Magnesium in PDB 6iv8: The Selenomethionine(Semet)-Derived CAS13D Binary Complex

The structure of The Selenomethionine(Semet)-Derived CAS13D Binary Complex, PDB code: 6iv8 was solved by B.Zhang, Y.M.Ye, W.W.Ye, S.Y.Ouyang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.92 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.164, 145.733, 249.383, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21

The binding sites of Magnesium atom in the The Selenomethionine(Semet)-Derived CAS13D Binary Complex (pdb code 6iv8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Selenomethionine(Semet)-Derived CAS13D Binary Complex, PDB code: 6iv8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Selenomethionine(Semet)-Derived CAS13D Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Selenomethionine(Semet)-Derived CAS13D Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:17.0 occ:1.00 O B:HOH241 2.0 13.7 1.0 OP1 B:C-7 2.0 16.8 1.0 O B:HOH252 2.1 16.4 1.0 O B:HOH287 2.1 16.8 1.0 O B:HOH272 2.1 18.0 1.0 O A:HOH1084 2.1 22.4 1.0 P B:C-7 3.3 17.8 1.0 O3' B:U-8 3.7 18.3 1.0 OD2 A:ASP178 3.9 28.5 1.0 OP2 B:C-7 4.0 16.2 1.0 O A:HOH1167 4.2 24.3 1.0 O B:HOH205 4.2 17.9 1.0 O A:HOH1001 4.2 42.4 1.0 OP2 B:A-2 4.2 19.4 1.0 O A:HOH1114 4.3 19.4 1.0 O B:HOH281 4.3 16.7 1.0 O B:HOH294 4.4 26.8 1.0 OP2 B:A-5 4.4 21.1 1.0 O5' B:C-7 4.4 15.6 1.0 O B:HOH221 4.5 23.4 1.0 OD1 A:ASP178 4.6 30.3 1.0 C5' B:C-7 4.6 17.0 1.0 CG A:ASP178 4.7 27.1 1.0 OP1 B:A-3 4.8 24.2 1.0 C5' B:U-6 4.9 22.3 1.0

Magnesium binding site 2 out of 2 in the The Selenomethionine(Semet)-Derived CAS13D Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Selenomethionine(Semet)-Derived CAS13D Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:36.8 occ:0.97 O D:HOH232 1.9 27.4 1.0 O D:HOH226 2.0 38.4 1.0 OP1 D:C-7 2.1 33.9 1.0 O C:HOH1041 2.1 34.0 1.0 O D:HOH241 2.2 39.6 1.0 O C:HOH1050 2.2 40.5 1.0 P D:C-7 3.3 35.6 1.0 O3' D:U-8 3.7 34.9 1.0 OP2 D:C-7 4.0 36.6 1.0 OD2 C:ASP178 4.0 54.9 1.0 O D:HOH234 4.1 44.4 1.0 O C:HOH1031 4.2 44.0 1.0 OP2 D:A-5 4.3 43.0 1.0 OP2 D:A-2 4.3 47.5 1.0 O D:HOH223 4.3 37.6 1.0 O D:HOH229 4.4 38.3 1.0 O5' D:C-7 4.5 41.2 1.0 OD1 C:ASP178 4.5 48.0 1.0 CG C:ASP178 4.7 38.6 1.0 C5' D:C-7 4.7 46.4 1.0 OP1 D:A-3 4.9 46.8 1.0 CD2 C:TYR174 5.0 47.9 1.0

B.Zhang, Y.Ye, W.Ye, V.Perculija, H.Jiang, Y.Chen, Y.Li, J.Chen, J.Lin, S.Wang, Q.Chen, Y.S.Han, S.Ouyang. Two Hepn Domains Dictate Crispr Rna Maturation and Target Cleavage in CAS13D. Nat Commun V. 10 2544 2019.
ISSN: ESSN 2041-1723
PubMed: 31186424
DOI: 10.1038/S41467-019-10507-3