Sodium in PDB 1txz: Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp-Ribose

The structure of Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp-Ribose, PDB code: 1txz was solved by D.Kumaran, S.Swaminathan, S.K.Burley, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.437, 37.931, 62.514, 90.00, 112.30, 90.00
R / Rfree (%)	20 / 23.5

The binding sites of Sodium atom in the Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp-Ribose (pdb code 1txz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp-Ribose, PDB code: 1txz:

Sodium binding site 1 out of 1 in the Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp-Ribose


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 Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na289 b:26.7 occ:1.00 O A:PRO78 2.5 26.9 1.0 N A:ASP90 2.9 27.3 1.0 O1A A:APR285 2.9 23.4 1.0 CG A:ASP90 3.1 27.4 1.0 OD2 A:ASP90 3.2 28.2 1.0 C2D A:APR285 3.3 36.1 1.0 CB A:ASP90 3.4 26.0 1.0 N A:PHE89 3.5 28.8 1.0 OD1 A:ASP90 3.6 29.0 1.0 O A:GLY87 3.6 31.9 1.0 CA A:ASP90 3.7 26.6 1.0 C A:PRO78 3.7 25.9 1.0 CB A:PHE89 3.8 27.0 1.0 C A:PHE89 3.8 28.5 1.0 O3A A:APR285 3.9 23.4 1.0 O1D A:APR285 3.9 42.4 1.0 CA A:PHE89 3.9 28.6 1.0 C5D A:APR285 3.9 32.1 1.0 CG A:PRO78 3.9 24.5 1.0 PA A:APR285 3.9 22.4 1.0 O2D A:APR285 4.0 37.7 1.0 C1D A:APR285 4.1 37.3 1.0 C A:GLY88 4.2 29.1 1.0 C3D A:APR285 4.2 35.6 1.0 O4D A:APR285 4.3 38.0 1.0 C4D A:APR285 4.4 34.3 1.0 CD A:PRO78 4.4 27.8 1.0 CA A:GLY79 4.5 26.2 1.0 CA A:GLY88 4.5 28.9 1.0 N A:PRO78 4.6 25.7 1.0 N A:GLY79 4.6 25.9 1.0 CA A:PRO78 4.6 25.9 1.0 O2A A:APR285 4.7 21.7 1.0 C A:GLY87 4.7 31.7 1.0 CB A:PRO78 4.7 26.5 1.0 O5D A:APR285 4.8 26.3 1.0 C A:ASP90 5.0 25.4 1.0 O A:PHE89 5.0 29.6 1.0 O A:GLY88 5.0 28.0 1.0

D.Kumaran, S.Eswaramoorthy, F.W.Studier, S.Swaminathan. Structure and Mechanism of Adp-Ribose-1''-Monophosphatase (Appr-1''-Pase), A Ubiquitous Cellular Processing Enzyme. Protein Sci. V. 14 719 2005.
ISSN: ISSN 0961-8368
PubMed: 15722447
DOI: 10.1110/PS.041132005