Magnesium in PDB 6d92: Ternary Rsago Complex with Guide Rna and Target Dna Containing A-A Non-Canonical Pair at Position 3

The structure of Ternary Rsago Complex with Guide Rna and Target Dna Containing A-A Non-Canonical Pair at Position 3, PDB code: 6d92 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)	42.81 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.237, 118.942, 118.559, 90.00, 95.72, 90.00
R / Rfree (%)	19.8 / 24

The binding sites of Magnesium atom in the Ternary Rsago Complex with Guide Rna and Target Dna Containing A-A Non-Canonical Pair at Position 3 (pdb code 6d92). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Rsago Complex with Guide Rna and Target Dna Containing A-A Non-Canonical Pair at Position 3, PDB code: 6d92:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Rsago Complex with Guide Rna and Target Dna Containing A-A Non-Canonical Pair at Position 3


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 and Target Dna Containing A-A Non-Canonical Pair at Position 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:21.4 occ:1.00 OP1 C:A3 2.0 24.2 1.0 OP3 C:U1 2.1 20.0 1.0 O A:HOH972 2.1 21.2 1.0 O C:HOH206 2.2 21.7 1.0 OXT A:LEU777 2.2 24.9 1.0 O A:LEU777 2.2 21.2 1.0 C A:LEU777 2.5 24.3 1.0 P C:U1 3.3 21.5 1.0 P C:A3 3.4 23.3 1.0 OP1 C:U1 3.6 22.9 1.0 O3' C:U2 3.8 23.6 1.0 NZ A:LYS506 3.9 21.5 1.0 NH2 A:ARG731 3.9 35.2 1.0 CA A:LEU777 4.0 22.4 1.0 OE1 A:GLN478 4.0 23.6 1.0 NE2 A:GLN478 4.2 22.7 1.0 O A:HOH962 4.2 33.6 1.0 O5' C:U1 4.2 23.1 1.0 OP2 C:U1 4.2 21.5 1.0 C5' C:U1 4.2 22.3 1.0 OP2 C:A3 4.3 22.0 1.0 NE A:ARG731 4.3 36.6 1.0 O C:HOH242 4.3 41.1 1.0 O5' C:A3 4.3 25.5 1.0 O C:HOH212 4.5 24.0 1.0 CD A:GLN478 4.6 22.6 1.0 O A:HOH968 4.6 27.8 1.0 CB A:LEU777 4.6 23.1 1.0 CZ A:ARG731 4.6 36.1 1.0 N A:LEU777 4.9 20.9 1.0 CE A:LYS506 4.9 20.4 1.0

Magnesium binding site 2 out of 2 in the Ternary Rsago Complex with Guide Rna and Target Dna Containing A-A Non-Canonical Pair at Position 3


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 and Target Dna Containing A-A Non-Canonical Pair at Position 3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:26.0 occ:1.00 OP1 H:A3 2.0 26.3 1.0 OP3 H:U1 2.0 23.4 1.0 O F:HOH1018 2.1 28.4 1.0 O H:HOH234 2.1 25.8 1.0 O F:LEU777 2.2 27.5 1.0 OXT F:LEU777 2.3 28.3 1.0 C F:LEU777 2.5 29.5 1.0 P H:U1 3.3 23.7 1.0 P H:A3 3.3 26.0 1.0 OP1 H:U1 3.6 22.9 1.0 O3' H:U2 3.7 26.8 1.0 NZ F:LYS506 3.9 25.9 1.0 NH2 F:ARG731 4.0 43.0 1.0 CA F:LEU777 4.1 26.0 1.0 O F:HOH950 4.1 33.3 1.0 OE1 F:GLN478 4.1 27.0 1.0 C5' H:U1 4.2 26.2 1.0 NE2 F:GLN478 4.2 23.4 1.0 O5' H:U1 4.2 26.8 1.0 O H:HOH242 4.2 41.6 1.0 OP2 H:U1 4.3 24.0 1.0 O5' H:A3 4.3 28.2 1.0 OP2 H:A3 4.3 25.2 1.0 NE F:ARG731 4.3 38.6 1.0 O H:HOH208 4.5 32.6 1.0 O F:HOH1036 4.6 31.9 1.0 CB F:LEU777 4.6 28.7 1.0 CD F:GLN478 4.6 25.7 1.0 CZ F:ARG731 4.6 41.5 1.0 CE F:LYS506 4.8 24.8 1.0 N F:LEU777 4.9 24.5 1.0

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