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

Protein crystallography data

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

Other elements in 3c9f:

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

Zinc (Zn) 2 atoms

Sodium Binding Sites:

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 3c9f

Go back to Sodium Binding Sites List in 3c9f
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 3c9f

Go back to Sodium Binding Sites List in 3c9f
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 3c9f

Go back to Sodium Binding Sites List in 3c9f
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 3c9f

Go back to Sodium Binding Sites List in 3c9f
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

Reference:

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.
Page generated: Tue Dec 15 06:04:13 2020

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