Sodium in PDB 2xjr: X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D2-D3)

The structure of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D2-D3), PDB code: 2xjr 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)	19.35 / 1.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.460, 61.910, 106.430, 90.00, 90.00, 90.00
R / Rfree (%)	11.321 / 13.996

The structure of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and MAN5(D2-D3) 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(D2-D3) (pdb code 2xjr). 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(D2-D3), PDB code: 2xjr:
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(D2-D3)


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(D2-D3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1273 b:14.1 occ:1.00 O A:HOH2374 1.7 15.5 0.5 OD1 A:ASP82 2.2 18.5 1.0 OE1 A:GLN98 2.3 12.2 0.4 O A:HOH2170 2.4 38.0 1.0 OD1 A:ASN84 2.4 11.0 1.0 O A:HOH2033 2.4 13.7 1.0 O A:HOH2389 2.5 11.3 0.2 O A:HOH2192 2.7 22.8 0.5 O A:HOH2108 2.7 20.5 0.8 CD A:GLN98 3.2 13.2 0.4 CG A:ASP82 3.3 16.5 1.0 CG A:ASN84 3.4 8.7 1.0 NE2 A:GLN98 3.4 12.0 0.4 ND2 A:ASN84 3.6 14.3 1.0 O A:HOH2375 3.6 18.8 0.5 OD2 A:ASP82 3.9 22.6 1.0 O A:HOH2389 4.0 15.8 0.2 O A:TYR83 4.5 7.8 1.0 N A:GLN98 4.5 7.9 1.0 OG1 A:THR230 4.6 13.0 1.0 O A:HOH2376 4.6 44.3 1.0 CG A:GLN98 4.6 12.4 0.4 O A:HOH2319 4.6 24.0 0.8 CB A:ASP82 4.6 12.5 1.0 CD1 A:TRP228 4.6 7.6 1.0 C A:ASP82 4.6 10.9 1.0 O A:HOH2120 4.7 27.4 1.0 CA A:ASP82 4.7 10.5 1.0 CB A:ASN84 4.8 7.7 1.0 CA A:PRO97 4.8 8.0 1.0 C A:TYR83 4.8 7.4 1.0 O A:ASP82 4.9 15.9 1.0 OE1 A:GLU99 4.9 14.7 1.0 N A:TYR83 4.9 8.3 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(D2-D3)


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(D2-D3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1275 b:16.4 occ:1.00 O A:HOH2338 3.0 46.0 1.0 O A:HOH2047 3.0 14.2 1.0 O A:HOH2186 3.0 34.9 1.0 N A:PRO95 3.5 7.8 1.0 CB A:PRO86 3.6 8.4 1.0 C A:PHE94 3.7 7.4 1.0 CD A:PRO95 3.7 8.6 1.0 CA A:PRO86 3.8 7.1 1.0 CG A:PRO86 3.8 9.2 1.0 CA A:PRO95 3.9 7.7 1.0 CA A:PHE94 4.1 7.9 1.0 O A:HOH2403 4.1 17.7 0.3 CG2 A:THR93 4.1 13.7 1.0 CB A:PRO95 4.2 8.1 1.0 O A:PHE94 4.2 8.2 1.0 N A:PHE94 4.3 8.5 1.0 N A:PRO86 4.3 6.5 1.0 O A:HOH2225 4.4 38.1 1.0 O A:THR93 4.4 11.4 1.0 CG A:PRO95 4.5 10.1 1.0 C A:THR93 4.5 9.7 1.0 CD A:PRO86 4.6 7.5 1.0 O A:HOH2372 4.7 56.8 1.0 O A:HOH2016 4.9 10.1 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