Sodium in PDB 2xjt: X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D1)

The structure of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D1), PDB code: 2xjt was solved by M.Veelders, S.Brueckner, D.Ott, C.Unverzagt, H.-U.Moesch, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.33 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.320, 62.010, 106.360, 90.00, 90.00, 90.00
R / Rfree (%)	13.045 / 15.316

The structure of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D1) also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D1) (pdb code 2xjt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D1), PDB code: 2xjt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1273 b:12.2 occ:1.00 O A:HOH2182 2.1 24.3 0.7 OD1 A:ASP82 2.3 17.9 1.0 OE1 A:GLN98 2.3 9.3 0.3 O A:HOH2158 2.4 29.0 1.0 O A:HOH2184 2.4 27.9 1.0 O A:HOH2332 2.4 14.2 1.0 OD1 A:ASN84 2.5 11.6 1.0 O A:HOH2154 2.6 24.5 1.0 CD A:GLN98 3.3 10.4 0.3 CG A:ASN84 3.4 10.4 1.0 CG A:ASP82 3.4 15.7 1.0 O A:HOH2183 3.6 64.5 0.7 ND2 A:ASN84 3.7 17.5 1.0 NE2 A:GLN98 3.7 10.8 0.3 OD2 A:ASP82 3.9 22.1 1.0 OG1 A:THR230 4.5 14.3 1.0 N A:GLN98 4.5 9.6 1.0 O A:TYR83 4.6 8.4 1.0 O A:HOH2064 4.6 25.8 1.0 O A:HOH2186 4.6 27.6 1.0 CB A:ASP82 4.6 13.0 1.0 CD1 A:TRP228 4.7 8.1 1.0 CG A:GLN98 4.7 9.1 0.3 C A:ASP82 4.7 12.1 1.0 CA A:ASP82 4.8 11.8 1.0 CA A:PRO97 4.8 9.8 1.0 CB A:ASN84 4.8 9.6 1.0 C A:TYR83 4.8 8.4 1.0 OE1 A:GLU99 4.9 16.7 1.0 N A:TYR83 4.9 9.6 1.0 O A:ASP82 4.9 15.5 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1275 b:16.5 occ:1.00 O A:HOH2177 3.0 29.3 0.5 O A:HOH2073 3.0 21.6 0.5 O A:HOH2162 3.0 15.2 1.0 O A:HOH2103 3.2 25.6 0.5 N A:PRO95 3.5 10.1 1.0 CB A:PRO86 3.6 9.9 1.0 C A:PHE94 3.7 9.7 1.0 CD A:PRO95 3.7 10.4 1.0 CA A:PRO86 3.8 8.9 1.0 CG A:PRO86 3.8 10.5 1.0 CA A:PRO95 3.9 10.1 1.0 CA A:PHE94 4.1 10.4 1.0 CG2 A:THR93 4.1 14.9 1.0 O A:PHE94 4.2 10.0 1.0 CB A:PRO95 4.2 10.1 1.0 N A:PHE94 4.3 10.8 1.0 N A:PRO86 4.3 8.0 1.0 O A:THR93 4.5 12.9 1.0 CG A:PRO95 4.5 11.9 1.0 O A:HOH2224 4.5 28.1 0.5 C A:THR93 4.5 12.0 1.0 O A:HOH2082 4.7 27.7 0.5 CD A:PRO86 4.7 9.2 1.0 O A:HOH2161 4.9 11.6 1.0

M.Veelders, S.Brueckner, D.Ott, C.Unverzagt, H.-U.Moesch, L.-O.Essen. Structural Basis of Flocculin-Mediated Social Behavior in Yeast Proc.Natl.Acad.Sci.Usa V. 107 22511 2010.
ISSN: ISSN 0027-8424
PubMed: 21149680
DOI: 10.1073/PNAS.1013210108