Magnesium in PDB 7qqp: SPCAS9 Bound to AAVS1 Off-TARGET3 Dna Substrate

The structure of SPCAS9 Bound to AAVS1 Off-TARGET3 Dna Substrate, PDB code: 7qqp 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)	47.96 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.606, 67.73, 188.09, 90, 111.27, 90
R / Rfree (%)	19.4 / 22.5

The structure of SPCAS9 Bound to AAVS1 Off-TARGET3 Dna Substrate also contains other interesting chemical elements:

Potassium

(K)

10 atoms

The binding sites of Magnesium atom in the SPCAS9 Bound to AAVS1 Off-TARGET3 Dna Substrate (pdb code 7qqp). 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 AAVS1 Off-TARGET3 Dna Substrate, PDB code: 7qqp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SPCAS9 Bound to AAVS1 Off-TARGET3 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 AAVS1 Off-TARGET3 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:81.2 occ:1.00 O A:HOH202 1.9 87.0 1.0 O B:HOH1546 2.0 93.7 1.0 O A:HOH275 2.0 72.2 1.0 O B:HOH1634 2.0 65.0 1.0 O A:HOH210 2.2 103.6 1.0 O A:HOH217 2.3 53.7 1.0 O A:HOH223 3.7 85.7 1.0 O4 A:U22 3.8 48.4 1.0 O A:HOH226 4.1 62.8 1.0 O A:HOH277 4.1 66.5 1.0 OP2 A:G21 4.2 44.4 1.0 O A:HOH265 4.3 47.9 1.0 N7 A:G21 4.5 37.7 1.0 O B:HOH1575 4.5 58.2 1.0 NH1 B:ARG403 4.6 48.5 1.0 K A:K103 4.7 74.0 1.0 O A:HOH231 4.7 71.2 1.0 C4 A:U22 4.7 43.8 1.0

Magnesium binding site 2 out of 2 in the SPCAS9 Bound to AAVS1 Off-TARGET3 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 AAVS1 Off-TARGET3 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:49.2 occ:1.00 O A:HOH227 2.0 49.1 1.0 OP1 A:U50 2.0 60.0 1.0 O A:HOH247 2.0 41.5 1.0 O A:HOH234 2.1 46.4 1.0 O A:HOH261 2.1 44.9 1.0 O A:HOH203 2.4 39.5 1.0 P A:U50 3.3 48.9 1.0 OP2 A:U50 3.8 48.6 1.0 O B:HOH1540 4.1 39.9 1.0 O5' A:U50 4.1 47.2 1.0 O6 A:G62 4.1 67.5 1.0 NZ B:LYS1123 4.2 47.5 1.0 O B:HOH1621 4.2 62.1 1.0 O3' A:A49 4.4 51.4 1.0 OP1 A:A51 4.4 36.6 1.0 OP1 A:A52 4.4 46.7 1.0 O6 A:G53 4.5 47.8 1.0 C5' A:U50 4.5 41.7 1.0 O A:HOH233 4.5 64.7 1.0 OP2 A:A52 4.6 53.1 1.0 N7 A:G53 4.6 45.7 1.0 O A:HOH252 4.9 53.9 1.0 O A:HOH260 5.0 48.7 1.0 N1 A:G62 5.0 44.0 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