Magnesium in PDB 7lyt: Cryo-Em Structure of Casphi-2 (CAS12J) Bound to Crrna and Phosphorothioate-Dna

The structure of Cryo-Em Structure of Casphi-2 (CAS12J) Bound to Crrna and Phosphorothioate-Dna also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Cryo-Em Structure of Casphi-2 (CAS12J) Bound to Crrna and Phosphorothioate-Dna (pdb code 7lyt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Casphi-2 (CAS12J) Bound to Crrna and Phosphorothioate-Dna, PDB code: 7lyt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Casphi-2 (CAS12J) Bound to Crrna and Phosphorothioate-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Casphi-2 (CAS12J) Bound to Crrna and Phosphorothioate-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:72.2 occ:1.00 OD1 A:ASP394 2.1 70.1 1.0 OD2 A:ASP695 2.1 71.6 1.0 S2P D:SC12 2.6 74.8 1.0 CG A:ASP394 3.0 70.1 1.0 HA A:ASP695 3.1 71.6 1.0 CG A:ASP695 3.2 71.6 1.0 OD2 A:ASP394 3.3 70.1 1.0 HH21 A:ARG678 3.4 73.4 1.0 HH22 A:ARG678 3.4 73.4 1.0 HB3 A:ASP695 3.6 71.6 1.0 NH2 A:ARG678 3.7 73.4 1.0 CB A:ASP695 3.8 71.6 1.0 C5' D:SC12 3.8 74.8 1.0 CA A:ASP695 3.9 71.6 1.0 O A:LEU395 3.9 69.5 1.0 O5' D:SC12 4.0 74.8 1.0 P D:SC12 4.1 74.8 1.0 MG A:MG803 4.1 74.8 1.0 OD1 A:ASP695 4.2 71.6 1.0 HB2 A:ALA699 4.2 70.5 1.0 CB A:ASP394 4.3 70.1 1.0 HB3 A:ASP394 4.3 70.1 1.0 HB3 A:ALA699 4.5 70.5 1.0 HB1 A:ALA699 4.5 70.5 1.0 HA3 A:GLY396 4.5 69.0 1.0 CB A:ALA699 4.6 70.5 1.0 N A:ASP695 4.7 71.6 1.0 C A:LEU395 4.7 69.5 1.0 HB2 A:ASP695 4.7 71.6 1.0 O A:ASP394 4.7 70.1 1.0 C A:ASP394 4.8 70.1 1.0 OG A:SER664 4.9 73.5 1.0 HB2 A:ASP394 4.9 70.1 1.0 C A:ASP695 5.0 71.6 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Casphi-2 (CAS12J) Bound to Crrna and Phosphorothioate-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Casphi-2 (CAS12J) Bound to Crrna and Phosphorothioate-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:74.8 occ:1.00 OD2 A:ASP394 2.1 70.1 1.0 S2P D:SC12 2.4 74.8 1.0 OE1 A:GLU606 3.0 71.6 1.0 CG A:ASP394 3.1 70.1 1.0 HB2 A:SER664 3.4 73.5 1.0 O3' D:SC11 3.5 80.5 1.0 OD1 A:ASP394 3.6 70.1 1.0 P D:SC12 3.7 74.8 1.0 C4' D:SC11 3.9 80.5 1.0 CD A:GLU606 3.9 71.6 1.0 HG1 A:THR663 3.9 72.9 1.0 HB1 A:ALA699 3.9 70.5 1.0 OE2 A:GLU606 4.1 71.6 1.0 C3' D:SC11 4.1 80.5 1.0 MG A:MG802 4.1 72.2 1.0 HB2 A:PRO660 4.2 73.0 1.0 HB2 A:ASP394 4.2 70.1 1.0 CB A:ASP394 4.2 70.1 1.0 OG1 A:THR663 4.2 72.9 1.0 HA A:ASP394 4.3 70.1 1.0 CB A:SER664 4.4 73.5 1.0 C5' D:SC12 4.6 74.8 1.0 HB2 A:ALA699 4.7 70.5 1.0 H A:SER664 4.7 73.5 1.0 O5' D:SC12 4.7 74.8 1.0 H A:LEU395 4.7 69.5 1.0 CB A:ALA699 4.7 70.5 1.0 HB3 A:PRO660 4.7 73.0 1.0 O A:LEU395 4.8 69.5 1.0 CA A:ASP394 4.8 70.1 1.0 HD11 A:LEU703 4.8 70.3 1.0 OG A:SER664 4.8 73.5 1.0 C5' D:SC11 4.8 80.5 1.0 HB3 A:GLU606 4.9 71.6 1.0 OP1 D:SC12 4.9 74.8 1.0 CB A:PRO660 4.9 73.0 1.0 O4' D:SC11 4.9 80.5 1.0 HB3 A:SER664 4.9 73.5 1.0 HH21 A:ARG678 4.9 73.4 1.0 HB3 A:ASP394 5.0 70.1 1.0 O5' D:SC11 5.0 80.5 1.0

P.Pausch, K.M.Soczek, D.A.Herbst, C.A.Tsuchida, B.Al-Shayeb, J.F.Banfield, E.Nogales, J.A.Doudna. Dna Interference States of the Hypercompact Crispr-Casphi Effector Nat.Struct.Mol.Biol. 2021.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-021-00632-3