Magnesium in PDB 5y36: Cryo-Em Structure of SPCAS9-Sgrna-Dna Ternary Complex

The binding sites of Magnesium atom in the Cryo-Em Structure of SPCAS9-Sgrna-Dna Ternary Complex (pdb code 5y36). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of SPCAS9-Sgrna-Dna Ternary Complex, PDB code: 5y36:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of SPCAS9-Sgrna-Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of SPCAS9-Sgrna-Dna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:0.0 occ:1.00 OP2 D:DA34 1.8 0.0 1.0 OD2 A:ASP986 2.0 0.0 1.0 NE2 A:HIS982 2.7 0.0 1.0 CD2 A:HIS982 2.7 0.0 1.0 CG A:ASP986 3.1 0.0 1.0 ND1 A:HIS983 3.1 0.0 1.0 P D:DA34 3.2 0.0 1.0 CE1 A:HIS983 3.5 0.0 1.0 CB A:ASP986 3.6 0.0 1.0 OP1 D:DA34 3.7 0.0 1.0 CE1 A:HIS982 3.8 0.0 1.0 MG D:MG101 3.8 0.0 1.0 CG A:HIS982 3.9 0.0 1.0 O3' D:DC33 4.0 0.0 1.0 CG A:HIS983 4.0 0.0 1.0 OD1 A:ASP986 4.1 0.0 1.0 CA A:HIS983 4.2 0.0 1.0 CB A:ALA10 4.3 0.0 1.0 O5' D:DA34 4.3 0.0 1.0 ND1 A:HIS982 4.4 0.0 1.0 NE2 A:HIS983 4.5 0.0 1.0 O A:HIS982 4.5 0.0 1.0 N A:HIS983 4.6 0.0 1.0 CB A:HIS983 4.6 0.0 1.0 C A:HIS982 4.6 0.0 1.0 C5' D:DA34 4.7 0.0 1.0 CD2 A:HIS983 4.8 0.0 1.0 CB A:HIS982 4.9 0.0 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of SPCAS9-Sgrna-Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of SPCAS9-Sgrna-Dna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1402 b:0.0 occ:1.00 OD2 A:ASP861 2.1 0.0 1.0 OD1 A:ASP839 2.4 0.0 1.0 CG A:ASP839 2.7 0.0 1.0 CG A:ASP861 3.0 0.0 1.0 OD2 A:ASP839 3.1 0.0 1.0 CB A:ASP839 3.4 0.0 1.0 CB A:ASP861 3.6 0.0 1.0 CA A:ASP839 3.7 0.0 1.0 OD1 A:ASP861 3.8 0.0 1.0 OP2 C:DG23 4.0 0.0 1.0 O A:VAL838 4.3 0.0 1.0 OP1 C:DG23 4.5 0.0 1.0 N A:ASP839 4.6 0.0 1.0 N A:ALA840 4.6 0.0 1.0 C A:ASP839 4.7 0.0 1.0 P C:DG23 4.8 0.0 1.0 C A:VAL838 4.8 0.0 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of SPCAS9-Sgrna-Dna Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of SPCAS9-Sgrna-Dna Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:0.0 occ:1.00 OP1 D:DA34 2.1 0.0 1.0 P D:DA34 3.2 0.0 1.0 OP2 D:DA34 3.5 0.0 1.0 NH2 A:ARG925 3.5 0.0 1.0 MG A:MG1401 3.8 0.0 1.0 C5' D:DA34 3.9 0.0 1.0 NH1 A:ARG925 3.9 0.0 1.0 OE1 A:GLU762 3.9 0.0 1.0 CZ A:ARG925 4.1 0.0 1.0 O5' D:DA34 4.1 0.0 1.0 CB A:GLU762 4.4 0.0 1.0 O3' D:DC33 4.5 0.0 1.0 CB A:ALA764 4.6 0.0 1.0 O A:ILE11 4.7 0.0 1.0 CD A:GLU762 4.7 0.0 1.0 CB A:ALA10 4.9 0.0 1.0

C.Huai, G.Li, R.Yao, Y.Zhang, M.Cao, L.Kong, C.Jia, H.Yuan, H.Chen, D.Lu, Q.Huang. Structural Insights Into Dna Cleavage Activation of Crispr-CAS9 System Nat Commun V. 8 1375 2017.
ISSN: ESSN 2041-1723
PubMed: 29123204
DOI: 10.1038/S41467-017-01496-2