Magnesium in PDB 7qqt: SPCAS9 Bound to Fancf Off-TARGET1 Dna Substrate

The structure of SPCAS9 Bound to Fancf Off-TARGET1 Dna Substrate, PDB code: 7qqt 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)	47.58 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.591, 66.733, 187.02, 90, 111.03, 90
R / Rfree (%)	20.3 / 23.8

The structure of SPCAS9 Bound to Fancf 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 Fancf Off-TARGET1 Dna Substrate (pdb code 7qqt). 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-TARGET1 Dna Substrate, PDB code: 7qqt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SPCAS9 Bound to Fancf 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 Fancf 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:HOH290 2.2 68.6 1.0 O A:HOH253 2.2 58.4 1.0 O A:HOH314 2.2 64.3 1.0 O A:HOH340 2.3 37.4 1.0 OP2 A:G21 3.4 49.3 1.0 O4 A:U22 3.9 35.8 1.0 N7 A:G21 4.0 29.4 1.0 O A:HOH285 4.1 37.0 1.0 O B:HOH1738 4.2 41.2 1.0 O A:HOH265 4.4 60.5 1.0 O A:HOH286 4.4 31.1 1.0 NH1 B:ARG403 4.4 34.8 1.0 C8 A:G21 4.6 37.8 1.0 O A:HOH250 4.7 32.7 1.0 C4 A:U22 4.8 36.2 1.0 O A:HOH313 4.9 49.8 1.0 P A:G21 4.9 47.6 1.0

Magnesium binding site 2 out of 2 in the SPCAS9 Bound to Fancf 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 Fancf Off-TARGET1 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:34.9 occ:1.00 OP1 A:U50 2.0 37.1 1.0 O A:HOH291 2.1 34.3 1.0 O A:HOH257 2.1 30.3 1.0 O A:HOH208 2.1 40.2 1.0 O A:HOH269 2.2 29.9 1.0 O A:HOH213 2.2 26.6 1.0 P A:U50 3.3 38.9 1.0 OP2 A:U50 3.9 45.7 1.0 O A:HOH203 3.9 35.3 1.0 O B:HOH1629 3.9 19.2 1.0 O6 A:G62 4.0 40.6 1.0 O5' A:U50 4.1 37.5 1.0 O A:HOH330 4.2 39.2 1.0 O A:HOH224 4.2 49.9 1.0 O6 A:G53 4.4 30.1 1.0 OP1 A:A51 4.5 25.5 1.0 NZ B:LYS1123 4.5 29.8 1.0 O3' A:A49 4.5 41.4 1.0 C5' A:U50 4.6 32.1 1.0 OP1 A:A52 4.6 28.5 1.0 N7 A:G53 4.6 31.8 1.0 OP2 A:A52 4.8 29.1 1.0 C6 A:G62 4.9 37.0 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