Sodium in PDB 1ty8: Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp

The structure of Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp, PDB code: 1ty8 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 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.948, 38.054, 63.137, 90.00, 111.75, 90.00
R / Rfree (%)	19 / 24.4

The structure of Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp (pdb code 1ty8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp, PDB code: 1ty8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:22.9 occ:1.00 O1A A:ADP285 2.5 18.9 1.0 O A:PRO78 2.7 14.1 1.0 O A:HOH376 2.8 17.9 1.0 CG A:ASP90 3.0 16.9 1.0 O A:HOH332 3.0 19.0 1.0 N A:ASP90 3.1 13.7 1.0 OD2 A:ASP90 3.1 16.5 1.0 O A:GLY87 3.2 17.4 1.0 CB A:ASP90 3.3 15.0 1.0 OD1 A:ASP90 3.3 18.4 1.0 N A:PHE89 3.6 15.8 1.0 PA A:ADP285 3.7 15.8 1.0 CA A:ASP90 3.8 15.2 1.0 C A:PRO78 3.8 12.5 1.0 CG A:PRO78 3.9 14.1 1.0 O3A A:ADP285 3.9 13.1 1.0 C A:PHE89 4.1 16.4 1.0 CB A:PHE89 4.1 15.2 1.0 CA A:PHE89 4.2 16.3 1.0 C A:GLY88 4.2 17.1 1.0 NA A:NA302 4.2 26.4 1.0 C A:GLY87 4.3 19.8 1.0 CD A:PRO78 4.3 14.7 1.0 CA A:GLY88 4.4 16.7 1.0 O2A A:ADP285 4.5 15.4 1.0 CA A:GLY79 4.5 12.4 1.0 N A:GLY79 4.6 10.8 1.0 N A:PRO78 4.7 13.2 1.0 CB A:PRO78 4.7 14.3 1.0 CA A:PRO78 4.7 13.7 1.0 O A:HOH369 4.8 19.2 1.0 O5' A:ADP285 4.8 19.4 1.0 N A:GLY88 4.8 17.8 1.0 O A:GLY88 5.0 13.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp


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 Yeast YMX7, An Adp-Ribose-1''-Monophosphatase, Complexed with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:26.4 occ:1.00 OG1 A:THR148 2.6 5.6 1.0 O A:PRO78 2.7 14.1 1.0 O A:GLY79 2.7 9.7 1.0 O2B A:ADP285 2.8 11.5 1.0 C A:GLY79 3.1 11.0 1.0 O A:HOH369 3.2 19.2 1.0 C A:PRO78 3.3 12.5 1.0 CA A:GLY79 3.4 12.4 1.0 N A:GLY79 3.6 10.8 1.0 O1B A:ADP285 3.6 12.3 1.0 PB A:ADP285 3.7 12.7 1.0 CG2 A:VAL149 3.7 17.6 1.0 O3A A:ADP285 3.9 13.1 1.0 CB A:THR148 4.1 9.6 1.0 O A:HOH332 4.1 19.0 1.0 N A:ASN80 4.1 11.9 1.0 NA A:NA301 4.2 22.9 1.0 O A:HOH376 4.2 17.9 1.0 N A:VAL149 4.4 13.5 1.0 CG1 A:VAL149 4.4 12.9 1.0 CA A:PRO78 4.5 13.7 1.0 N A:THR148 4.5 10.1 1.0 CB A:VAL149 4.6 15.7 1.0 CB A:PRO78 4.6 14.3 1.0 CA A:THR148 4.7 9.4 1.0 CA A:ASN80 4.8 10.7 1.0 C A:THR148 4.8 13.7 1.0 CG2 A:THR148 4.9 8.7 1.0 OD2 A:ASP90 4.9 16.5 1.0 O1A A:ADP285 4.9 18.9 1.0 PA A:ADP285 4.9 15.8 1.0

D.Kumaran, S.Swaminathan. Crystal Structure of Yeast Hypothetical Protein YMX7 To Be Published.