Sodium in PDB 1u02: Crystal Structure of Trehalose-6-Phosphate Phosphatase Related Protein

The structure of Crystal Structure of Trehalose-6-Phosphate Phosphatase Related Protein, PDB code: 1u02 was solved by N.R.Krishnamurthy, D.Kumaran, S.Swaminathan, S.K.Burley, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.92
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.995, 45.056, 53.391, 90.00, 90.65, 90.00
R / Rfree (%)	19.7 / 21.6

The structure of Crystal Structure of Trehalose-6-Phosphate Phosphatase Related Protein also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Trehalose-6-Phosphate Phosphatase Related Protein (pdb code 1u02). 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 Trehalose-6-Phosphate Phosphatase Related Protein, PDB code: 1u02:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Trehalose-6-Phosphate Phosphatase Related Protein


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 Trehalose-6-Phosphate Phosphatase Related Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na241 b:28.2 occ:1.00 O A:HOH296 2.5 17.6 1.0 OD1 A:ASP9 2.7 13.7 1.0 OG A:SER22 2.7 15.3 1.0 O A:PRO14 2.9 13.1 1.0 O A:HOH275 3.5 20.4 1.0 CG A:ASP9 3.6 13.9 1.0 CB A:SER22 3.6 13.5 1.0 NH2 A:ARG47 3.8 11.6 1.0 CB A:ASP9 3.9 12.9 1.0 C A:PRO14 3.9 15.4 1.0 CA A:ILE15 4.0 16.0 1.0 CG2 A:VAL13 4.0 15.3 1.0 N A:ILE16 4.1 17.3 1.0 CG1 A:ILE16 4.2 13.9 1.0 CA A:ASP9 4.3 12.2 1.0 N A:ILE15 4.4 15.4 1.0 O2 A:GOL251 4.4 32.9 1.0 C A:ILE15 4.5 16.7 1.0 CD1 A:ILE15 4.6 19.9 1.0 OD2 A:ASP9 4.7 15.6 1.0 CD1 A:ILE16 4.8 16.3 1.0 N A:GLY10 4.9 14.4 1.0 CA A:SER22 4.9 13.3 1.0 C2 A:GOL251 4.9 29.9 1.0 CB A:VAL13 5.0 14.4 1.0 CA A:PRO19 5.0 12.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Trehalose-6-Phosphate Phosphatase Related Protein


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 Trehalose-6-Phosphate Phosphatase Related Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na242 b:29.6 occ:1.00 O A:HOH423 2.2 22.6 1.0 O A:HOH286 3.0 19.2 1.0 N A:TYR212 3.1 17.4 1.0 O A:GLY10 3.4 15.9 1.0 O A:HOH381 3.4 47.1 1.0 CB A:ASP211 3.6 20.8 1.0 CA A:ASP211 3.6 20.0 1.0 CD2 A:TYR212 3.7 18.3 1.0 C A:ASP211 3.8 17.9 1.0 CB A:TYR212 3.8 16.9 1.0 CA A:TYR212 4.0 16.4 1.0 C A:GLY10 4.1 15.5 1.0 CG A:TYR212 4.2 17.1 1.0 CG1 A:VAL198 4.3 18.2 1.0 CA A:GLY10 4.4 14.8 1.0 CA A:PRO14 4.6 15.2 1.0 CE2 A:TYR212 4.8 18.9 1.0 O A:VAL13 4.8 14.0 1.0 O A:ASP211 4.9 16.2 1.0 CG A:ASP211 5.0 22.4 1.0

K.N.Rao, D.Kumaran, J.Seetharaman, J.B.Bonanno, S.K.Burley, S.Swaminathan. Crystal Structure of Trehalose-6-Phosphate Phosphatase-Related Protein: Biochemical and Biological Implications. Protein Sci. V. 15 1735 2006.
ISSN: ISSN 0961-8368
PubMed: 16815921
DOI: 10.1110/PS.062096606