Magnesium in PDB 9l12: Crystal Structure of CAS12H Ternary Complex

The structure of Crystal Structure of CAS12H Ternary Complex, PDB code: 9l12 was solved by W.Xiang, J.Chen, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.42 / 3.81
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	155.527, 155.527, 479.655, 90, 90, 120
R / Rfree (%)	33.4 / 33.9

The binding sites of Magnesium atom in the Crystal Structure of CAS12H Ternary Complex (pdb code 9l12). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of CAS12H Ternary Complex, PDB code: 9l12:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of CAS12H Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of CAS12H Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:12.5 occ:1.00 OD1 A:ASN467 2.2 12.8 1.0 OD2 A:ASP465 2.2 10.3 1.0 OD1 A:ASP465 2.3 8.5 1.0 CG A:ASP465 2.6 9.3 1.0 CG A:ASN467 2.8 16.7 1.0 ND2 A:ASN467 2.8 14.5 1.0 NH2 A:ARG718 3.1 15.7 1.0 OG A:SER706 3.2 7.6 1.0 OD1 A:ASP740 3.4 13.1 1.0 OE1 A:GLU658 3.7 13.8 1.0 OE2 A:GLU658 3.9 13.8 1.0 NH1 A:ARG718 3.9 18.2 1.0 CZ A:ARG718 3.9 18.4 1.0 CB A:ASP465 4.1 10.1 1.0 CB A:ASN467 4.1 27.1 1.0 CD A:GLU658 4.2 11.0 1.0 CG A:ASP740 4.3 12.7 1.0 NZ A:LYS702 4.4 17.1 1.0 CB A:SER706 4.4 6.5 1.0 O A:LEU466 4.5 19.4 1.0 C A:LEU466 4.6 13.5 1.0 N A:ASN467 4.6 17.9 1.0 N A:LEU466 4.7 6.2 1.0 OD2 A:ASP740 4.9 12.1 1.0 CA A:ASN467 4.9 31.1 1.0 C A:ASP465 4.9 10.2 1.0 CA A:ASP465 5.0 12.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of CAS12H Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of CAS12H Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg901 b:19.8 occ:1.00 OD1 E:ASP465 2.1 10.1 1.0 OD2 E:ASP465 2.2 16.5 1.0 CG E:ASP465 2.3 15.0 1.0 ND2 E:ASN467 2.3 29.0 1.0 CG E:ASN467 2.3 25.4 1.0 OD1 E:ASN467 2.4 18.3 1.0 O E:LEU466 2.6 21.8 1.0 C E:LEU466 2.6 19.4 1.0 N E:LEU466 2.9 21.2 1.0 N E:ASN467 3.0 25.2 1.0 CA E:LEU466 3.3 15.2 1.0 OE1 E:GLU658 3.3 21.4 1.0 C E:ASP465 3.4 18.2 1.0 CB E:ASN467 3.4 32.3 1.0 CB E:ASP465 3.6 18.1 1.0 CA E:ASN467 3.7 34.5 1.0 OD1 E:ASP740 3.9 20.5 1.0 CA E:ASP465 4.0 15.8 1.0 O E:ASP465 4.1 18.1 1.0 CD E:GLU658 4.2 16.6 1.0 CG E:ASP740 4.4 22.8 1.0 CB E:LEU466 4.5 14.4 1.0 OE2 E:GLU658 4.6 20.4 1.0 OD2 E:ASP740 4.6 24.2 1.0 NH2 E:ARG718 4.8 11.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of CAS12H Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of CAS12H Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg901 b:15.3 occ:1.00 ND2 I:ASN467 2.3 12.9 1.0 OD1 I:ASN467 2.7 8.8 1.0 CG I:ASN467 2.8 13.1 1.0 OD1 I:ASP465 3.0 13.7 1.0 OD2 I:ASP465 3.3 15.9 1.0 OE2 I:GLU658 3.5 13.8 1.0 CG I:ASP465 3.6 14.8 1.0 NH2 I:ARG718 3.6 15.7 1.0 CB I:SER706 3.8 16.9 1.0 OG I:SER706 3.8 18.0 1.0 OE1 I:GLU658 4.0 10.2 1.0 CD I:GLU658 4.2 13.5 1.0 CB I:ASN467 4.3 22.5 1.0 NH1 I:ARG718 4.5 15.5 1.0 CZ I:ARG718 4.5 14.3 1.0 OD1 I:ASP740 4.5 25.6 1.0 O I:LEU466 4.5 12.1 1.0 OG1 I:THR705 4.6 75.0 1.0 CA I:SER706 4.8 14.9 1.0 N I:SER706 4.8 17.4 1.0

W.Xiang, X.Lin, Y.Yang, L.Huang, Y.Chen, J.Chen, L.Liu. CAS12H Is A Crrna-Guided Dna Nickase That Can Be Utilized For Precise Gene Editing. Cell Rep V. 44 15718 2025.
ISSN: ESSN 2211-1247
PubMed: 40372912
DOI: 10.1016/J.CELREP.2025.115718