Sodium in PDB 4zac: Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form.

The structure of Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form., PDB code: 4zac 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)	54.19 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	114.410, 96.180, 116.640, 90.00, 96.58, 90.00
R / Rfree (%)	16.3 / 19.2

The structure of Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Manganese	(Mn)	4 atoms

The binding sites of Sodium atom in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. (pdb code 4zac). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form., PDB code: 4zac:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:27.2 occ:1.00 O A:HOH958 2.0 36.7 1.0 O A:HOH1040 2.1 36.7 1.0 O A:HOH1061 2.3 40.8 1.0 O A:HOH1067 2.4 47.3 1.0 OD1 A:ASP62 2.4 25.9 1.0 OD1 A:ASP310 2.6 32.4 1.0 OD2 A:ASP62 2.7 28.3 1.0 CG A:ASP62 2.9 25.0 1.0 CG A:ASP310 3.6 30.9 1.0 CB A:ASP310 4.1 25.4 1.0 CE1 A:HIS127 4.1 29.3 1.0 CG A:LYS61 4.2 45.9 1.0 CB A:ASP62 4.4 25.0 1.0 CA A:ASP310 4.4 24.9 1.0 NE2 A:HIS127 4.6 34.1 1.0 OD2 A:ASP310 4.6 35.6 1.0 O A:HOH950 4.7 41.6 1.0 N A:ASN311 4.8 20.9 1.0 O A:HOH715 4.8 33.8 1.0 OD1 A:ASN311 4.8 31.2 1.0

Sodium binding site 2 out of 3 in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:22.8 occ:1.00 O B:HOH939 2.0 33.6 1.0 O B:HOH949 2.2 36.3 1.0 O B:HOH1015 2.4 38.3 1.0 O B:HOH1004 2.4 35.1 1.0 OD1 B:ASP62 2.4 22.3 1.0 OD1 B:ASP310 2.5 28.1 1.0 OD2 B:ASP62 2.5 25.4 1.0 CG B:ASP62 2.8 22.5 1.0 CG B:ASP310 3.5 21.5 1.0 CE1 B:HIS127 4.1 26.8 1.0 CB B:ASP310 4.1 21.5 1.0 CB B:ASP62 4.4 21.0 1.0 CA B:ASP310 4.4 21.1 1.0 OD2 B:ASP310 4.4 33.9 1.0 NE2 B:HIS127 4.5 33.5 1.0 O B:HOH950 4.6 36.6 1.0 O B:HOH712 4.7 31.1 1.0 OD1 B:ASN311 4.8 29.8 1.0 N B:ASN311 4.9 20.2 1.0 O B:HOH1000 4.9 46.5 1.0

Sodium binding site 3 out of 3 in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na604 b:38.6 occ:1.00 O C:HOH863 1.9 42.5 1.0 O C:HOH928 2.3 42.5 1.0 OD1 C:ASP310 2.3 36.2 1.0 OD1 C:ASP62 2.6 35.0 1.0 OD2 C:ASP62 2.8 38.9 1.0 CG C:ASP62 3.0 38.4 1.0 CG C:ASP310 3.4 35.6 1.0 CB C:ASP310 4.0 33.5 1.0 CE1 C:HIS127 4.1 42.2 1.0 CA C:ASP310 4.3 32.5 1.0 OD2 C:ASP310 4.4 38.0 1.0 CB C:ASP62 4.5 37.5 1.0 NE2 C:HIS127 4.6 39.8 1.0 N C:ASN311 4.8 30.6 1.0

K.A.Payne, M.D.White, K.Fisher, B.Khara, S.S.Bailey, D.Parker, N.J.Rattray, D.K.Trivedi, R.Goodacre, R.Beveridge, P.Barran, S.E.Rigby, N.S.Scrutton, S.Hay, D.Leys. New Cofactor Supports Alpha , Beta-Unsaturated Acid Decarboxylation Via 1,3-Dipolar Cycloaddition. Nature V. 522 502 2015.
ISSN: ESSN 1476-4687
PubMed: 26083754
DOI: 10.1038/NATURE14560