Magnesium in PDB 8d2o: Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2)

The binding sites of Magnesium atom in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2) (pdb code 8d2o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2), PDB code: 8d2o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:56.3 occ:1.00 ND1 A:HIS750 2.2 35.9 1.0 OD2 A:ASP18 2.5 38.3 1.0 CE1 A:HIS750 2.7 36.4 1.0 CG A:ASP18 3.3 33.6 1.0 O A:HOH1303 3.4 37.9 1.0 CG A:HIS750 3.4 34.6 1.0 CB A:ASP18 3.5 36.9 1.0 CA A:HIS750 4.0 34.0 1.0 NE2 A:HIS750 4.0 38.0 1.0 CB A:HIS750 4.0 36.5 1.0 OD2 A:ASP753 4.2 44.2 1.0 O A:HOH1302 4.2 41.8 1.0 CD2 A:HIS750 4.3 33.5 1.0 OD1 A:ASP18 4.4 32.9 1.0 CB A:ASP753 4.5 40.0 1.0 CD2 A:HIS749 4.5 39.5 1.0 NE2 A:HIS749 4.7 42.6 1.0 CA A:ASP18 4.8 37.8 1.0 O A:HIS750 4.8 26.8 1.0 C A:ASP18 4.8 36.3 1.0 N A:HIS750 4.8 37.0 1.0 CG A:ASP753 4.8 46.0 1.0 O A:ASP18 4.8 39.1 1.0 C A:HIS750 4.9 33.2 1.0

Magnesium binding site 2 out of 5 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:32.2 occ:1.00 OP1 B:U22 2.8 29.6 1.0 OP2 B:A23 2.8 30.6 1.0 O A:ARG137 3.3 19.6 1.0 O5' B:U22 3.4 21.5 1.0 CG A:ARG139 3.5 17.3 1.0 N A:ARG139 3.5 14.1 1.0 C5' B:U22 3.5 19.7 1.0 P B:A23 3.6 29.0 1.0 P B:U22 3.7 14.7 1.0 OP1 B:A23 3.7 24.7 1.0 O3' B:U22 3.9 28.9 1.0 C A:ARG137 4.0 14.4 1.0 CA A:HIS138 4.0 7.1 1.0 C A:HIS138 4.2 14.8 1.0 N A:HIS138 4.2 15.3 1.0 C3' B:U22 4.3 26.5 1.0 O A:ALA136 4.3 19.1 1.0 NE A:ARG139 4.3 13.4 1.0 CA A:ARG139 4.4 14.5 1.0 C4' B:U22 4.4 22.0 1.0 CD A:ARG139 4.4 13.0 1.0 CB A:ARG139 4.4 10.3 1.0 NH2 A:ARG80 4.4 20.3 1.0 N A:GLY140 4.5 22.3 1.0 OP2 B:U22 4.5 33.6 1.0 C A:ARG139 4.9 19.3 1.0 O3' B:G21 4.9 15.7 1.0 O A:GLY140 5.0 25.6 1.0

Magnesium binding site 3 out of 5 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:30.3 occ:1.00 OP2 B:C48 3.0 17.9 1.0 C5 B:U49 3.2 29.8 1.0 OP2 B:U49 3.2 20.6 1.0 O5' B:C48 3.2 29.6 1.0 CE1 A:HIS138 3.6 17.6 1.0 NE2 A:HIS138 3.6 14.8 1.0 P B:C48 3.7 15.9 1.0 C6 B:C48 3.8 23.7 1.0 C6 B:U49 4.0 31.0 1.0 MG B:MG203 4.0 24.4 1.0 C3' B:C48 4.0 24.3 1.0 C5 B:C48 4.1 24.9 1.0 C4 B:U49 4.2 28.3 1.0 O4 B:U49 4.3 28.8 1.0 C5' B:C48 4.4 22.2 1.0 P B:U49 4.4 16.0 1.0 OP1 B:C48 4.4 28.4 1.0 N1 B:C48 4.6 28.2 1.0 C4' B:C48 4.6 25.4 1.0 O3' B:C48 4.7 22.3 1.0 C2' B:C48 4.8 24.6 1.0 O5' B:U49 4.8 37.2 1.0 O4' B:C48 4.9 27.8 1.0 ND1 A:HIS138 4.9 17.1 1.0 C1' B:C48 5.0 27.5 1.0 CD2 A:HIS138 5.0 4.8 1.0

Magnesium binding site 4 out of 5 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:24.4 occ:1.00 OP2 B:U49 2.8 20.6 1.0 OP2 B:A50 3.1 35.0 1.0 O5' B:U49 3.3 37.2 1.0 CG A:ARG137 3.3 14.9 1.0 P B:U49 3.5 16.0 1.0 NH2 A:ARG77 3.7 20.7 1.0 CB A:ARG137 3.9 19.6 1.0 MG B:MG202 4.0 30.3 1.0 C6 B:U49 4.1 31.0 1.0 NE2 A:HIS138 4.1 14.8 1.0 OP1 B:U49 4.2 32.9 1.0 C5 B:U49 4.3 29.8 1.0 C3' B:U49 4.3 26.7 1.0 C5' B:U49 4.5 23.4 1.0 P B:A50 4.5 33.1 1.0 CE1 A:HIS138 4.6 17.6 1.0 CD A:ARG137 4.6 13.1 1.0 O3' B:U49 4.8 24.7 1.0 NE A:ARG137 4.9 5.2 1.0 C4' B:U49 4.9 24.6 1.0 O3' B:C48 4.9 22.3 1.0

Magnesium binding site 5 out of 5 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Post- Cleavage 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:29.5 occ:1.00 OP1 B:A53 2.9 5.0 1.0 OP1 B:C52 3.1 41.0 1.0 C5' B:A53 3.4 21.8 1.0 O6 B:G72 3.5 32.7 1.0 OP2 B:A54 3.5 33.4 1.0 N1 B:G72 3.5 21.0 1.0 C6 B:G72 3.9 28.4 1.0 C5' B:C52 4.0 26.4 1.0 O5' B:A53 4.0 28.5 1.0 P B:A53 4.0 10.5 1.0 P B:A54 4.2 23.1 1.0 OP1 B:A54 4.3 23.1 1.0 P B:C52 4.3 20.9 1.0 O5' B:C52 4.3 36.1 1.0 C4' B:A53 4.5 10.6 1.0 O3' B:A53 4.5 25.1 1.0 C2 B:G72 4.6 24.8 1.0 CD A:ARG71 4.7 11.8 1.0 N2 B:G72 4.7 23.9 1.0 O3' B:C52 4.8 33.6 1.0 C3' B:A53 4.8 10.4 1.0 C4' B:C52 5.0 21.3 1.0

A.Das, J.Rai, M.O.Roth, Y.Shu, M.L.Medina, M.R.Barakat, H.Li. Coupled Catalytic States and the Role of Metal Coordination in CAS9 Nat Catal V. 6 969 2023.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-023-01031-1