Magnesium in PDB 8y0a: Crystal Structure of LBCAS12A in Complex with Crrna and 18NT Target Dna

The structure of Crystal Structure of LBCAS12A in Complex with Crrna and 18NT Target Dna, PDB code: 8y0a was solved by X.Lin, J.Chen, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.87 / 3.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.777, 142.673, 209.126, 90, 90, 90
R / Rfree (%)	23.8 / 29.4

The binding sites of Magnesium atom in the Crystal Structure of LBCAS12A in Complex with Crrna and 18NT Target Dna (pdb code 8y0a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of LBCAS12A in Complex with Crrna and 18NT Target Dna, PDB code: 8y0a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of LBCAS12A in Complex with Crrna and 18NT Target Dna


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 LBCAS12A in Complex with Crrna and 18NT Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:17.7 occ:1.00 OP2 B:A-4 2.2 33.5 1.0 O A:THR716 2.5 31.0 1.0 C A:THR716 3.6 29.8 1.0 OD1 A:ASP708 3.7 35.6 1.0 P B:A-4 3.7 36.1 1.0 OP2 B:U-5 4.1 36.9 1.0 N A:THR716 4.2 28.7 1.0 O5' B:A-4 4.3 29.9 1.0 O5' B:U-5 4.3 30.4 1.0 C A:GLY715 4.3 33.2 1.0 CA A:THR716 4.5 25.2 1.0 CA A:PRO717 4.5 20.7 1.0 OP1 B:U-5 4.5 43.1 1.0 P B:U-5 4.5 36.6 1.0 N A:PRO717 4.5 24.4 1.0 O A:GLY715 4.5 38.1 1.0 OP1 B:A-4 4.6 39.9 1.0 C A:PRO717 4.6 26.3 1.0 OD1 A:ASN718 4.6 33.5 1.0 C3' B:U-5 4.7 36.0 1.0 O3' B:U-5 4.7 33.0 1.0 N A:ASN718 4.7 28.3 1.0 CG A:ASP708 4.8 32.5 1.0 CA A:GLY715 4.9 39.4 1.0 N7 B:A-4 5.0 30.6 1.0 O A:PRO717 5.0 28.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of LBCAS12A in Complex with Crrna and 18NT Target Dna


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 LBCAS12A in Complex with Crrna and 18NT Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1302 b:4.2 occ:1.00 NH1 A:ARG887 3.5 31.8 1.0 NH1 A:ARG883 3.6 36.7 1.0 NE A:ARG883 3.7 33.7 1.0 CZ A:ARG883 4.1 34.3 1.0 CZ A:ARG887 4.6 31.1 1.0 O4' B:A10 4.8 44.7 1.0 CD A:ARG883 4.8 33.7 1.0 NH2 A:ARG887 4.8 25.5 1.0 CG A:GLU880 4.9 60.7 1.0 OE1 A:GLU880 4.9 81.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of LBCAS12A in Complex with Crrna and 18NT Target Dna


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 LBCAS12A in Complex with Crrna and 18NT Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1301 b:2.0 occ:1.00 NH1 E:ARG883 3.0 28.0 1.0 NE E:ARG883 3.5 29.5 1.0 CZ E:ARG883 3.7 26.0 1.0 NH1 E:ARG887 4.0 28.1 1.0 CD E:ARG883 4.8 28.4 1.0 NH2 E:ARG883 5.0 22.1 1.0 O4' F:A10 5.0 38.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of LBCAS12A in Complex with Crrna and 18NT Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of LBCAS12A in Complex with Crrna and 18NT Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1302 b:12.1 occ:1.00 OP2 F:A-4 2.2 33.6 1.0 O E:THR716 2.4 27.9 1.0 C E:THR716 3.5 25.3 1.0 P F:A-4 3.6 37.9 1.0 OD1 E:ASP708 3.8 40.9 1.0 N E:THR716 3.9 27.8 1.0 C E:GLY715 4.0 31.4 1.0 OP2 F:U-5 4.2 36.0 1.0 OP1 F:U-5 4.2 37.8 1.0 O5' F:A-4 4.2 29.6 1.0 O E:GLY715 4.3 37.1 1.0 CA E:THR716 4.3 24.0 1.0 O5' F:U-5 4.3 23.2 1.0 OP1 F:A-4 4.4 30.8 1.0 P F:U-5 4.4 29.6 1.0 N E:PRO717 4.4 23.8 1.0 CA E:GLY715 4.5 29.8 1.0 CA E:PRO717 4.5 23.6 1.0 C E:PRO717 4.6 25.8 1.0 O3' F:U-5 4.7 32.0 1.0 OD1 E:ASN718 4.7 35.1 1.0 N E:ASN718 4.7 23.0 1.0 C3' F:U-5 4.8 30.9 1.0 CB E:THR716 4.9 28.2 1.0 CG E:ASP708 4.9 32.6 1.0 O E:PRO717 5.0 30.3 1.0

J.Chen, X.Lin, W.Xiang, Y.Chen, Y.Zhao, L.Huang, L.Liu. Dna Target Binding-Induced Pre-Crrna Processing in Type II and V Crispr-Cas Systems. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 39676682
DOI: 10.1093/NAR/GKAE1241