Manganese in PDB 4ogc: Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii

The structure of Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii, PDB code: 4ogc was solved by F.Jiang, E.Ma, S.Lin, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.30 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.610, 132.560, 80.040, 90.00, 95.38, 90.00
R / Rfree (%)	19.4 / 23.3

The structure of Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Manganese atom in the Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii (pdb code 4ogc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii, PDB code: 4ogc:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1202 b:58.9 occ:1.00 OD2 A:ASP17 2.1 46.3 1.0 ND1 A:HIS736 2.2 59.3 1.0 O A:HOH1302 2.3 28.2 1.0 CE1 A:HIS736 2.9 55.4 1.0 CG A:ASP17 3.1 46.5 1.0 CG A:HIS736 3.4 56.5 1.0 OD1 A:ASP17 3.4 54.3 1.0 OD2 A:ASP739 3.7 64.0 1.0 MN A:MN1206 3.8 64.8 1.0 CB A:HIS736 3.9 55.0 1.0 NE2 A:HIS736 4.1 49.7 1.0 CA A:HIS736 4.1 55.9 1.0 CD2 A:HIS736 4.3 49.6 1.0 O A:ASP17 4.4 46.9 1.0 CB A:ASP17 4.4 41.9 1.0 OG A:SER22 4.7 60.8 1.0 CD2 A:HIS735 4.7 73.2 1.0 CG A:ASP739 4.7 61.6 1.0 CA A:GLY19 4.8 50.8 1.0 NE2 A:HIS735 4.8 73.9 1.0 O A:VAL18 4.8 47.4 1.0 CB A:ASP739 4.9 55.0 1.0 C A:ASP17 4.9 42.1 1.0 N A:GLY19 4.9 50.5 1.0 N A:HIS736 4.9 60.4 1.0 C A:VAL18 5.0 43.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Type II-C CAS9 Enzyme From Actinomyces Naeslundii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1206 b:64.8 occ:1.00 OE1 A:GLU505 2.1 71.0 1.0 OD1 A:ASP17 2.1 54.3 1.0 CD A:GLU505 3.0 70.2 1.0 CG A:ASP17 3.2 46.5 1.0 O A:HOH1302 3.3 28.2 1.0 CG A:GLU505 3.6 63.9 1.0 OD2 A:ASP17 3.7 46.3 1.0 MN A:MN1202 3.8 58.9 1.0 OE2 A:GLU505 3.8 72.2 1.0 OD2 A:ASP739 4.0 64.0 1.0 OG1 A:THR706 4.1 58.5 1.0 O A:VAL18 4.3 47.4 1.0 O A:GLY703 4.4 59.9 1.0 CB A:GLU505 4.4 57.3 1.0 CB A:ASP17 4.5 41.9 1.0 CG A:ASP739 4.5 61.6 1.0 CB A:ASP739 4.6 55.0 1.0 O A:HIS506 4.8 66.9 1.0 O A:GLU505 4.9 58.9 1.0 CA A:ASP17 5.0 42.0 1.0

M.Jinek, F.Jiang, D.W.Taylor, S.H.Sternberg, E.Kaya, E.Ma, C.Anders, M.Hauer, K.Zhou, S.Lin, M.Kaplan, A.T.Iavarone, E.Charpentier, E.Nogales, J.A.Doudna. Structures of CAS9 Endonucleases Reveal Rna-Mediated Conformational Activation. Science V. 343 47997 2014.
ISSN: ISSN 0036-8075
PubMed: 24505130
DOI: 10.1126/SCIENCE.1247997