Magnesium in PDB 7qqq: SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate

The structure of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate, PDB code: 7qqq 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)	46.03 / 2.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.99, 67.91, 187.819, 90, 111.22, 90
R / Rfree (%)	18.9 / 23.5

The structure of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate also contains other interesting chemical elements:

Potassium

(K)

13 atoms

The binding sites of Magnesium atom in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate (pdb code 7qqq). 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-TARGET4 Dna Substrate, PDB code: 7qqq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SPCAS9 Bound to AAVS1 Off-TARGET4 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-TARGET4 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:81.6 occ:1.00 O A:HOH208 1.9 89.4 1.0 O B:HOH1549 2.0 94.7 1.0 O A:HOH270 2.0 91.7 1.0 O A:HOH215 2.3 71.5 1.0 O A:HOH268 2.6 44.8 1.0 O A:HOH261 2.9 61.9 1.0 O A:HOH242 3.8 54.4 1.0 O4 A:U22 3.9 36.7 1.0 NH1 B:ARG403 4.7 47.5 1.0 OP2 A:G21 4.7 60.3 1.0 O A:HOH237 4.8 32.8 1.0 N6 A:A48 4.8 39.0 1.0 N7 A:G21 4.8 44.5 1.0 CZ B:PHE164 4.9 41.8 1.0 NH2 B:ARG403 4.9 40.7 1.0 C4 A:U22 4.9 52.0 1.0 N6 A:A49 5.0 44.0 1.0 CZ B:ARG403 5.0 47.6 1.0

Magnesium binding site 2 out of 2 in the SPCAS9 Bound to AAVS1 Off-TARGET4 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-TARGET4 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:47.8 occ:1.00 OP1 A:U50 1.9 50.3 1.0 O A:HOH241 1.9 55.7 1.0 O A:HOH214 2.0 53.3 1.0 O A:HOH255 2.1 50.7 1.0 O A:HOH223 2.1 43.6 1.0 O A:HOH205 2.1 50.9 1.0 P A:U50 3.1 49.1 1.0 OP2 A:U50 3.6 47.9 1.0 O A:HOH240 3.7 33.8 1.0 O5' A:U50 3.9 42.0 1.0 O6 A:G62 4.1 51.8 1.0 OP1 A:A51 4.3 42.9 1.0 NZ B:LYS1123 4.3 58.0 1.0 O3' A:A49 4.3 47.5 1.0 C5' A:U50 4.4 43.1 1.0 OP1 A:A52 4.5 58.6 1.0 OP2 A:A52 4.6 49.3 1.0 O6 A:G53 4.7 49.7 1.0 N7 A:G53 4.8 49.5 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