Magnesium in PDB 9ar4: Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam

The binding sites of Magnesium atom in the Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam (pdb code 9ar4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam, PDB code: 9ar4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:48.2 occ:1.00 OP2 B:A101 2.1 62.3 1.0 O B:HOH304 2.2 38.9 1.0 O B:HOH306 2.3 43.6 1.0 O B:HOH309 2.8 53.3 1.0 P B:A101 3.4 38.0 1.0 N7 B:G94 3.6 40.3 1.0 O4 B:U95 4.0 49.7 1.0 OP1 B:A101 4.0 49.2 1.0 O6 B:G94 4.1 46.1 1.0 C3' B:G100 4.2 54.9 1.0 O3' B:G100 4.2 52.0 1.0 C5 B:C93 4.3 34.7 1.0 O B:HOH305 4.4 39.2 1.0 C5 B:G94 4.4 44.4 1.0 OP2 B:G94 4.5 41.6 1.0 C8 B:G94 4.5 37.0 1.0 O5' B:A101 4.6 48.2 1.0 C5' B:G100 4.6 53.7 1.0 C6 B:G94 4.6 40.8 1.0 C5' B:A101 4.6 48.7 1.0 C4 B:C93 4.7 32.3 1.0 OP2 B:C93 4.7 36.3 1.0 O B:HOH301 4.8 50.8 1.0 C6 B:C93 4.8 32.2 1.0 N4 B:C93 4.8 33.0 1.0 C4 B:U95 4.9 50.7 1.0

Magnesium binding site 2 out of 6 in the Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:43.4 occ:1.00 OP1 B:U102 2.6 54.9 1.0 O B:HOH308 2.9 45.7 1.0 OG1 A:THR812 3.0 33.2 1.0 OP2 B:U102 3.1 49.3 1.0 P B:U102 3.3 43.8 1.0 CG2 A:THR812 3.4 17.6 1.0 CB A:THR812 3.8 24.5 1.0 CB A:SER810 3.8 18.7 1.0 OG A:SER810 3.8 34.8 1.0 N A:THR812 4.3 20.6 1.0 N A:ILE811 4.4 22.0 1.0 O3' B:A101 4.5 51.5 1.0 O5' B:U102 4.5 55.1 1.0 C5' B:U102 4.5 50.6 1.0 CA A:SER810 4.6 15.1 1.0 CA A:THR812 4.7 15.9 1.0 OP2 B:G91 4.9 34.9 1.0 C A:SER810 5.0 26.9 1.0

Magnesium binding site 3 out of 6 in the Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:37.7 occ:1.00 O A:HOH1201 2.0 34.1 1.0 OD2 A:ASP8 2.1 42.3 1.0 ND1 A:HIS720 2.1 33.6 1.0 OP3 D:DG27 2.2 46.3 0.0 OP2 D:DG27 2.3 49.0 1.0 CE1 A:HIS720 2.7 32.0 1.0 P D:DG27 2.8 46.9 1.0 CG A:ASP8 3.2 36.2 1.0 CG A:HIS720 3.4 32.3 1.0 O A:HOH1204 3.4 24.8 1.0 MG A:MG1102 3.4 33.5 1.0 OD2 A:ASP723 3.6 44.9 1.0 OD1 A:ASP8 3.6 43.8 1.0 O A:HOH1207 3.6 31.0 1.0 O5' D:DG27 3.7 49.0 1.0 NE2 A:HIS720 3.9 29.7 1.0 CB A:HIS720 4.0 29.1 1.0 OP1 D:DG27 4.0 45.5 1.0 CA A:HIS720 4.1 28.6 1.0 CD2 A:HIS720 4.3 24.1 1.0 C5' D:DG27 4.3 45.6 1.0 ND1 A:HIS719 4.4 32.7 1.0 CE1 A:HIS719 4.4 25.8 1.0 O A:HOH1208 4.4 39.5 1.0 CB A:ASP8 4.5 25.1 1.0 CG A:ASP723 4.6 42.2 1.0 NZ A:LYS711 4.7 60.0 1.0 OG A:SER13 4.7 32.8 1.0 O A:ASP8 4.7 30.7 1.0 CB A:ASP723 4.7 24.2 1.0 N A:HIS720 4.8 24.4 1.0

