Magnesium in PDB 7qr1: SPCAS9 Bound to Trac Off-TARGET2 Dna Substrate

The structure of SPCAS9 Bound to Trac Off-TARGET2 Dna Substrate, PDB code: 7qr1 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)	47.54 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.42, 66.795, 187.24, 90, 111.41, 90
R / Rfree (%)	20.6 / 23.1

The structure of SPCAS9 Bound to Trac Off-TARGET2 Dna Substrate also contains other interesting chemical elements:

Potassium

(K)

14 atoms

The binding sites of Magnesium atom in the SPCAS9 Bound to Trac Off-TARGET2 Dna Substrate (pdb code 7qr1). 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 Trac Off-TARGET2 Dna Substrate, PDB code: 7qr1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SPCAS9 Bound to Trac Off-TARGET2 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 Trac Off-TARGET2 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:68.4 occ:1.00 O B:HOH1580 1.9 69.1 1.0 O A:HOH205 2.0 70.5 1.0 O A:HOH292 2.1 65.9 1.0 O A:HOH284 2.1 70.1 1.0 O A:HOH244 2.1 68.1 1.0 O A:HOH291 2.3 60.5 1.0 O4 A:U22 3.8 39.5 1.0 O A:HOH283 3.9 53.4 1.0 OP2 A:G21 4.2 52.4 1.0 O A:HOH246 4.4 73.2 1.0 N7 A:G21 4.4 40.3 1.0 O A:HOH260 4.5 54.0 1.0 NH1 B:ARG403 4.5 44.8 1.0 K A:K105 4.5 73.0 1.0 O A:HOH280 4.7 53.9 1.0 O B:HOH1568 4.7 58.6 1.0 C4 A:U22 4.8 41.7 1.0 CZ B:ARG403 4.9 47.6 1.0 NH2 B:ARG403 5.0 49.1 1.0

Magnesium binding site 2 out of 2 in the SPCAS9 Bound to Trac Off-TARGET2 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 Trac Off-TARGET2 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:53.4 occ:1.00 O A:HOH226 2.0 53.4 1.0 O A:HOH216 2.0 53.4 1.0 O A:HOH275 2.0 53.4 1.0 O A:HOH206 2.1 53.4 1.0 OP1 A:U50 2.1 68.6 1.0 O A:HOH201 2.1 53.4 1.0 P A:U50 3.3 53.5 1.0 O A:HOH207 3.6 64.4 1.0 O A:HOH227 3.7 53.4 1.0 OP2 A:U50 3.8 57.9 1.0 O A:HOH212 3.8 58.9 1.0 O5' A:U50 4.0 49.9 1.0 O6 A:G62 4.0 55.2 1.0 OP1 A:A51 4.4 40.9 1.0 O6 A:G53 4.4 50.9 1.0 C5' A:U50 4.4 49.5 1.0 NZ B:LYS1123 4.5 49.5 1.0 O3' A:A49 4.6 48.2 1.0 O B:HOH1665 4.6 63.2 1.0 OP1 A:A52 4.8 47.7 1.0 OP2 A:A52 4.8 43.1 1.0 OG1 B:THR73 4.9 39.7 1.0 N7 A:G53 5.0 47.5 1.0 C6 A:G62 5.0 53.7 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