Magnesium in PDB 7qqv: SPCAS9 Bound to Fancf Off-TARGET3 Dna Substrate

The structure of SPCAS9 Bound to Fancf Off-TARGET3 Dna Substrate, PDB code: 7qqv 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)	47.81 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	179.019, 67.145, 187.767, 90, 111.14, 90
R / Rfree (%)	19.5 / 23

The structure of SPCAS9 Bound to Fancf 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 Fancf Off-TARGET3 Dna Substrate (pdb code 7qqv). 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-TARGET3 Dna Substrate, PDB code: 7qqv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SPCAS9 Bound to Fancf 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 Fancf Off-TARGET3 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:82.4 occ:1.00 O B:HOH1842 2.3 51.2 1.0 O A:HOH323 2.4 55.8 1.0 O A:HOH341 2.4 59.5 1.0 O A:HOH346 3.0 71.3 1.0 O4 A:U22 3.4 45.1 1.0 O A:HOH303 3.7 42.2 1.0 OP2 A:G21 3.7 47.9 1.0 O A:HOH304 3.8 34.1 1.0 O A:HOH306 4.3 47.3 1.0 C4 A:U22 4.3 45.9 1.0 N7 A:G21 4.4 44.5 1.0 C5 A:U22 4.5 46.5 1.0 O A:HOH261 4.7 49.0 1.0 O A:HOH241 4.7 57.9 1.0 C8 A:G21 5.0 47.1 1.0 N6 A:A48 5.0 41.1 1.0

Magnesium binding site 2 out of 2 in the SPCAS9 Bound to Fancf 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 Fancf Off-TARGET3 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:38.2 occ:1.00 O A:HOH253 2.0 29.1 1.0 O A:HOH220 2.0 34.7 1.0 OP1 A:U50 2.1 44.2 1.0 O A:HOH250 2.1 37.0 1.0 O A:HOH315 2.2 38.8 1.0 O A:HOH259 2.2 37.2 1.0 P A:U50 3.4 45.1 1.0 O A:HOH289 3.7 37.3 1.0 OP2 A:U50 3.9 41.5 1.0 O A:HOH214 3.9 46.8 1.0 O6 A:G62 3.9 47.1 1.0 O5' A:U50 4.1 41.4 1.0 O A:HOH347 4.3 55.2 1.0 NZ B:LYS1123 4.3 36.6 1.0 OP1 A:A51 4.4 32.3 1.0 O A:HOH339 4.4 54.5 1.0 O6 A:G53 4.4 40.0 1.0 C5' A:U50 4.4 38.9 1.0 OP2 A:A52 4.5 43.1 1.0 OP1 A:A52 4.5 45.2 1.0 O A:HOH212 4.5 47.8 1.0 O3' A:A49 4.6 43.0 1.0 N7 A:G53 4.6 43.7 1.0 O A:HOH326 4.8 62.9 1.0 C6 A:G62 4.9 45.2 1.0 N1 A:G62 5.0 45.2 1.0 P A:A52 5.0 42.1 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