Magnesium in PDB 8s9v: Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State

The binding sites of Magnesium atom in the Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State (pdb code 8s9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State, PDB code: 8s9v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:36.4 occ:1.00 O A:HOH904 1.6 33.2 1.0 H1 G:HOH207 1.6 31.1 1.0 H2 A:HOH904 1.6 33.2 1.0 O G:HOH202 1.7 32.0 1.0 O A:HOH903 1.8 31.8 1.0 H2 A:HOH903 1.8 31.8 1.0 O G:HOH207 2.0 31.1 1.0 OP1 G:A43 2.0 26.4 1.0 OD1 A:ASP140 2.1 26.3 1.0 H1 G:HOH202 2.2 32.0 1.0 H2 G:HOH202 2.3 32.0 1.0 H1 A:HOH904 2.4 33.2 1.0 H1 A:HOH903 2.6 31.8 1.0 H2 G:HOH207 2.6 31.1 1.0 CG A:ASP140 3.2 26.3 1.0 P G:A43 3.4 26.4 1.0 CA A:ASP140 3.8 26.3 1.0 CB A:ASP140 3.8 26.3 1.0 C5' G:A43 3.8 26.4 1.0 O5' G:A43 4.0 26.4 1.0 O2' G:C44 4.2 26.5 1.0 OD2 A:ASP140 4.2 26.3 1.0 O3' G:U42 4.2 25.3 1.0 N A:ASP140 4.3 26.3 1.0 OP2 G:A43 4.5 26.4 1.0 C5' G:U45 4.8 25.1 1.0 C4' G:A43 4.9 26.4 1.0 O3' G:C44 5.0 26.5 1.0 C3' G:A43 5.0 26.4 1.0 C A:ASP140 5.0 26.3 1.0

Magnesium binding site 2 out of 5 in the Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:27.1 occ:1.00 H2 A:HOH902 1.6 25.9 1.0 O A:HOH902 1.7 25.9 1.0 O A:HOH901 1.7 22.1 1.0 OD2 A:ASP26 1.8 24.2 1.0 OD1 A:ASP26 1.9 24.2 1.0 CG A:ASP26 2.1 24.2 1.0 H1 A:HOH901 2.2 22.1 1.0 H2 A:HOH901 2.3 22.1 1.0 H1 A:HOH902 2.4 25.9 1.0 H1 G:HOH203 2.7 26.2 1.0 O G:HOH203 3.2 26.2 1.0 O4' G:C44 3.3 26.5 1.0 O A:LEU142 3.6 20.0 1.0 CB A:ASP26 3.6 24.2 1.0 H2 G:HOH203 3.7 26.2 1.0 CA A:ARG143 3.7 20.7 1.0 O3' G:A43 3.9 26.4 1.0 N A:PHE144 4.0 20.2 1.0 C6 G:C44 4.2 26.5 1.0 OP2 G:C44 4.2 26.5 1.0 C5' G:C44 4.2 26.5 1.0 CD2 A:PHE144 4.3 20.2 1.0 C A:ARG143 4.3 20.7 1.0 C1' G:C44 4.3 26.5 1.0 C4' G:C44 4.3 26.5 1.0 C A:LEU142 4.4 20.0 1.0 N1 G:C44 4.5 26.5 1.0 N A:ARG143 4.5 20.7 1.0 CA A:ASP26 4.5 24.2 1.0 CB A:ARG143 4.6 20.7 1.0 P G:C44 4.6 26.5 1.0 N A:ASP26 4.7 24.2 1.0 O4' G:A43 4.9 26.4 1.0 C5 G:C44 4.9 26.5 1.0 C4' G:A43 4.9 26.4 1.0 CE2 A:PHE144 4.9 20.2 1.0 O5' G:C44 4.9 26.5 1.0 C1' G:A43 4.9 26.4 1.0

Magnesium binding site 3 out of 5 in the Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:42.6 occ:1.00 H2 A:HOH906 1.6 40.6 1.0 H1 G:HOH210 1.6 36.3 1.0 O G:HOH205 1.7 37.5 1.0 O G:HOH210 1.8 36.3 1.0 O A:HOH906 1.9 40.6 1.0 H2 G:HOH210 2.1 36.3 1.0 H1 G:HOH205 2.1 37.5 1.0 H2 G:HOH205 2.3 37.5 1.0 H1 A:HOH905 2.4 39.0 1.0 H2 A:HOH905 2.6 39.0 1.0 H1 A:HOH906 2.6 40.6 1.0 O A:HOH905 2.6 39.0 1.0 OD1 D:ASP33 3.3 32.4 1.0 CA D:ASP33 3.8 32.4 1.0 CB D:ASP33 3.9 32.4 1.0 O5' G:G38 4.0 24.3 1.0 CG D:ASP33 4.0 32.4 1.0 C5' G:G38 4.1 24.3 1.0 O D:ASP33 4.2 32.4 1.0 C D:ASP33 4.5 32.4 1.0 CA D:GLY28 4.7 45.4 1.0 C8 G:G38 4.8 24.3 1.0 O D:THR32 4.8 36.7 1.0 N D:ASP33 4.8 32.4 1.0

