Magnesium in PDB 6ltu: Crystal Structure of CAS12I2 Ternary Complex with Double MG2+ Bound in Catalytic Pocket

The structure of Crystal Structure of CAS12I2 Ternary Complex with Double MG2+ Bound in Catalytic Pocket, PDB code: 6ltu was solved by X.Huang, W.Sun, Z.Cheng, M.Chen, X.Li, J.Wang, G.Sheng, W.Gong, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.87 / 2.57
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	94.329, 123.575, 281.218, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 22.9

The binding sites of Magnesium atom in the Crystal Structure of CAS12I2 Ternary Complex with Double MG2+ Bound in Catalytic Pocket (pdb code 6ltu). 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 CAS12I2 Ternary Complex with Double MG2+ Bound in Catalytic Pocket, PDB code: 6ltu:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of CAS12I2 Ternary Complex with Double MG2+ Bound in Catalytic Pocket


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 CAS12I2 Ternary Complex with Double MG2+ Bound in Catalytic Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:24.0 occ:1.00 OP1 E:DC24 2.0 41.2 1.0 OD2 A:ASP599 2.1 34.9 1.0 O E:HOH101 2.1 43.8 1.0 OD1 A:ASN601 2.2 36.9 1.0 O A:HOH1253 2.3 29.9 1.0 OD1 A:ASP1019 2.4 39.0 1.0 CG A:ASP599 2.8 36.5 1.0 OD1 A:ASP599 2.9 38.8 1.0 CG A:ASN601 3.3 35.8 1.0 P E:DC24 3.4 41.7 1.0 CG A:ASP1019 3.5 43.4 1.0 ND2 A:ASN601 3.9 35.8 1.0 MG A:MG1102 3.9 41.1 1.0 O5' E:DC24 4.1 43.9 1.0 CB A:ASP1019 4.1 41.4 1.0 OP2 E:DC24 4.2 41.6 1.0 CB A:ASP599 4.3 31.6 1.0 CA A:ASP1019 4.3 40.3 1.0 O A:GLN600 4.4 35.9 1.0 O A:HOH1242 4.4 35.1 1.0 C5' E:DC24 4.4 40.1 1.0 OD2 A:ASP1019 4.4 44.1 1.0 CB A:ALA1022 4.4 39.1 1.0 OG A:SER883 4.5 42.2 1.0 O3' E:DC23 4.5 38.2 1.0 NH2 A:ARG900 4.5 42.8 1.0 CB A:ASN601 4.6 36.9 1.0 OP2 E:DT25 4.7 48.4 1.0 NH1 A:ARG991 4.8 45.8 1.0 C A:GLN600 4.9 35.6 1.0 O A:HOH1209 4.9 45.0 1.0 NH1 A:ARG900 4.9 43.5 1.0 CA A:ASN601 4.9 34.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of CAS12I2 Ternary Complex with Double MG2+ Bound in Catalytic Pocket


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 CAS12I2 Ternary Complex with Double MG2+ Bound in Catalytic Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:41.1 occ:1.00 OD1 A:ASP599 2.1 38.8 1.0 O A:HOH1242 2.2 35.1 1.0 OE2 A:GLU833 2.2 34.6 1.0 O A:HOH1209 2.4 45.0 1.0 O3' E:DC23 2.6 38.2 1.0 OP1 E:DC24 2.7 41.2 1.0 CD A:GLU833 3.1 43.2 1.0 P E:DC24 3.3 41.7 1.0 CG A:ASP599 3.3 36.5 1.0 OE1 A:GLU833 3.4 46.1 1.0 C3' E:DC23 3.8 47.3 1.0 MG A:MG1101 3.9 24.0 1.0 OG A:SER883 4.1 42.2 1.0 O A:GLN600 4.1 35.9 1.0 C4' E:DC23 4.1 46.8 1.0 OD2 A:ASP599 4.2 34.9 1.0 OG1 A:THR882 4.2 47.9 1.0 CB A:ASP599 4.3 31.6 1.0 O E:HOH101 4.3 43.8 1.0 OP2 E:DC24 4.3 41.6 1.0 C2' E:DC23 4.3 49.0 1.0 O5' E:DC24 4.4 43.9 1.0 C5' E:DC24 4.4 40.1 1.0 N A:GLN600 4.4 36.1 1.0 CG A:GLU833 4.5 35.8 1.0 CA A:ASP599 4.6 34.2 1.0 CD1 A:ILE1026 4.6 36.9 1.0 CB A:ALA1022 4.8 39.1 1.0 C A:ASP599 4.9 37.9 1.0 C A:GLN600 5.0 35.6 1.0 O4' E:DC23 5.0 49.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of CAS12I2 Ternary Complex with Double MG2+ Bound in Catalytic Pocket


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 CAS12I2 Ternary Complex with Double MG2+ Bound in Catalytic Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:40.7 occ:1.00 O B:HOH224 2.1 32.4 1.0 O B:HOH245 2.1 28.2 1.0 O A:HOH1225 2.1 39.7 1.0 O A:HOH1221 2.1 37.2 1.0 O A:HOH1415 2.2 31.3 1.0 O B:HOH217 2.2 36.7 1.0 O4 B:U12 3.9 34.4 1.0 O A:ARG745 4.1 34.9 1.0 O2 B:C15 4.1 34.4 1.0 N3 B:C15 4.1 37.6 1.0 O A:THR744 4.2 42.1 1.0 O B:HOH230 4.2 26.7 1.0 OP2 B:C11 4.4 34.9 1.0 O B:HOH248 4.4 49.5 1.0 O B:HOH229 4.4 35.2 1.0 CA A:ARG745 4.5 36.9 1.0 C4 B:U12 4.5 39.1 1.0 C2 B:C15 4.6 38.0 1.0 O A:HOH1360 4.7 40.7 1.0 C5 B:U12 4.7 37.4 1.0 C A:ARG745 4.7 37.0 1.0 O A:HOH1404 5.0 40.9 1.0

X.Huang, W.Sun, Z.Cheng, M.Chen, X.Li, J.Wang, G.Sheng, W.Gong, Y.Wang. Structural Basis For Two Metal-Ion Catalysis of Dna Cleavage By CAS12I2. Nat Commun V. 11 5241 2020.
ISSN: ESSN 2041-1723
PubMed: 33067443
DOI: 10.1038/S41467-020-19072-6