Magnesium in PDB 7zo1: SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate

The structure of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate, PDB code: 7zo1 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)	46.51 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.41, 69.2, 188.46, 90, 111.77, 90
R / Rfree (%)	21.2 / 25

The structure of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate also contains other interesting chemical elements:

Potassium

(K)

8 atoms

The binding sites of Magnesium atom in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate (pdb code 7zo1). 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 CD34 Off-TARGET9 Dna Substrate, PDB code: 7zo1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:56.7 occ:1.00 OP1 A:U50 2.0 46.2 1.0 O A:HOH222 2.2 45.7 1.0 O A:HOH229 2.2 48.8 1.0 O A:HOH245 2.2 57.4 1.0 O A:HOH278 2.2 48.2 1.0 O A:HOH258 2.2 46.2 1.0 P A:U50 3.4 51.5 1.0 O6 A:G62 3.9 52.7 1.0 O A:HOH206 4.1 47.6 1.0 OP2 A:U50 4.1 49.8 1.0 O5' A:U50 4.1 48.8 1.0 O B:HOH1561 4.2 40.9 1.0 O6 A:G53 4.3 56.5 1.0 NZ B:LYS1123 4.3 57.1 1.0 OP1 A:A51 4.4 38.7 1.0 OP2 A:A52 4.4 56.4 1.0 OP1 A:A52 4.4 59.5 1.0 C5' A:U50 4.5 41.1 1.0 N7 A:G53 4.5 52.7 1.0 O3' A:A49 4.5 49.3 1.0 O A:HOH302 4.6 56.1 1.0 N1 A:G62 4.7 49.4 1.0 C6 A:G62 4.7 46.7 1.0 O A:HOH210 4.8 54.0 1.0 P A:A52 4.9 49.6 1.0 O A:HOH276 5.0 59.2 1.0

Magnesium binding site 2 out of 2 in the SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:68.5 occ:1.00 O A:HOH231 2.2 75.4 1.0 O B:HOH1524 2.2 88.8 1.0 O B:HOH1658 2.2 73.2 1.0 O A:HOH201 2.2 71.2 1.0 O B:HOH1664 2.2 46.9 1.0 O A:HOH282 2.2 63.4 1.0 O A:HOH288 3.7 53.2 1.0 O4 A:U22 4.0 42.5 1.0 O A:HOH300 4.2 60.9 1.0 NH1 B:ARG403 4.2 59.3 1.0 OP2 A:G21 4.3 69.3 1.0 O A:HOH218 4.4 52.1 1.0 N7 A:G21 4.4 48.0 1.0 K A:K105 4.5 73.2 1.0 O A:HOH242 4.7 65.7 1.0 CZ B:ARG403 4.8 57.5 1.0 O A:HOH256 4.8 59.2 1.0 C4 A:U22 4.9 51.4 1.0 O A:HOH283 4.9 41.2 1.0 NH2 B:ARG403 5.0 70.9 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