Magnesium in PDB 6d95: Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair

The structure of Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair, PDB code: 6d95 was solved by Y.Liu, D.Esyunina, I.Olovnikov, M.Teplova, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.44 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.197, 119.978, 118.692, 90.00, 95.51, 90.00
R / Rfree (%)	21 / 25

The binding sites of Magnesium atom in the Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair (pdb code 6d95). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair, PDB code: 6d95:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:27.4 occ:1.00 OP1 B:A3 1.8 33.3 1.0 O A:HOH855 2.0 28.6 1.0 OP3 B:U1 2.1 30.7 1.0 O B:HOH214 2.1 28.5 1.0 O A:LEU777 2.2 28.6 1.0 OXT A:LEU777 2.3 29.8 1.0 C A:LEU777 2.6 30.3 1.0 P B:A3 3.3 30.3 1.0 P B:U1 3.3 28.7 1.0 OP1 B:U1 3.6 28.6 1.0 O3' B:U2 3.7 31.3 1.0 NH2 A:ARG731 4.0 37.8 1.0 OE1 A:GLN478 4.0 34.7 1.0 NZ A:LYS506 4.1 32.1 1.0 CA A:LEU777 4.1 27.6 1.0 C5' B:U1 4.1 30.0 1.0 O5' B:U1 4.1 32.3 1.0 O A:HOH904 4.2 32.7 1.0 OP2 B:A3 4.2 29.6 1.0 O5' B:A3 4.2 30.5 1.0 O B:HOH233 4.2 43.5 1.0 NE2 A:GLN478 4.2 26.4 1.0 OP2 B:U1 4.3 26.7 1.0 NE A:ARG731 4.3 39.6 1.0 O B:HOH206 4.4 35.4 1.0 CD A:GLN478 4.6 30.3 1.0 O A:HOH851 4.6 36.6 1.0 CZ A:ARG731 4.7 36.5 1.0 CB A:LEU777 4.7 27.4 1.0 N A:LEU777 4.9 26.6 1.0

Magnesium binding site 2 out of 4 in the Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:39.2 occ:1.00 O B:HOH230 1.9 46.2 1.0 OP2 B:C7 2.0 37.1 1.0 O A:HOH830 2.2 38.0 1.0 O B:HOH209 2.2 36.6 1.0 O B:HOH208 2.2 31.9 1.0 O A:HOH1057 2.3 36.4 1.0 P B:C7 3.3 39.4 1.0 O5' B:C7 3.8 41.7 1.0 O3' B:G6 3.9 41.6 1.0 O B:HOH223 3.9 41.4 1.0 OD1 A:ASP640 4.0 48.2 1.0 O B:HOH245 4.1 38.0 1.0 O B:HOH237 4.2 39.5 1.0 O2' B:G6 4.4 38.8 1.0 OP2 B:A8 4.4 33.8 1.0 N7 B:A8 4.5 31.6 1.0 OP1 B:C7 4.6 42.0 1.0 O A:HOH1025 4.6 66.4 1.0 O C:HOH125 4.7 29.0 1.0 N6 B:A8 4.9 30.2 1.0 C3' B:G6 4.9 40.6 1.0

Magnesium binding site 3 out of 4 in the Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:30.3 occ:1.00 OP1 H:A3 1.9 31.0 1.0 OP3 H:U1 2.1 30.1 1.0 O H:HOH223 2.1 28.8 1.0 O F:HOH865 2.1 31.2 1.0 OXT F:LEU777 2.1 30.9 1.0 O F:LEU777 2.1 29.1 1.0 C F:LEU777 2.5 32.0 1.0 P H:U1 3.3 30.4 1.0 P H:A3 3.3 32.0 1.0 OP1 H:U1 3.6 34.2 1.0 O3' H:U2 3.8 31.4 1.0 NZ F:LYS506 3.8 31.6 1.0 NH2 F:ARG731 4.0 38.4 1.0 CA F:LEU777 4.0 30.0 1.0 OE1 F:GLN478 4.1 34.7 1.0 NE2 F:GLN478 4.1 28.6 1.0 C5' H:U1 4.2 33.1 1.0 NE F:ARG731 4.2 40.3 1.0 O5' H:U1 4.2 34.0 1.0 OP2 H:A3 4.2 29.4 1.0 O H:HOH207 4.2 44.8 1.0 O5' H:A3 4.3 33.0 1.0 OP2 H:U1 4.3 33.4 1.0 O F:HOH854 4.4 35.8 1.0 CD F:GLN478 4.6 31.2 1.0 O F:HOH887 4.6 35.4 1.0 CB F:LEU777 4.6 31.6 1.0 CZ F:ARG731 4.6 41.4 1.0 CE F:LYS506 4.8 32.0 1.0 N F:LEU777 4.8 32.0 1.0 O F:PHE776 5.0 29.2 1.0

Magnesium binding site 4 out of 4 in the Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ternary Rsago Complex with Guide Rna Paired and Target Dna Containing A8-A8' Non-Canonical Pair within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg102 b:48.1 occ:1.00 O H:HOH204 2.0 40.1 1.0 O H:HOH241 2.0 49.0 1.0 OP2 H:C7 2.1 32.9 0.5 O H:HOH224 2.1 41.1 1.0 O H:HOH231 2.1 36.5 1.0 O H:HOH234 2.2 36.8 1.0 P H:C7 3.3 35.3 0.5 O5' H:C7 3.6 35.4 0.5 O3' H:G6 3.8 32.7 0.5 OP2 H:A8 4.2 41.0 1.0 O5' H:C7 4.3 56.1 0.5 OP2 H:C7 4.4 58.8 0.5 N7 H:A8 4.5 37.8 1.0 O2' H:G6 4.6 31.3 0.5 OP1 H:C7 4.6 34.8 0.5 P H:C7 4.7 59.8 0.5 O J:HOH114 4.8 33.9 1.0 OP1 H:C7 4.8 59.8 0.5 N6 H:A8 4.9 37.0 1.0 C5 H:C7 5.0 44.0 0.5 C6 H:C7 5.0 43.2 0.5 C3' H:G6 5.0 32.8 0.5 C6 H:C7 5.0 45.1 0.5

Y.Liu, D.Esyunina, I.Olovnikov, M.Teplova, A.Kulbachinskiy, A.A.Aravin, D.J.Patel. Accommodation of Helical Imperfections in Rhodobacter Sphaeroides Argonaute Ternary Complexes with Guide Rna and Target Dna. Cell Rep V. 24 453 2018.
ISSN: ESSN 2211-1247
PubMed: 29996105
DOI: 10.1016/J.CELREP.2018.06.021