Sodium in PDB 4zaz: Structure of Ubix Y169F in Complex with A Covalent Adduct Formed Between Reduced Fmn and Dimethylallyl Monophosphate

The structure of Structure of Ubix Y169F in Complex with A Covalent Adduct Formed Between Reduced Fmn and Dimethylallyl Monophosphate, PDB code: 4zaz was solved by M.D.White, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.30 / 1.45
Space group	F 2 3
Cell size a, b, c (Å), α, β, γ (°)	142.260, 142.260, 142.260, 90.00, 90.00, 90.00
R / Rfree (%)	10.3 / 14.7

The binding sites of Sodium atom in the Structure of Ubix Y169F in Complex with A Covalent Adduct Formed Between Reduced Fmn and Dimethylallyl Monophosphate (pdb code 4zaz). 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 Structure of Ubix Y169F in Complex with A Covalent Adduct Formed Between Reduced Fmn and Dimethylallyl Monophosphate, PDB code: 4zaz:

Sodium binding site 1 out of 1 in the Structure of Ubix Y169F in Complex with A Covalent Adduct Formed Between Reduced Fmn and Dimethylallyl Monophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Ubix Y169F in Complex with A Covalent Adduct Formed Between Reduced Fmn and Dimethylallyl Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:32.3 occ:1.00 O A:HOH552 2.5 50.9 1.0 O A:HOH404 2.7 45.9 1.0 O A:HOH509 3.3 18.2 1.0 N A:LYS40 3.3 15.9 0.5 N A:LYS40 3.3 15.9 0.5 CA A:SER39 3.8 14.3 1.0 CG A:LYS40 3.9 23.0 0.5 CB A:SER39 3.9 15.7 1.0 CB A:LYS40 3.9 22.5 0.5 CG A:GLN81 4.0 21.7 1.0 CB A:LYS40 4.0 21.6 0.5 C A:SER39 4.1 14.8 1.0 O A:HOH547 4.2 36.2 1.0 CA A:LYS40 4.2 17.2 0.5 CA A:LYS40 4.3 16.9 0.5 NE2 A:GLN81 4.5 32.3 1.0 CB A:GLN81 4.5 18.9 1.0 CD A:LYS40 4.5 35.6 0.5 ND2 A:ASN118 4.5 28.8 1.0 CD A:GLN81 4.7 24.3 1.0 O A:HOH514 4.9 34.2 1.0 OG A:SER39 5.0 14.7 1.0

M.D.White, K.A.Payne, K.Fisher, S.A.Marshall, D.Parker, N.J.Rattray, D.K.Trivedi, R.Goodacre, S.E.Rigby, N.S.Scrutton, S.Hay, D.Leys. Ubix Is A Flavin Prenyltransferase Required For Bacterial Ubiquinone Biosynthesis. Nature V. 522 497 2015.
ISSN: ESSN 1476-4687
PubMed: 26083743
DOI: 10.1038/NATURE14559