Manganese 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:

Calcium	(Ca)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Structural Basis For Dnase Activity of A Conserved Protein Implicated in Crispr-Mediated Antiviral Defense, PDB code: 3god:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 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 Manganese with other atoms in the Mn 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:Mn325 b:51.3 occ:1.00 NE2 A:HIS254 2.3 36.6 1.0 OD2 A:ASP268 2.4 34.9 1.0 O A:HOH526 2.5 40.4 1.0 O A:HOH451 2.5 36.4 1.0 OE1 A:GLU190 2.5 38.1 1.0 CE1 A:HIS254 2.8 33.1 1.0 OD1 A:ASP268 2.9 26.5 1.0 CD A:GLU190 3.0 38.8 1.0 CG A:ASP268 3.0 24.9 1.0 OE2 A:GLU190 3.2 41.9 1.0 CD2 A:HIS254 3.5 33.9 1.0 O A:HOH362 3.8 26.5 1.0 O A:HOH662 3.9 35.5 1.0 ND1 A:HIS254 3.9 30.2 1.0 NH1 A:ARG140 4.2 24.7 0.5 CG A:GLU190 4.3 38.0 1.0 CG A:HIS254 4.3 29.1 1.0 O A:HOH437 4.3 35.3 1.0 NH2 A:ARG140 4.4 29.4 0.5 CB A:ASP268 4.5 22.1 1.0 O A:HOH487 4.7 35.1 1.0 NZ A:LYS271 4.7 31.6 1.0 CZ A:ARG140 4.8 29.3 0.5

Manganese binding site 2 out of 4 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 Manganese with other atoms in the Mn 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:Mn325 b:48.8 occ:1.00 OE1 B:GLU190 2.3 39.0 1.0 NE2 B:HIS254 2.4 34.8 1.0 OD2 B:ASP268 2.4 34.7 1.0 CD B:GLU190 2.9 38.1 1.0 CE1 B:HIS254 2.9 28.0 1.0 OD1 B:ASP268 3.0 25.7 1.0 CG B:ASP268 3.1 24.8 1.0 OE2 B:GLU190 3.1 38.8 1.0 CD2 B:HIS254 3.6 30.0 1.0 NH1 B:ARG140 3.9 25.3 0.5 O B:HOH348 4.0 37.1 1.0 ND1 B:HIS254 4.1 29.8 1.0 O B:HOH436 4.1 25.8 1.0 CG B:GLU190 4.1 34.8 1.0 NH2 B:ARG140 4.4 28.4 0.5 CG B:HIS254 4.5 25.6 1.0 CB B:ASP268 4.5 21.6 1.0 CZ B:ARG140 4.6 29.0 0.5 O B:HOH535 4.8 34.6 1.0

Manganese binding site 3 out of 4 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 Manganese with other atoms in the Mn binding site number 3 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 C:Mn325 b:69.5 occ:1.00 O C:HOH506 2.4 42.6 1.0 NE2 C:HIS254 2.7 38.1 1.0 CE1 C:HIS254 3.3 33.6 1.0 OD2 C:ASP268 3.6 35.2 1.0 O C:HOH508 3.8 47.5 1.0 CD2 C:HIS254 3.8 33.9 1.0 O C:HOH553 4.2 49.6 1.0 OD1 C:ASP268 4.4 32.8 1.0 CG C:ASP268 4.4 29.5 1.0 ND1 C:HIS254 4.5 31.6 1.0 CG C:HIS254 4.8 35.4 1.0 OE1 C:GLU190 5.0 42.6 1.0

Manganese binding site 4 out of 4 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 Manganese with other atoms in the Mn binding site number 4 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 D:Mn325 b:73.9 occ:1.00 NE2 D:HIS254 2.8 42.8 1.0 CE1 D:HIS254 3.3 34.9 1.0 OD2 D:ASP268 3.5 37.5 1.0 CD2 D:HIS254 3.8 37.1 1.0 CG D:ASP268 4.4 30.9 1.0 OD1 D:ASP268 4.4 32.8 1.0 ND1 D:HIS254 4.5 37.1 1.0 NZ D:LYS271 4.7 46.1 1.0 CG D:HIS254 4.8 39.6 1.0 OE1 D:GLU190 4.8 49.6 1.0 OE2 D:GLU190 4.8 42.9 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