Sodium in PDB 3c9f: Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314

The structure of Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314, PDB code: 3c9f was solved by Y.Patskovsky, R.Romero, M.Gilmore, M.Eberle, K.Bain, D.Smith, S.R.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.946, 106.740, 150.656, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.5

The structure of Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314 (pdb code 3c9f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314, PDB code: 3c9f:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:44.8 occ:1.00 O A:HOH639 2.3 42.0 1.0 O A:HOH870 2.4 48.8 1.0 O A:HOH806 2.4 32.4 1.0 O A:HOH906 2.5 50.4 1.0 O A:HIS477 2.5 38.7 1.0 C A:HIS477 3.6 37.3 1.0 O A:HOH707 4.1 28.1 1.0 N A:HIS477 4.1 33.8 1.0 O A:HOH914 4.2 50.8 1.0 CA A:HIS477 4.3 38.4 1.0 CB A:HIS477 4.3 40.4 1.0 O A:HOH864 4.4 45.1 1.0 OD1 A:ASP254 4.6 38.7 1.0 N A:ASP478 4.6 37.6 1.0 CA A:ASP478 4.8 40.6 1.0 CG2 A:THR476 5.0 27.6 1.0 O A:HOH813 5.0 44.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:59.9 occ:1.00 O B:HOH838 2.4 42.0 1.0 OD1 B:ASN94 2.5 46.5 1.0 O B:THR91 2.6 44.5 1.0 O B:ASP89 2.9 38.5 1.0 O B:HOH823 3.4 50.6 1.0 CG B:ASN94 3.7 35.1 1.0 O B:HOH716 3.7 58.0 1.0 C B:THR91 3.7 42.1 1.0 C B:ASP89 3.9 37.3 1.0 N B:ASN94 4.1 41.5 1.0 O B:HOH886 4.1 50.7 1.0 CA B:SER92 4.3 48.4 1.0 CA B:ASP89 4.4 30.0 1.0 OG B:SER92 4.4 57.4 1.0 CA B:ASN94 4.4 42.4 1.0 N B:SER92 4.4 45.1 1.0 C B:PRO93 4.5 40.6 1.0 ND2 B:ASN94 4.5 48.6 1.0 N B:THR91 4.6 37.3 1.0 CB B:ASN94 4.6 44.4 1.0 CB B:SER92 4.7 54.1 1.0 C B:ILE90 4.8 37.5 1.0 OE1 B:GLU411 4.8 57.9 1.0 CA B:THR91 4.8 39.9 1.0 N B:ILE90 4.9 31.6 1.0 CB B:ASP89 4.9 31.6 1.0 O B:PRO93 5.0 39.1 1.0 O B:HOH1056 5.0 53.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na604 b:44.6 occ:1.00 O B:HOH735 2.3 43.9 1.0 O B:HIS477 2.3 25.5 1.0 O B:HOH648 2.4 25.2 1.0 O B:HOH998 2.4 44.8 1.0 O B:HOH999 2.5 48.6 1.0 O B:HOH1039 2.9 54.4 1.0 C B:HIS477 3.5 21.6 1.0 O B:HOH675 3.8 28.7 1.0 N B:HIS477 4.0 23.4 1.0 CA B:HIS477 4.2 27.3 1.0 O B:HOH953 4.2 44.5 1.0 CB B:HIS477 4.3 24.8 1.0 O B:HOH1052 4.5 62.0 1.0 N B:ASP478 4.5 26.8 1.0 O B:HOH722 4.5 43.2 1.0 O B:HOH885 4.6 53.6 1.0 OD1 B:ASP254 4.6 27.0 1.0 CA B:ASP478 4.7 27.0 1.0 O B:ARG253 4.9 21.7 1.0 CG2 B:THR476 4.9 15.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of 5'-Nucleotidase From Candida Albicans SC5314 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:54.4 occ:1.00 O B:HOH764 2.3 40.2 1.0 O B:HOH742 2.3 41.2 1.0 O A:HOH736 2.5 37.2 1.0 O B:LYS314 2.5 26.5 1.0 O B:HOH747 2.7 41.7 1.0 O B:HOH883 2.9 48.3 1.0 C B:LYS314 3.5 22.1 1.0 O B:HOH980 3.6 48.0 1.0 OD2 B:ASP317 4.0 42.3 1.0 O B:HOH770 4.0 46.5 1.0 O B:HOH1025 4.1 54.1 1.0 CB B:ASP317 4.1 31.4 1.0 CA B:LYS314 4.2 22.0 1.0 CD B:LYS314 4.4 28.2 1.0 O B:ASP313 4.4 30.9 1.0 N B:ASP317 4.4 26.0 1.0 CG B:ASP317 4.4 38.9 1.0 NZ B:LYS314 4.5 38.1 1.0 N B:GLU315 4.6 24.5 1.0 N B:PHE316 4.7 27.5 1.0 CG B:LYS314 4.8 23.4 1.0 CE B:LYS314 4.8 35.0 1.0 CA B:ASP317 4.9 28.1 1.0 O A:HOH706 4.9 33.8 1.0 CA B:GLU315 4.9 26.2 1.0

Y.Patskovsky, R.Romero, M.Gilmore, M.Eberle, K.Bain, D.Smith, S.R.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of 5'-Nucleotidase From Candida Albicans. To Be Published.