Sodium in PDB 3fd6: Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate

All present enzymatic activity of Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate:
2.7.9.3;

The structure of Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate, PDB code: 3fd6 was solved by K.T.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.96 / 1.95
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	67.618, 67.618, 182.551, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 19.6

The structure of Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate (pdb code 3fd6). 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 Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate, PDB code: 3fd6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate


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 Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na398 b:36.1 occ:1.00 O B:HOH429 2.6 7.0 1.0 O A:ASP69 2.7 16.9 1.0 O1B A:ADP393 2.7 37.3 1.0 OG1 A:THR85 3.0 12.3 1.0 C A:ASP69 3.3 15.3 1.0 O A:HOH447 3.5 14.5 1.0 PB A:ADP393 3.6 34.0 1.0 O A:MET68 3.7 20.6 1.0 O3B A:ADP393 3.8 32.9 1.0 CA A:ASP69 3.8 13.1 1.0 O A:HOH563 3.8 20.6 1.0 O2' A:ADP393 3.8 16.6 1.0 CG A:ASP110 3.8 19.2 1.0 OD1 A:ASP110 3.9 18.7 1.0 OD2 A:ASP110 4.0 19.1 1.0 O3A A:ADP393 4.1 20.9 1.0 CB A:THR85 4.1 15.4 1.0 N A:THR70 4.2 15.0 1.0 C3' A:ADP393 4.2 13.2 1.0 C2' A:ADP393 4.3 18.1 1.0 O3' A:ADP393 4.3 10.2 1.0 CB A:ASP110 4.4 13.6 1.0 CA A:THR70 4.4 18.8 1.0 O A:HOH445 4.5 13.7 1.0 C A:MET68 4.6 20.6 1.0 N A:ASP69 4.6 13.4 1.0 CA A:THR85 4.7 16.8 1.0 O A:THR86 4.8 15.4 1.0 MG A:MG396 4.8 16.0 1.0 O A:HOH470 4.9 15.2 1.0 N A:THR86 4.9 15.6 1.0 CB A:ASP69 4.9 14.7 1.0 O B:GLY162 5.0 25.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate


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 Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na398 b:20.9 occ:1.00 O3B B:ADP393 2.5 6.3 1.0 O B:ASP69 2.6 15.8 1.0 OG1 B:THR85 2.6 18.8 1.0 O B:HOH422 2.8 18.9 1.0 OD2 B:ASP110 3.3 16.5 1.0 O A:HOH421 3.3 30.7 1.0 O B:HOH591 3.5 15.9 1.0 CB B:THR85 3.5 16.0 1.0 CG B:ASP110 3.5 16.5 1.0 PB B:ADP393 3.5 13.7 1.0 C B:ASP69 3.7 18.5 1.0 O B:THR86 3.9 17.7 1.0 O1B B:ADP393 3.9 10.5 1.0 CB B:ASP110 4.0 15.5 1.0 O B:HOH430 4.0 11.2 1.0 CA B:THR85 4.1 15.7 1.0 OD1 B:ASP110 4.1 15.7 1.0 N B:THR86 4.1 16.6 1.0 O2' B:ADP393 4.2 11.1 1.0 O2B B:ADP393 4.3 14.5 1.0 O B:HOH435 4.3 12.5 1.0 CA B:ASP69 4.4 19.0 1.0 MG B:MG396 4.6 13.1 1.0 C B:THR85 4.6 15.6 1.0 N B:THR70 4.7 18.4 1.0 MG B:MG397 4.8 22.2 1.0 CG2 B:THR85 4.8 12.6 1.0 C2' B:ADP393 4.9 16.1 1.0 CA B:THR70 4.9 14.8 1.0 O3A B:ADP393 4.9 19.8 1.0 C B:THR86 4.9 18.8 1.0 O B:HOH560 4.9 20.2 1.0 O B:MET68 4.9 17.2 1.0 O A:GLY162 4.9 18.4 1.0

K.T.Wang, J.Wang, L.F.Li, X.D.Su. Crystal Structures of Catalytic Intermediates of Human Selenophosphate Synthetase 1. J.Mol.Biol. V. 390 747 2009.
ISSN: ISSN 0022-2836
PubMed: 19477186
DOI: 10.1016/J.JMB.2009.05.032