Magnesium binding site 4 out of 5 in the Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:24.8 occ:1.00 H2 D:HOH703 1.6 26.8 1.0 O D:HOH703 1.7 26.8 1.0 O D:HOH701 1.8 28.7 1.0 H1 D:HOH703 2.0 26.8 1.0 H1 D:HOH701 2.1 28.7 1.0 H2 D:HOH701 2.6 28.7 1.0 O4' G:C32 2.6 27.7 1.0 O D:LEU397 2.7 20.3 1.0 OD1 D:ASP246 3.1 27.8 1.0 O3' G:C31 3.2 27.7 1.0 OD2 D:ASP246 3.2 27.8 1.0 O G:HOH208 3.5 27.3 1.0 O5' G:C32 3.5 27.7 1.0 C1' G:C32 3.5 27.7 1.0 CG D:ASP246 3.5 27.8 1.0 CA D:TYR398 3.6 24.4 1.0 C D:LEU397 3.7 20.3 1.0 H1 G:HOH208 3.8 27.3 1.0 C4' G:C32 3.8 27.7 1.0 C6 G:C32 3.8 27.7 1.0 N1 G:C32 3.8 27.7 1.0 P G:C32 4.0 27.7 1.0 C5' G:C32 4.0 27.7 1.0 N D:TYR398 4.1 24.4 1.0 H2 G:HOH208 4.1 27.3 1.0 C4' G:C31 4.3 27.7 1.0 CB D:TYR398 4.3 24.4 1.0 C3' G:C31 4.3 27.7 1.0 OP2 G:C32 4.4 27.7 1.0 H1 G:HOH204 4.5 32.0 1.0 O4' G:C31 4.6 27.7 1.0 MG G:MG101 4.6 33.1 1.0 C D:TYR398 4.7 24.4 1.0 C5 G:C32 4.7 27.7 1.0 C1' G:C31 4.7 27.7 1.0 N D:SER399 4.8 22.8 1.0 C2 G:C32 4.8 27.7 1.0 C2' G:C32 4.9 27.7 1.0 C3' G:C32 4.9 27.7 1.0 CB D:ASP246 4.9 27.8 1.0 H2 D:HOH702 4.9 30.8 1.0 O D:HOH702 5.0 30.8 1.0 CA D:LEU397 5.0 20.3 1.0

Magnesium binding site 5 out of 5 in the Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crispr-Cas Type III-D Effector Complex Bound to A Self-Target Rna in the Pre-Cleavage State within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:33.1 occ:1.00 H2 D:HOH702 1.6 30.8 1.0 H1 D:HOH702 1.7 30.8 1.0 O G:HOH209 1.7 33.5 1.0 H1 G:HOH209 1.7 33.5 1.0 O D:HOH702 1.7 30.8 1.0 O G:HOH201 2.0 33.5 1.0 H1 G:HOH204 2.0 32.0 1.0 OP2 G:C32 2.1 27.7 1.0 O G:HOH204 2.2 32.0 1.0 H2 G:HOH201 2.4 33.5 1.0 H2 G:HOH209 2.5 33.5 1.0 H1 G:HOH201 2.6 33.5 1.0 H1 D:HOH701 2.9 28.7 1.0 H2 G:HOH204 3.0 32.0 1.0 O D:LEU243 3.1 32.0 1.0 P G:C32 3.4 27.7 1.0 O G:HOH206 3.5 34.6 1.0 O D:HOH701 3.6 28.7 1.0 H2 D:HOH701 3.7 28.7 1.0 O5' G:C32 3.7 27.7 1.0 H1 G:HOH206 3.8 34.6 1.0 O2' G:C31 3.8 27.7 1.0 H2 G:HOH206 4.0 34.6 1.0 O3' G:C31 4.0 27.7 1.0 O D:HOH703 4.1 26.8 1.0 C D:LEU243 4.3 32.0 1.0 H2 G:HOH208 4.4 27.3 1.0 O G:HOH208 4.5 27.3 1.0 OP1 G:C32 4.6 27.7 1.0 H1 D:HOH703 4.6 26.8 1.0 H1 G:HOH208 4.6 27.3 1.0 MG D:MG602 4.6 24.8 1.0 H2 D:HOH703 4.7 26.8 1.0 C2' G:C31 4.9 27.7 1.0

E.A.Schwartz, J.P.K.Bravo, F.Ahsan, L.A.Macias, J.S.Brodbelt, G.Palermo, P.C.Fineran, R.D.Fagerlund, D.W.Taylor. Rna Targeting and Cleavage By the Type III-Dv Crispr Effector Complex Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-47506-Y