Magnesium in PDB 7qr8: SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate

The structure of SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate, PDB code: 7qr8 was solved by M.Pacesa, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.12 / 2.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.278, 68.029, 186.741, 90, 110.74, 90
R / Rfree (%)	22.2 / 25

The structure of SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate also contains other interesting chemical elements:

Potassium

(K)

10 atoms

The binding sites of Magnesium atom in the SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate (pdb code 7qr8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate, PDB code: 7qr8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:69.8 occ:1.00 O A:HOH226 1.9 57.1 1.0 O A:HOH230 2.1 55.3 1.0 O B:HOH1613 2.1 69.7 1.0 OP2 A:G21 3.8 52.1 1.0 O A:HOH201 3.8 58.7 1.0 O A:HOH237 3.9 45.9 1.0 O4 A:U22 4.1 47.7 1.0 O A:HOH228 4.3 52.4 1.0 O A:HOH208 4.6 58.5 1.0 N7 A:G21 4.9 44.1 1.0 NH2 B:ARG403 4.9 53.3 1.0 C4 A:U22 5.0 45.5 1.0

Magnesium binding site 2 out of 2 in the SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:53.3 occ:1.00 O A:HOH205 2.1 51.6 1.0 O A:HOH212 2.1 57.8 1.0 O A:HOH204 2.1 58.1 1.0 OP1 A:U50 2.1 51.7 1.0 O A:HOH223 3.1 46.3 1.0 P A:U50 3.3 44.5 1.0 O6 A:G62 3.6 53.9 1.0 OP1 A:A51 3.6 46.8 1.0 OP2 A:U50 3.8 43.0 1.0 O5' A:U50 3.9 46.4 1.0 C5' A:U50 4.2 44.8 1.0 O6 A:G53 4.4 58.6 1.0 OP1 A:A52 4.4 50.9 1.0 OP2 A:A52 4.5 55.6 1.0 O3' A:A49 4.6 44.8 1.0 C6 A:G62 4.6 47.3 1.0 N1 A:G62 4.7 53.4 1.0 NZ B:LYS1123 4.9 51.5 1.0 N7 A:G53 4.9 52.6 1.0 OG1 B:THR73 4.9 47.4 1.0 C5' A:A51 4.9 45.5 1.0 P A:A52 5.0 46.3 1.0

M.Pacesa, C.H.Lin, A.Clery, A.Saha, P.R.Arantes, K.Bargsten, M.J.Irby, F.H.Allain, G.Palermo, P.Cameron, P.D.Donohoue, M.Jinek. Structural Basis For CAS9 Off-Target Activity. Cell V. 185 4067 2022.
ISSN: ISSN 1097-4172
PubMed: 36306733
DOI: 10.1016/J.CELL.2022.09.026