Sodium in PDB 2r85: Crystal Structure of Purp From Pyrococcus Furiosus Complexed with Amp

The structure of Crystal Structure of Purp From Pyrococcus Furiosus Complexed with Amp, PDB code: 2r85 was solved by Y.Zhang, R.H.White, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.88 / 1.70
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	123.205, 123.205, 376.298, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 18.6

The structure of Crystal Structure of Purp From Pyrococcus Furiosus Complexed with Amp also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Purp From Pyrococcus Furiosus Complexed with Amp (pdb code 2r85). 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 Purp From Pyrococcus Furiosus Complexed with Amp, PDB code: 2r85:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Purp From Pyrococcus Furiosus Complexed with Amp


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 Purp From Pyrococcus Furiosus Complexed with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na600 b:15.1 occ:1.00 O A:ILE284 2.3 11.0 1.0 O A:GLU98 2.4 14.3 1.0 O A:HOH747 2.4 27.5 1.0 O A:HOH613 2.4 16.7 1.0 O A:HOH746 2.5 34.7 1.0 OE2 A:GLU104 2.6 17.4 1.0 C A:ILE284 3.5 11.6 1.0 C A:GLU98 3.5 14.0 1.0 CD A:GLU104 3.5 17.4 1.0 N A:ILE284 3.9 12.3 1.0 OE1 A:GLU104 4.0 18.6 1.0 CB A:GLU98 4.1 13.0 1.0 CA A:GLU98 4.1 13.2 1.0 OE2 A:GLU283 4.2 28.2 1.0 CA A:ILE284 4.3 12.1 1.0 CG2 A:ILE284 4.4 13.7 1.0 CB A:GLU283 4.4 15.0 1.0 O A:HOH757 4.4 31.3 1.0 N A:SER285 4.4 10.8 1.0 OE2 A:GLU98 4.5 14.6 1.0 N A:SER99 4.5 14.3 0.7 N A:SER99 4.5 14.5 0.3 CG A:GLU104 4.5 14.5 1.0 O A:HOH758 4.6 29.2 1.0 CA A:SER285 4.6 11.3 1.0 CG A:GLU98 4.7 13.4 1.0 CA A:SER99 4.8 14.9 0.7 C A:GLU283 4.8 13.3 1.0 CA A:SER99 4.8 15.1 0.3 CA A:GLU283 4.9 14.1 1.0 CG A:GLU283 4.9 20.3 1.0 OG A:SER285 5.0 13.8 1.0 CB A:ILE284 5.0 13.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Purp From Pyrococcus Furiosus Complexed with Amp


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 Purp From Pyrococcus Furiosus Complexed with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na600 b:16.0 occ:1.00 O B:ILE284 2.2 13.2 0.3 O B:HOH679 2.3 27.1 1.0 O B:ILE284 2.4 13.1 0.7 O B:GLU98 2.4 18.1 1.0 O B:HOH681 2.4 17.9 1.0 OE2 B:GLU104 2.4 18.1 1.0 O B:HOH680 2.5 29.2 1.0 CD B:GLU104 3.4 19.1 1.0 C B:ILE284 3.4 13.5 0.3 C B:ILE284 3.5 13.6 0.7 C B:GLU98 3.5 17.9 1.0 N B:ILE284 3.9 13.8 0.3 OE1 B:GLU104 3.9 19.4 1.0 N B:ILE284 3.9 13.9 0.7 OE1 B:GLU283 4.1 26.4 1.0 O B:HOH864 4.1 40.5 1.0 CB B:GLU98 4.2 17.2 1.0 CA B:GLU98 4.2 17.3 1.0 CA B:ILE284 4.2 13.4 0.3 CA B:ILE284 4.3 13.6 0.7 CB B:GLU283 4.4 16.1 1.0 N B:SER285 4.4 13.3 1.0 CG B:GLU104 4.4 17.4 1.0 O B:HOH682 4.5 29.8 1.0 CA B:SER285 4.5 13.5 1.0 OE2 B:GLU98 4.5 17.5 1.0 N B:SER99 4.6 18.2 0.3 N B:SER99 4.6 18.4 0.7 CG2 B:ILE284 4.7 13.8 0.7 CB B:ILE284 4.7 13.4 0.3 CG B:GLU98 4.8 17.4 1.0 C B:GLU283 4.8 14.3 1.0 CA B:SER99 4.8 18.6 0.3 OG B:SER285 4.9 15.7 1.0 CA B:SER99 4.9 19.2 0.7 CG B:GLU283 4.9 19.8 1.0 CA B:GLU283 4.9 15.1 1.0 CD B:GLU283 4.9 24.2 1.0

Y.Zhang, R.H.White, S.E.Ealick. Crystal Structure and Function of 5-Formaminoimidazole-4-Carboxamide Ribonucleotide Synthetase From Methanocaldococcus Jannaschii. Biochemistry V. 47 205 2008.
ISSN: ISSN 0006-2960
PubMed: 18069798
DOI: 10.1021/BI701406G