Magnesium in PDB 7qqx: SPCAS9 Bound to Fancf Off-TARGET5 Dna Substrate

The structure of SPCAS9 Bound to Fancf Off-TARGET5 Dna Substrate, PDB code: 7qqx 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)	48.00 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.534, 67.378, 188.387, 90, 110.9, 90
R / Rfree (%)	18.2 / 21.6

The structure of SPCAS9 Bound to Fancf Off-TARGET5 Dna Substrate also contains other interesting chemical elements:

Potassium

(K)

9 atoms

The binding sites of Magnesium atom in the SPCAS9 Bound to Fancf Off-TARGET5 Dna Substrate (pdb code 7qqx). 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 Fancf Off-TARGET5 Dna Substrate, PDB code: 7qqx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:77.7 occ:1.00 O A:HOH201 1.9 87.1 1.0 O B:HOH1813 2.0 72.0 1.0 O A:HOH214 2.1 78.2 1.0 O B:HOH1679 2.2 77.4 1.0 O A:HOH337 2.3 53.7 1.0 O A:HOH295 2.6 39.6 1.0 O A:HOH278 3.3 51.1 1.0 O4 A:U22 3.9 42.7 1.0 O A:HOH340 4.0 67.0 1.0 O A:HOH248 4.1 42.9 1.0 O A:HOH291 4.2 50.2 1.0 OP2 A:G21 4.4 48.7 1.0 O A:HOH262 4.5 28.2 1.0 NH1 B:ARG403 4.6 52.8 1.0 O A:HOH269 4.6 59.2 1.0 N7 A:G21 4.7 41.9 1.0 O A:HOH312 4.8 50.0 1.0 C4 A:U22 4.9 41.9 1.0 N6 A:A48 4.9 33.8 1.0 NH2 B:ARG403 5.0 60.6 1.0 CZ B:ARG403 5.0 56.9 1.0

Magnesium binding site 2 out of 2 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:33.4 occ:1.00 OP1 A:U50 2.1 43.8 1.0 O A:HOH218 2.1 38.7 1.0 O A:HOH282 2.1 38.1 1.0 O A:HOH257 2.1 36.2 1.0 O A:HOH301 2.1 34.8 1.0 O A:HOH204 2.2 42.9 1.0 P A:U50 3.4 43.7 1.0 O A:HOH209 3.9 39.7 1.0 O6 A:G62 3.9 44.5 1.0 O B:HOH1593 4.0 27.3 1.0 OP2 A:U50 4.1 49.6 1.0 O5' A:U50 4.1 40.1 1.0 O A:HOH332 4.2 64.4 1.0 OP1 A:A51 4.3 38.0 1.0 NZ B:LYS1123 4.3 41.4 1.0 OP2 A:A52 4.3 31.1 1.0 O6 A:G53 4.4 40.4 1.0 O A:HOH202 4.5 80.3 1.0 N7 A:G53 4.5 37.4 1.0 O3' A:A49 4.5 44.3 1.0 OP1 A:A52 4.5 44.4 1.0 C5' A:U50 4.6 36.1 1.0 C6 A:G62 4.9 40.2 1.0 N1 A:G62 4.9 39.9 1.0 P A:A52 4.9 38.7 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