Sodium in PDB 3god: Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense

The structure of Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense, PDB code: 3god was solved by B.Wiedenheft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.97 / 2.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.870, 110.960, 130.250, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 25.8

The structure of Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense (pdb code 3god). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense, PDB code: 3god:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense within 5.0Å range: probe atom residue distance (Å) B Occ A:Na326 b:38.2 occ:1.00 O A:GLY216 2.5 28.1 1.0 O A:HOH542 2.7 32.4 1.0 O A:GLY87 2.7 31.7 1.0 O A:GLY218 3.4 29.7 1.0 C A:GLY216 3.6 26.8 1.0 C A:GLY87 3.9 29.2 1.0 C A:GLY218 4.4 29.9 1.0 CA A:GLY216 4.5 26.0 1.0 N A:GLY218 4.5 27.4 1.0 N A:SER217 4.5 25.4 1.0 C A:SER217 4.5 30.0 1.0 CG A:ARG224 4.5 25.2 1.0 CA A:GLY87 4.6 26.0 1.0 CA A:SER217 4.6 28.3 1.0 CG2 A:THR89 4.6 30.0 1.0 OD2 A:ASP227 4.8 23.4 1.0 CD A:ARG224 4.9 26.9 1.0 N A:GLY88 4.9 29.9 1.0 O A:HOH358 5.0 22.1 1.0

Sodium binding site 2 out of 2 in the Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense within 5.0Å range: probe atom residue distance (Å) B Occ B:Na327 b:32.4 occ:1.00 O B:HOH667 2.1 41.8 1.0 O B:GLY216 2.2 31.3 1.0 O B:HOH373 2.4 38.0 1.0 O B:HOH365 2.5 26.7 1.0 O B:GLY87 2.8 36.1 1.0 O B:GLY218 3.1 33.1 1.0 C B:GLY216 3.3 30.9 1.0 C B:GLY87 4.0 35.1 1.0 CA B:GLY216 4.1 26.3 1.0 C B:GLY218 4.1 32.2 1.0 C B:SER217 4.2 31.6 1.0 N B:GLY218 4.3 30.9 1.0 N B:SER217 4.3 28.9 1.0 O B:SER217 4.4 33.4 1.0 CA B:SER217 4.4 31.9 1.0 CG2 B:THR89 4.5 36.9 1.0 OD2 B:ASP227 4.6 22.9 1.0 CG B:ARG224 4.6 26.9 1.0 CA B:GLY87 4.7 33.4 1.0 O B:HOH413 4.8 42.5 1.0 CA B:GLY218 4.8 27.9 1.0 O B:HOH352 4.9 27.9 1.0 N B:GLY88 5.0 34.0 1.0

B.Wiedenheft, K.Zhou, M.Jinek, S.M.Coyle, W.Ma, J.A.Doudna. Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Genome Defense. Structure V. 17 904 2009.
ISSN: ISSN 0969-2126
PubMed: 19523907
DOI: 10.1016/J.STR.2009.03.019