Magnesium binding site 4 out of 6 in the Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:33.5 occ:1.00 OP2 D:DG27 2.1 49.0 1.0 OD1 A:ASP8 2.1 43.8 1.0 O A:HOH1208 2.1 39.5 1.0 OE1 A:GLU500 2.4 33.6 1.0 O A:HOH1207 2.5 31.0 1.0 CG A:ASP8 2.8 36.2 1.0 OD2 A:ASP8 3.1 42.3 1.0 CD A:GLU500 3.1 35.0 1.0 O A:HOH1203 3.2 42.8 1.0 MG A:MG1101 3.4 37.7 1.0 OE2 A:GLU500 3.4 34.8 1.0 P D:DG27 3.5 46.9 1.0 C5' D:DG27 3.8 45.6 1.0 CB A:ASP8 4.1 25.1 1.0 O5' D:DG27 4.2 49.0 1.0 CG A:GLU500 4.2 26.5 1.0 CA A:ASP8 4.3 28.9 1.0 OP1 D:DG27 4.3 45.5 1.0 CB A:GLU500 4.4 27.7 1.0 OP3 D:DG27 4.4 46.3 0.0 C A:ASP8 4.5 22.9 1.0 N A:ILE9 4.6 16.6 1.0 O A:ILE9 4.7 39.9 1.0 O A:HOH1204 4.8 24.8 1.0 O A:HOH1201 4.9 34.1 1.0 OD2 A:ASP723 4.9 44.9 1.0 O A:ASP8 5.0 30.7 1.0

Magnesium binding site 5 out of 6 in the Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:38.4 occ:1.00 OP2 C:DC15 2.1 34.3 1.0 OD1 A:ASP581 2.1 37.6 1.0 O A:HOH1205 2.2 19.5 1.0 O3' P:DC14 2.2 14.9 1.0 OD1 A:ASN605 2.2 49.0 1.0 O C:HOH202 2.6 32.5 1.0 C3' P:DC14 3.2 7.5 1.0 CG A:ASP581 3.3 37.1 1.0 CG A:ASN605 3.4 44.3 1.0 P C:DC15 3.4 37.5 1.0 O5' C:DC15 3.7 29.3 1.0 ND2 A:ASN605 3.9 41.1 1.0 CB A:ASP581 4.0 30.8 1.0 N A:HIS582 4.1 28.4 1.0 CA A:ASP581 4.1 29.5 1.0 O A:HIS582 4.1 45.2 1.0 O A:ASN605 4.2 43.0 1.0 C4' P:DC14 4.2 8.5 1.0 OP1 C:DC15 4.2 33.2 1.0 OD2 A:ASP581 4.3 43.9 1.0 O A:GLY609 4.3 37.3 1.0 C2' P:DC14 4.4 7.0 1.0 OP3 C:DC15 4.4 31.6 1.0 NZ A:LYS608 4.5 39.8 1.0 CB A:ASN605 4.6 44.5 1.0 C A:ASP581 4.6 32.9 1.0 O5' P:DC14 4.6 16.0 1.0 C5' P:DC14 4.6 5.4 1.0 CA A:ASN605 4.7 45.9 1.0 C A:ASN605 4.8 47.9 1.0 C A:HIS582 4.9 38.6 1.0 CA A:HIS582 4.9 31.3 1.0 CD A:LYS608 5.0 41.1 1.0

Magnesium binding site 6 out of 6 in the Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of THERMOCAS9 in Post-Cleavage State Bound with the Dna Containing Nnnncca Pam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:33.7 occ:1.00 OP1 B:C93 2.1 43.4 1.0 OG1 A:THR478 2.5 20.9 1.0 O B:HOH305 2.7 39.2 1.0 O A:ARG475 3.2 29.9 1.0 NE2 A:GLN479 3.2 18.5 1.0 P B:C93 3.3 40.2 1.0 O5' B:C93 3.6 41.1 1.0 C5' B:C93 3.6 33.6 1.0 CE A:MET806 3.6 25.9 1.0 CA A:ARG475 3.7 4.1 1.0 CB A:THR478 3.7 10.8 1.0 CG A:GLN479 3.7 11.8 1.0 C A:ARG475 3.8 16.8 1.0 CD A:GLN479 3.9 17.9 1.0 N A:GLN479 4.0 13.0 1.0 CG A:ARG475 4.0 13.4 1.0 O B:HOH302 4.1 35.5 1.0 CB A:ARG475 4.2 13.9 1.0 OP2 B:C93 4.3 36.3 1.0 C A:THR478 4.4 9.0 1.0 O3' B:G92 4.4 35.3 1.0 SD A:MET806 4.5 42.2 1.0 CA A:THR478 4.5 19.6 1.0 NE A:ARG475 4.6 31.6 1.0 OP2 B:G94 4.6 41.6 1.0 CB A:GLN479 4.7 8.4 1.0 CA A:GLN479 4.7 12.4 1.0 O A:MET474 4.7 21.7 1.0 CG2 A:THR478 4.8 9.9 1.0 C4' B:C93 4.8 32.9 1.0 N A:ARG475 4.9 19.0 1.0 CD A:ARG475 4.9 10.9 1.0 O B:HOH309 4.9 53.3 1.0 O3' B:C93 5.0 43.3 1.0 N A:THR478 5.0 13.3 1.0

M.Roth, Y.Shu, D.Trasanidis, Y.Zhao, R.Hoffman, J.Van Der Oost, H.Li. Molecular Basis For Epigenetic-Sensitive Editing By CAS9 To Be Published.