Sodium in PDB 2rg8: Crystal Structure of Programmed For Cell Death 4 Middle MA3 Domain

The structure of Crystal Structure of Programmed For Cell Death 4 Middle MA3 Domain, PDB code: 2rg8 was solved by R.Garces, C.Suzuki, G.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.68 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.680, 70.060, 110.880, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25.1

The structure of Crystal Structure of Programmed For Cell Death 4 Middle MA3 Domain also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Programmed For Cell Death 4 Middle MA3 Domain (pdb code 2rg8). 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 Programmed For Cell Death 4 Middle MA3 Domain, PDB code: 2rg8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Programmed For Cell Death 4 Middle MA3 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 Programmed For Cell Death 4 Middle MA3 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4 b:19.1 occ:1.00 OD2 A:ASP271 2.7 18.0 1.0 O A:HOH308 2.9 9.0 1.0 O A:SER220 3.0 6.5 1.0 CG A:ARG267 3.6 14.1 1.0 C A:SER220 3.7 8.6 1.0 CA A:ALA268 3.7 9.4 1.0 CG A:ASP271 3.8 18.2 1.0 CA A:SER220 3.8 7.6 1.0 CD1 A:ILE273 3.8 11.2 1.0 CB A:SER220 3.8 8.2 1.0 O A:ARG267 3.9 10.7 1.0 N A:ALA268 3.9 8.7 1.0 C A:ARG267 4.0 11.2 1.0 CB A:ASP271 4.1 16.9 1.0 N A:SER224 4.2 7.7 1.0 CB A:LEU223 4.2 8.6 1.0 CB A:SER224 4.3 13.2 1.0 CB A:ALA268 4.4 7.4 1.0 O A:HOH352 4.4 21.5 1.0 CD A:ARG267 4.4 17.1 1.0 OG A:SER220 4.4 7.8 1.0 NE A:ARG267 4.4 19.9 1.0 CB A:ARG267 4.5 11.3 1.0 CG1 A:ILE273 4.6 12.4 1.0 CA A:SER224 4.6 10.4 1.0 OD1 A:ASP271 4.9 18.6 1.0 N A:LYS221 4.9 7.9 1.0 C A:LEU223 4.9 9.0 1.0 CD1 A:LEU223 4.9 10.1 1.0 CA A:ARG267 4.9 11.5 1.0 C A:ALA268 4.9 11.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Programmed For Cell Death 4 Middle MA3 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 Programmed For Cell Death 4 Middle MA3 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3 b:14.4 occ:1.00 OD2 B:ASP271 2.6 20.2 1.0 O B:HOH307 2.8 8.7 1.0 O B:SER220 2.8 7.5 1.0 C B:SER220 3.5 6.9 1.0 CA B:SER220 3.7 7.7 1.0 CG B:ASP271 3.7 17.9 1.0 CA B:ALA268 3.8 9.5 1.0 CB B:SER220 3.8 7.2 1.0 CD1 B:ILE273 3.8 15.3 1.0 O B:ARG267 3.8 11.7 1.0 N B:ALA268 3.8 8.7 1.0 C B:ARG267 3.9 9.9 1.0 CB B:ASP271 4.1 17.5 1.0 NH1 B:ARG267 4.2 25.7 1.0 CB B:ARG267 4.2 10.6 1.0 CB B:LEU223 4.2 10.2 1.0 OG B:SER220 4.2 8.9 1.0 N B:SER224 4.2 7.8 1.0 CB B:SER224 4.4 11.8 1.0 CB B:ALA268 4.4 8.8 1.0 O B:HOH323 4.4 23.5 1.0 CG1 B:ILE273 4.6 13.7 1.0 CZ B:ARG267 4.6 23.8 1.0 CA B:SER224 4.7 10.8 1.0 CA B:ARG267 4.7 10.5 1.0 N B:LYS221 4.7 8.1 1.0 NH2 B:ARG267 4.8 26.0 1.0 OD1 B:ASP271 4.8 21.6 1.0 CD2 B:LEU223 4.9 14.2 1.0 C B:LEU223 5.0 10.4 1.0 C B:ALA268 5.0 10.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Programmed For Cell Death 4 Middle MA3 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 Programmed For Cell Death 4 Middle MA3 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na5 b:16.7 occ:1.00 O A:HOH310 2.6 8.7 1.0 O B:HOH312 2.9 14.8 1.0 O B:LEU260 3.0 6.7 1.0 CE2 B:PHE264 3.4 9.0 1.0 CD2 B:PHE264 3.5 9.1 1.0 CG B:GLN263 3.5 7.0 1.0 CD B:ARG216 3.6 6.2 1.0 CB B:GLN263 3.7 7.5 1.0 C B:LEU260 3.8 6.4 1.0 CB B:ARG216 3.8 8.0 1.0 CZ B:PHE264 3.9 7.6 1.0 CA B:LEU260 4.0 6.2 1.0 CB B:LEU260 4.0 5.9 1.0 CD2 B:LEU260 4.0 7.6 1.0 CG B:PHE264 4.1 8.6 1.0 CG B:ARG216 4.2 5.9 1.0 N B:PHE264 4.2 6.7 1.0 OE1 A:GLU186 4.3 10.1 1.0 NE B:ARG216 4.4 7.3 1.0 CE1 B:PHE264 4.4 7.8 1.0 CD1 B:PHE264 4.5 8.4 1.0 O B:HOH333 4.6 20.5 1.0 C B:GLN263 4.6 5.5 1.0 CG B:LEU260 4.7 8.0 1.0 CA B:GLN263 4.7 7.7 1.0 CA B:PHE264 4.8 5.7 1.0 O A:HOH371 4.8 12.2 1.0 CB B:PHE264 4.8 7.4 1.0 CD B:GLN263 5.0 9.7 1.0

C.Suzuki, R.G.Garces, K.A.Edmonds, S.Hiller, S.G.Hyberts, A.Marintchev, G.Wagner. PDCD4 Inhibits Translation Initiation By Binding to EIF4A Using Both Its MA3 Domains. Proc.Natl.Acad.Sci.Usa V. 105 3274 2008.
ISSN: ISSN 0027-8424
PubMed: 18296639
DOI: 10.1073/PNAS.0712235105