Sodium in PDB 4c0l: Crystal Structure of Drosophila Miro Ef Hand and Cgtpase Domains Bound to One Magnesium Ion and Mg:Gdp (Mggdp-Miros)

The structure of Crystal Structure of Drosophila Miro Ef Hand and Cgtpase Domains Bound to One Magnesium Ion and Mg:Gdp (Mggdp-Miros), PDB code: 4c0l was solved by J.L.Klosowiak, P.J.Focia, Z.Wawrzak, S.Chakravarthy, E.C.Landahl, D.M.Freymann, S.E.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.825 / 3.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.510, 81.510, 154.950, 90.00, 90.00, 120.00
R / Rfree (%)	21.45 / 25.85

The structure of Crystal Structure of Drosophila Miro Ef Hand and Cgtpase Domains Bound to One Magnesium Ion and Mg:Gdp (Mggdp-Miros) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Drosophila Miro Ef Hand and Cgtpase Domains Bound to One Magnesium Ion and Mg:Gdp (Mggdp-Miros) (pdb code 4c0l). 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 Drosophila Miro Ef Hand and Cgtpase Domains Bound to One Magnesium Ion and Mg:Gdp (Mggdp-Miros), PDB code: 4c0l:

Sodium binding site 1 out of 1 in the Crystal Structure of Drosophila Miro Ef Hand and Cgtpase Domains Bound to One Magnesium Ion and Mg:Gdp (Mggdp-Miros)


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 Drosophila Miro Ef Hand and Cgtpase Domains Bound to One Magnesium Ion and Mg:Gdp (Mggdp-Miros) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1613 b:63.0 occ:1.00 OE2 A:GLU234 2.4 59.0 1.0 O A:LEU229 2.5 69.8 1.0 OD1 A:ASP223 2.8 60.2 1.0 OD1 A:ASP227 3.0 59.9 1.0 ND2 A:ASN231 3.2 62.8 1.0 OD2 A:ASP225 3.5 66.5 1.0 CD A:GLU234 3.5 53.5 1.0 N A:ASP225 3.6 58.5 1.0 CB A:ASP225 3.6 60.6 1.0 C A:LEU229 3.7 61.9 1.0 CG A:ASP227 3.8 65.6 1.0 N A:ILE224 3.8 56.6 1.0 CG A:ASP225 3.9 65.2 1.0 OD2 A:ASP227 3.9 71.6 1.0 CA A:ASP223 3.9 55.4 1.0 CG A:ASP223 4.0 64.0 1.0 C A:ASP223 4.0 60.8 1.0 N A:ASN231 4.1 56.2 1.0 CA A:ASP225 4.1 57.1 1.0 OE1 A:GLU234 4.3 51.1 1.0 CG A:ASN231 4.3 64.6 1.0 CG A:GLU234 4.4 48.8 1.0 CA A:LEU230 4.4 58.2 1.0 CG1 A:ILE224 4.5 47.1 1.0 CB A:ASP223 4.5 60.0 1.0 N A:LEU230 4.5 56.5 1.0 O A:CYS222 4.5 54.7 1.0 N A:GLY226 4.6 57.8 1.0 CB A:ASN231 4.6 59.4 1.0 C A:ILE224 4.6 55.7 1.0 N A:LEU229 4.7 62.2 1.0 CA A:LEU229 4.7 61.4 1.0 CA A:ILE224 4.7 54.0 1.0 C A:ASP225 4.8 58.9 1.0 C A:LEU230 4.8 60.3 1.0 O A:ASP223 4.9 60.3 1.0 N A:ASP227 4.9 65.9 1.0 OD1 A:ASP225 4.9 57.3 1.0 OD2 A:ASP223 5.0 65.1 1.0 CA A:ASN231 5.0 53.2 1.0

J.L.Klosowiak, P.J.Focia, S.Chakravarthy, E.C.Landahl, D.M.Freymann, S.E.Rice. Structural Coupling of the Ef Hand and C-Terminal Gtpase Domains in the Mitochondrial Protein Miro. Embo Rep. V. 14 968 2013.
ISSN: ISSN 1469-221X
PubMed: 24071720
DOI: 10.1038/EMBOR.2013.151