Magnesium in PDB 6d9k: Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair

The structure of Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair, PDB code: 6d9k 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)	43.54 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.119, 119.130, 118.134, 90.00, 95.60, 90.00
R / Rfree (%)	19.5 / 24.2

The binding sites of Magnesium atom in the Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair (pdb code 6d9k). 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-G Non-Canonical Pair, PDB code: 6d9k:
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-G 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 and Target Dna Containing A-G Non-Canonical Pair within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:35.4 occ:1.00 OP1 C:A3 2.0 39.3 1.0 OP3 C:U1 2.0 35.8 1.0 O C:HOH205 2.1 33.6 1.0 O A:HOH970 2.1 34.4 1.0 OXT A:LEU777 2.3 40.7 1.0 O A:LEU777 2.3 36.6 1.0 C A:LEU777 2.7 41.5 1.0 P C:U1 3.2 32.6 1.0 P C:A3 3.3 34.7 1.0 OP1 C:U1 3.4 31.4 1.0 O3' C:U2 3.8 33.3 1.0 NZ A:LYS506 3.9 34.1 1.0 O5' C:U1 4.1 37.1 1.0 OE1 A:GLN478 4.1 36.0 1.0 C5' C:U1 4.1 35.0 1.0 NH2 A:ARG731 4.1 42.9 1.0 NE2 A:GLN478 4.1 34.4 1.0 OP2 C:U1 4.2 33.1 1.0 CA A:LEU777 4.2 37.0 1.0 OP2 C:A3 4.2 30.1 1.0 O A:HOH923 4.2 38.8 1.0 O5' C:A3 4.3 33.5 1.0 NE A:ARG731 4.4 48.2 1.0 O C:HOH211 4.4 49.5 1.0 CD A:GLN478 4.6 34.2 1.0 O A:HOH961 4.6 43.4 1.0 CZ A:ARG731 4.7 45.9 1.0 CB A:LEU777 4.7 36.0 1.0 CE A:LYS506 5.0 31.6 1.0

Magnesium binding site 2 out of 2 in the Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G 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 and Target Dna Containing A-G Non-Canonical Pair within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:37.1 occ:1.00 OP1 H:A3 1.9 38.8 1.0 O H:HOH204 1.9 32.9 1.0 OP3 H:U1 2.0 35.4 1.0 O F:HOH955 2.1 32.6 1.0 O F:LEU777 2.2 45.0 1.0 OXT F:LEU777 2.3 48.0 1.0 C F:LEU777 2.6 49.1 1.0 P H:U1 3.2 35.6 1.0 P H:A3 3.3 39.5 1.0 OP1 H:U1 3.5 36.8 1.0 O3' H:U2 3.7 40.0 1.0 NZ F:LYS506 4.0 42.5 1.0 O5' H:U1 4.1 38.3 1.0 NH2 F:ARG731 4.1 48.8 1.0 C5' H:U1 4.1 37.8 1.0 CA F:LEU777 4.1 41.6 1.0 OE1 F:GLN478 4.1 38.9 1.0 NE2 F:GLN478 4.2 34.2 1.0 O5' H:A3 4.2 40.6 1.0 OP2 H:U1 4.3 38.6 1.0 OP2 H:A3 4.3 36.1 1.0 NE F:ARG731 4.3 54.5 1.0 O F:HOH921 4.4 44.7 1.0 CD F:GLN478 4.6 36.7 1.0 O F:HOH952 4.6 49.4 1.0 CB F:LEU777 4.7 39.5 1.0 CZ F:ARG731 4.7 50.1 1.0 CE F:LYS506 4.9 39.4 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