Magnesium in PDB 7qqr: SPCAS9 Bound to AAVS1 Off-TARGET5 Dna Substrate

The structure of SPCAS9 Bound to AAVS1 Off-TARGET5 Dna Substrate, PDB code: 7qqr 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)	47.70 / 2.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.637, 67.027, 187.803, 90, 111.35, 90
R / Rfree (%)	18.9 / 23.1

The structure of SPCAS9 Bound to AAVS1 Off-TARGET5 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-TARGET5 Dna Substrate (pdb code 7qqr). 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-TARGET5 Dna Substrate, PDB code: 7qqr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SPCAS9 Bound to AAVS1 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 AAVS1 Off-TARGET5 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:57.4 occ:1.00 OP1 A:U50 1.9 68.3 1.0 O A:HOH210 1.9 58.5 1.0 O A:HOH231 2.0 63.4 1.0 O A:HOH207 2.1 65.2 1.0 O A:HOH209 2.2 51.6 1.0 O A:HOH256 2.2 66.8 1.0 P A:U50 3.1 51.0 1.0 OP2 A:U50 3.6 54.7 1.0 O B:HOH1549 3.9 42.9 1.0 O5' A:U50 3.9 44.9 1.0 O6 A:G62 4.0 67.4 1.0 NZ B:LYS1123 4.2 65.6 1.0 C5' A:U50 4.2 41.5 1.0 O3' A:A49 4.3 56.5 1.0 OP1 A:A51 4.4 45.1 1.0 OP1 A:A52 4.5 58.0 1.0 OP2 A:A52 4.5 67.5 1.0 N7 A:G53 4.6 52.5 1.0 O6 A:G53 4.6 53.0 1.0 C6 A:G62 4.9 60.2 1.0 P A:A52 5.0 57.1 1.0 N1 A:G62 5.0 61.5 1.0

Magnesium binding site 2 out of 2 in the SPCAS9 Bound to AAVS1 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 AAVS1 Off-TARGET5 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:83.4 occ:1.00 O B:HOH1553 1.9 109.1 1.0 O A:HOH206 1.9 82.1 1.0 O B:HOH1621 2.0 75.4 1.0 O A:HOH245 2.1 76.6 1.0 O A:HOH233 2.2 73.1 1.0 O A:HOH249 3.1 69.0 1.0 O4 A:U22 4.1 48.5 1.0 OP2 A:G21 4.3 66.4 1.0 O B:HOH1526 4.3 62.4 1.0 O A:HOH234 4.3 43.6 1.0 NH1 B:ARG403 4.7 43.4 1.0 N7 A:G21 4.8 52.6 1.0 NH2 B:ARG403 4.9 56.8 1.0 CZ B:ARG403 4.9 54.2 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