Sodium in PDB 2xjp: X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and Mannose

The structure of X-Ray Structure of the N-Terminal Domain of the Flocculin FLO5 From Saccharomyces Cerevisiae in Complex with Calcium and Mannose, PDB code: 2xjp 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)	20.00 / 0.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.280, 61.820, 106.260, 90.00, 90.00, 90.00
R / Rfree (%)	10.523 / 12.236

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

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

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 Mannose (pdb code 2xjp). 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 Mannose, PDB code: 2xjp:
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 Mannose


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 Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1273 b:9.3 occ:1.00 O A:HOH2421 2.0 18.3 0.5 OD1 A:ASP82 2.3 13.1 1.0 O A:HOH2127 2.4 20.8 0.8 O A:HOH2031 2.4 10.9 1.0 OD1 A:ASN84 2.4 10.6 0.2 O A:HOH2263 2.4 17.0 0.6 O A:HOH2287 2.5 11.7 0.3 OD1 A:ASN84 2.5 8.6 0.8 O A:HOH2421 2.6 16.9 0.5 O A:HOH2287 2.6 18.4 0.7 O A:HOH2263 2.6 14.3 0.4 HD22 A:ASN84 3.2 11.4 0.0 O A:HOH2259 3.3 22.5 0.8 HD22 A:ASN84 3.3 9.7 0.0 CG A:ASP82 3.4 12.9 1.0 CG A:ASN84 3.4 6.4 0.2 CG A:ASN84 3.4 8.2 0.8 H A:GLN98 3.7 8.0 1.0 ND2 A:ASN84 3.7 11.4 0.8 ND2 A:ASN84 3.7 10.3 0.2 HG1 A:THR230 3.8 11.1 1.0 OD2 A:ASP82 3.8 17.7 0.6 HD1 A:TRP228 3.9 7.0 1.0 HA A:PRO97 3.9 7.6 1.0 HA A:ASP82 4.3 8.7 1.0 OG1 A:THR230 4.5 11.3 1.0 O A:TYR83 4.5 6.7 1.0 O A:HOH2114 4.5 24.3 1.0 N A:GLN98 4.5 8.1 1.0 CD1 A:TRP228 4.6 7.0 1.0 CB A:ASP82 4.6 10.4 1.0 O A:HOH2102 4.6 10.8 0.6 HB3 A:PRO97 4.7 9.4 1.0 O A:HOH2193 4.7 27.3 0.9 HD21 A:ASN84 4.7 11.4 0.0 HD21 A:ASN84 4.7 9.7 0.0 C A:ASP82 4.7 8.5 1.0 CB A:ASN84 4.7 9.2 0.2 CA A:ASP82 4.8 8.6 1.0 CA A:PRO97 4.8 7.6 1.0 HG21 A:THR230 4.8 15.0 1.0 HB2 A:GLN98 4.8 12.6 1.0 HA A:ASN84 4.8 6.5 0.8 HA A:ASN84 4.8 7.9 0.2 OE1 A:GLU99 4.8 9.5 0.8 C A:TYR83 4.8 6.3 1.0 CB A:ASN84 4.8 7.3 0.8 N A:TYR83 4.9 7.3 1.0 HB3 A:ASN84 5.0 8.9 0.2 HB3 A:GLN98 5.0 12.5 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 Mannose


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 Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1275 b:10.3 occ:1.00 O A:HOH2138 2.9 17.9 0.3 O A:HOH2168 3.0 25.9 0.9 O A:HOH2023 3.0 10.5 1.0 HB3 A:PRO86 3.1 7.6 1.0 HD3 A:PRO95 3.1 8.7 1.0 HG3 A:PRO86 3.1 7.9 1.0 HA A:PRO86 3.1 6.6 1.0 O A:HOH2310 3.2 24.2 0.5 O A:HOH2138 3.3 17.8 0.7 HG23 A:THR93 3.3 11.2 1.0 HA A:PRO95 3.5 7.6 1.0 N A:PRO95 3.5 7.8 1.0 HB3 A:PRO95 3.6 8.2 1.0 CB A:PRO86 3.6 7.7 1.0 C A:PHE94 3.7 7.5 1.0 CD A:PRO95 3.7 8.7 1.0 CA A:PRO86 3.8 6.7 1.0 HA A:PHE94 3.8 7.9 1.0 CG A:PRO86 3.8 8.0 1.0 CA A:PRO95 3.9 7.5 1.0 CB A:PRO95 4.1 8.2 1.0 CA A:PHE94 4.1 8.0 1.0 CG2 A:THR93 4.2 11.2 1.0 O A:PHE94 4.2 7.6 1.0 HG21 A:THR93 4.2 11.2 1.0 N A:PRO86 4.3 6.2 1.0 N A:PHE94 4.3 7.7 1.0 O A:HOH2416 4.4 30.1 0.5 HD2 A:PRO95 4.5 8.7 1.0 CG A:PRO95 4.5 10.0 1.0 HG2 A:PRO86 4.5 7.8 1.0 HB2 A:PRO86 4.6 7.6 1.0 HG22 A:THR93 4.6 11.2 1.0 O A:THR93 4.6 9.9 1.0 O A:HOH2399 4.6 28.2 0.5 C A:THR93 4.6 8.2 1.0 HG3 A:PRO95 4.6 9.7 1.0 CD A:PRO86 4.6 6.7 1.0 H A:PHE94 4.6 7.8 1.0 H A:CYS87 4.7 6.4 1.0 HD3 A:PRO86 4.8 6.7 1.0 O A:HOH2291 4.8 39.3 1.0 O A:HOH2012 4.9 8.7 1.0 C A:ILE85 4.9 6.1 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