Sodium in PDB 5c9f: Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii

The structure of Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii, PDB code: 5c9f was solved by M.Li, A.Gustchina, R.Cruz, M.Simoes, P.Curto, J.Martinez, C.Faro, I.Simoes, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.102, 94.153, 118.636, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.5

The structure of Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Sodium atom in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii (pdb code 5c9f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii, PDB code: 5c9f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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 A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:54.2 occ:1.00 O B:GLY202 2.8 90.9 1.0 CA B:GLY200 2.9 99.4 1.0 C B:GLY200 2.9 79.0 1.0 O B:GLY200 2.9 0.8 1.0 CB B:LEU204 3.1 52.2 1.0 N B:GLY200 3.3 0.3 1.0 N B:LEU204 3.5 55.7 1.0 N B:LEU201 3.7 74.8 1.0 C B:ASP203 3.7 80.3 1.0 O B:HOH444 3.9 52.5 1.0 CA B:LEU204 3.9 49.4 1.0 O B:ASP203 4.0 62.3 1.0 C B:GLY202 4.0 92.0 1.0 CD2 B:LEU204 4.1 46.9 1.0 CG B:LEU204 4.1 61.0 1.0 O B:LEU148 4.3 31.5 1.0 O B:HOH445 4.4 48.5 1.0 NZ B:LYS150 4.4 65.7 1.0 CA B:ASP203 4.4 62.4 1.0 C B:VAL199 4.5 50.7 1.0 CA B:LEU201 4.7 70.8 1.0 N B:ASP203 4.7 65.2 1.0 CA B:THR149 4.7 28.4 1.0 C B:LEU201 4.8 0.7 1.0 CD1 B:LEU204 4.8 68.0 1.0 N B:GLY202 4.9 80.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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 A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range: probe atom residue distance (Å) B Occ D:Na305 b:69.5 occ:1.00 O D:HOH449 2.2 52.0 1.0 O D:HOH412 2.4 42.4 1.0 OD1 D:ASP203 3.4 66.6 1.0 O D:HOH419 3.4 35.0 1.0 O D:HOH430 3.5 31.4 1.0 CE D:LYS150 3.5 38.3 1.0 NZ D:LYS150 3.7 42.3 1.0 CL D:CL303 3.7 34.9 1.0 CB D:LYS150 4.4 28.1 1.0 CG D:ASP203 4.5 51.8 1.0 O D:HOH416 4.6 50.1 1.0 CD D:LYS150 4.7 39.6 1.0 CA D:ASP203 4.9 35.8 1.0 CG D:LYS150 5.0 33.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii


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 A Retropepsin-Like Aspartic Protease From Rickettsia Conorii within 5.0Å range: probe atom residue distance (Å) B Occ D:Na306 b:46.6 occ:1.00 O D:GLY202 2.5 36.9 1.0 O D:GLY200 2.6 37.6 1.0 O D:HOH405 2.6 34.5 1.0 O D:HOH433 2.6 40.1 1.0 CL D:CL303 2.7 34.9 1.0 C D:GLY200 3.3 47.9 1.0 CA D:GLY200 3.6 39.6 1.0 NZ D:LYS150 3.6 42.3 1.0 CB D:LEU204 3.6 32.5 1.0 C D:GLY202 3.6 34.7 1.0 N D:LEU204 3.7 41.6 1.0 N D:GLY200 3.7 32.1 1.0 C D:ASP203 4.1 39.0 1.0 O D:HOH448 4.1 34.5 1.0 CA D:LEU204 4.3 30.6 1.0 N D:LEU201 4.3 40.4 1.0 CA D:ASP203 4.4 35.8 1.0 O D:LEU148 4.4 32.2 1.0 CG D:LYS150 4.4 33.2 1.0 N D:ASP203 4.4 41.0 1.0 N D:GLY202 4.4 41.4 1.0 N D:LYS150 4.5 22.9 1.0 C D:LEU201 4.5 47.3 1.0 CA D:GLY202 4.6 40.9 1.0 O D:HOH404 4.6 54.7 1.0 CA D:THR149 4.7 26.9 1.0 CE D:LYS150 4.8 38.3 1.0 CD2 D:LEU204 4.8 35.6 1.0 CG D:LEU204 4.8 33.4 1.0 CA D:LEU201 4.8 41.4 1.0 O D:ASP203 4.9 43.5 1.0 C D:VAL199 4.9 44.8 1.0 CD D:LYS150 5.0 39.6 1.0 O D:LEU201 5.0 53.8 1.0 C D:THR149 5.0 27.4 1.0

M.Li, A.Gustchina, R.Cruz, M.Simoes, P.Curto, J.Martinez, C.Faro, I.Simoes, A.Wlodawer. Structure of RC1339/Aprc From Rickettsia Conorii, A Retropepsin-Like Aspartic Protease. Acta Crystallogr. D Biol. V. 71 2109 2015CRYSTALLOGR..
ISSN: ESSN 1399-0047
PubMed: 26457434
DOI: 10.1107/S1399004715013905