Sodium in PDB 5c9d: 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: 5c9d 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)	41.85 / 2.59
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.290, 105.290, 90.996, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 29.8

The binding sites of Sodium atom in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii (pdb code 5c9d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of A Retropepsin-Like Aspartic Protease From Rickettsia Conorii, PDB code: 5c9d:

Sodium binding site 1 out of 1 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 A:Na301 b:88.1 occ:1.00 O B:HOH302 2.2 67.6 1.0 O A:GLY189 2.8 55.9 1.0 OE1 A:GLU110 3.1 77.0 1.0 OE2 A:GLU110 3.1 65.9 1.0 O B:ASN127 3.2 78.8 1.0 CD A:GLU110 3.5 77.0 1.0 CB A:ALA233 3.8 74.2 1.0 C A:GLY189 4.0 87.9 1.0 O B:ILE188 4.1 68.2 1.0 C B:ASN127 4.2 79.6 1.0 CE2 B:PHE129 4.3 67.6 1.0 CE1 A:TYR231 4.3 70.9 1.0 O A:HOH401 4.4 53.6 1.0 CB B:ASN127 4.4 87.0 1.0 CG2 B:ILE188 4.4 82.8 1.0 CA A:LYS190 4.5 78.0 1.0 N B:ASN127 4.6 0.3 1.0 N A:LYS190 4.6 69.4 1.0 CA B:ASN127 4.6 87.2 1.0 OH A:TYR231 4.7 75.2 1.0 CZ B:PHE129 4.8 64.7 1.0 CZ A:TYR231 4.9 72.4 1.0 CG A:GLU110 4.9 70.7 1.0 CG2 B:ILE126 4.9 0.4 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.,Sect.D V. 71 2119 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004715013930