75 From Candida Albicans


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 VPS75 From Candida Albicans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:50.5 occ:1.00 O B:ASP69 3.1 89.6 1.0 O B:ILE71 3.2 93.5 1.0 O B:ALA68 3.7 83.3 1.0 C B:ASP69 3.8 89.6 1.0 CA B:ASP69 4.0 93.1 1.0 C B:ILE71 4.3 92.4 1.0 C B:ALA68 4.7 84.2 1.0 N B:ILE71 4.7 88.9 1.0 N B:ASP69 4.8 88.9 1.0 N B:TYR70 4.8 90.6 1.0

Sodium binding site 3 out of 8 in the Crystal Structure of VPS75 From Candida Albicans


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 VPS75 From Candida Albicans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:42.0 occ:1.00 OD1 B:ASN215 3.8 69.5 1.0 NZ B:LYS218 4.2 74.7 1.0 OE1 A:GLU28 4.4 67.4 1.0 CB B:LEU214 4.6 68.8 1.0 OE2 A:GLU28 4.7 60.4 1.0 CD1 B:LEU214 4.8 72.2 1.0 CG B:ASN215 4.8 74.9 1.0

Sodium binding site 4 out of 8 in the Crystal Structure of VPS75 From Candida Albicans


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 VPS75 From Candida Albicans within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:75.3 occ:1.00 O C:SER225 2.7 93.0 1.0 O C:ILE222 3.5 76.8 1.0 C C:SER225 4.0 100.0 1.0 O C:ALA223 4.2 76.1 1.0 C C:ALA223 4.5 80.7 1.0 N C:SER225 4.5 93.1 1.0 CD1 C:LEU227 4.6 101.0 1.0 CA C:ALA223 4.7 82.9 1.0 C C:ILE222 4.7 74.5 1.0 CG C:LEU227 4.7 103.6 1.0 N C:LEU227 4.7 109.5 1.0 CA C:PRO226 4.8 110.0 1.0 N C:PRO226 4.9 105.5 1.0 CA C:SER225 4.9 92.4 1.0

Sodium binding site 5 out of 8 in the Crystal Structure of VPS75 From Candida Albicans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of VPS75 From Candida Albicans within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:46.9 occ:1.00 O C:HOH403 2.6 65.6 1.0 OE2 C:GLU28 2.9 55.9 1.0 CD C:GLU28 3.9 62.8 1.0 OH D:TYR43 3.9 57.9 1.0 OE1 C:GLU28 4.2 68.0 1.0 CG C:MET24 4.4 61.1 1.0 NZ D:LYS218 4.4 69.1 1.0 O D:LEU214 4.5 60.2 1.0 CH2 C:TRP20 4.9 66.1 1.0 CE C:MET24 4.9 61.2 1.0 CZ D:TYR43 5.0 59.7 1.0

Sodium binding site 6 out of 8 in the Crystal Structure of VPS75 From Candida Albicans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of VPS75 From Candida Albicans within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:53.1 occ:1.00 O F:ILE71 3.0 80.9 1.0 O F:ASP69 3.3 83.7 1.0 O F:ALA68 3.5 83.2 1.0 C F:ASP69 3.9 80.6 1.0 C F:ILE71 4.1 86.2 1.0 CA F:ASP69 4.2 86.4 1.0 C F:ALA68 4.6 78.8 1.0 N F:ILE71 4.6 82.2 1.0 N F:SER72 4.9 90.7 1.0 N F:ASP69 4.9 83.6 1.0 N F:TYR70 4.9 83.2 1.0 CD F:PRO73 4.9 82.1 1.0 CA F:SER72 4.9 91.6 1.0 CA F:ILE71 5.0 81.5 1.0

Sodium binding site 7 out of 8 in the Crystal Structure of VPS75 From Candida Albicans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of VPS75 From Candida Albicans within 5.0Å range: probe atom residue distance (Å) B Occ G:Na301 b:74.4 occ:1.00 O G:HOH404 3.4 52.6 1.0 O G:SER225 3.6 105.0 1.0 O G:ALA223 3.7 93.1 1.0 O G:ILE222 3.7 92.9 1.0 C G:ALA223 4.1 91.1 1.0 N G:SER225 4.4 97.4 1.0 C G:SER225 4.4 106.9 1.0 CA G:ALA223 4.4 89.1 1.0 N G:LEU224 4.8 90.3 1.0 C G:ILE222 4.8 87.6 1.0 OE1 G:GLU63 4.9 93.5 1.0

Sodium binding site 8 out of 8 in the Crystal Structure of VPS75 From Candida Albicans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of VPS75 From Candida Albicans within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:72.0 occ:1.00 O H:HOH402 2.5 58.9 1.0 O H:SER225 2.7 88.0 1.0 O H:ILE222 3.6 82.1 1.0 C H:SER225 3.9 90.4 1.0 O H:ALA223 4.4 82.6 1.0 CA H:PRO226 4.5 91.6 1.0 N H:PRO226 4.6 91.3 1.0 C H:ALA223 4.7 86.5 1.0 N H:SER225 4.7 88.9 1.0 C H:ILE222 4.8 83.7 1.0 CA H:SER225 4.9 88.8 1.0

W.Wang, X.Chen, Z.Yang, X.Chen, C.Li, M.Wang. Crystal Structure of Histone Chaperone VPS75 From Candida Albicans. Biochem.Biophys.Res.Commun. V. 578 136 2021.
ISSN: ESSN 1090-2104
PubMed: 34562653
DOI: 10.1016/J.BBRC.2021.09.030