Sodium in PDB 2x5x: The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode

The structure of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode, PDB code: 2x5x was solved by S.Wakadkar, S.Hermawan, D.Jendrossek, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.630, 140.580, 56.750, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 17.6

The structure of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode also contains other interesting chemical elements:

Iodine	(I)	8 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Sodium atom in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode (pdb code 2x5x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode, PDB code: 2x5x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1357 b:10.7 occ:1.00 I A:IOD1343 1.8 19.2 1.0 OG A:SER35 3.1 31.4 0.5 CA A:GLY20 3.6 9.3 1.0 N A:GLY20 3.8 9.0 1.0 CB A:SER35 4.3 18.8 0.5 O A:HOH2045 4.3 60.9 1.0 CB A:SER35 4.3 20.4 0.5 N A:SER35 4.4 12.7 1.0 O A:HOH2108 4.4 33.3 1.0 C A:GLY34 4.5 10.1 1.0 CA A:SER35 4.6 15.5 0.5 CA A:SER35 4.6 15.8 0.5 C A:GLY20 4.8 9.8 1.0 O A:GLY34 4.8 11.2 1.0 CA A:GLY34 5.0 10.3 1.0

Sodium binding site 2 out of 2 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1358 b:13.6 occ:1.00 O A:HOH2498 1.8 26.4 1.0 OH A:TYR204 3.3 34.5 1.0 CB A:SER250 3.6 22.1 1.0 CD1 A:TYR173 3.7 21.6 1.0 CE2 A:PHE251 3.7 22.0 1.0 OG A:SER250 3.7 23.1 1.0 CA A:TYR173 3.8 16.1 1.0 OD2 A:ASP284 3.8 28.4 1.0 CD2 A:PHE251 3.9 23.6 1.0 OD1 A:ASP284 3.9 31.7 1.0 CG A:ASP284 3.9 27.6 1.0 CB A:TYR173 4.0 19.4 1.0 N A:TYR173 4.0 14.4 1.0 CZ A:TYR204 4.2 26.7 1.0 O A:HOH2390 4.2 42.8 1.0 CE2 A:TYR204 4.2 22.6 1.0 CG A:TYR173 4.3 19.1 1.0 C A:TYR172 4.4 12.8 1.0 O A:HOH2345 4.5 20.2 1.0 CB A:TYR172 4.6 14.0 1.0 O A:TYR172 4.6 15.1 1.0 CE1 A:TYR173 4.7 26.6 1.0 CA A:SER250 4.8 20.9 1.0 CB A:ASP284 4.9 25.4 1.0 CZ A:PHE251 4.9 27.1 1.0 N A:SER250 5.0 19.2 1.0

S.Wakadkar, S.Hermawan, D.Jendrossek, A.C.Papageorgiou. The Structure of PHAZ7 at Atomic (1.2 A) Resolution Reveals Details of the Active Site and Suggests A Substrate-Binding Mode. Acta Crystallogr. Sect. F V. 66 648 2010STRUCT. Biol. Cryst. Commun..
ISSN: ESSN 1744-3091
PubMed: 20516591
DOI: 10.1107/S174430911001434X