Magnesium in PDB 6d8a: Rsago Ternary Complex with Guide Rna and Target Dna Containing A-A Bulge Within the Seed Segment of the Target Strand

The structure of Rsago Ternary Complex with Guide Rna and Target Dna Containing A-A Bulge Within the Seed Segment of the Target Strand, PDB code: 6d8a 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)	42.67 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.411, 118.985, 118.818, 90.00, 95.51, 90.00
R / Rfree (%)	19.8 / 23.9

The binding sites of Magnesium atom in the Rsago Ternary Complex with Guide Rna and Target Dna Containing A-A Bulge Within the Seed Segment of the Target Strand (pdb code 6d8a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rsago Ternary Complex with Guide Rna and Target Dna Containing A-A Bulge Within the Seed Segment of the Target Strand, PDB code: 6d8a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rsago Ternary Complex with Guide Rna and Target Dna Containing A-A Bulge Within the Seed Segment of the Target Strand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rsago Ternary Complex with Guide Rna and Target Dna Containing A-A Bulge Within the Seed Segment of the Target Strand within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:28.7 occ:1.00 OP1 C:A3 1.9 35.4 1.0 OP3 C:U1 1.9 32.4 1.0 O C:HOH206 2.0 32.2 1.0 O A:HOH915 2.1 30.6 1.0 O A:LEU777 2.3 27.7 1.0 OXT A:LEU777 2.3 33.6 1.0 C A:LEU777 2.6 33.6 1.0 P C:A3 3.2 27.2 1.0 P C:U1 3.3 30.6 1.0 HE22 A:GLN478 3.3 36.2 1.0 HH21 A:ARG731 3.4 48.5 1.0 HZ2 A:LYS506 3.4 37.2 1.0 HE A:ARG731 3.5 44.4 1.0 H5' C:U1 3.6 35.8 1.0 O3' C:U2 3.6 30.7 1.0 OP1 C:U1 3.6 29.8 1.0 OE1 A:GLN478 3.9 31.1 1.0 NE2 A:GLN478 4.1 30.2 1.0 O C:HOH212 4.1 31.8 1.0 O5' C:A3 4.1 30.0 1.0 CA A:LEU777 4.1 30.4 1.0 NZ A:LYS506 4.1 31.0 1.0 HZ3 A:LYS506 4.2 37.2 1.0 NH2 A:ARG731 4.2 40.4 1.0 O5' C:U1 4.2 37.9 1.0 C5' C:U1 4.2 29.8 1.0 OP2 C:U1 4.2 33.7 1.0 H5'' C:U1 4.2 35.8 1.0 HH21 A:ARG747 4.2 52.7 1.0 OP2 C:A3 4.2 32.4 1.0 HB3 A:LEU777 4.3 41.1 1.0 NE A:ARG731 4.3 37.0 1.0 HE3 A:LYS506 4.4 33.5 1.0 CD A:GLN478 4.4 28.2 1.0 HG2 A:ARG731 4.5 52.0 1.0 HA A:LEU777 4.6 36.4 1.0 CB A:LEU777 4.6 34.2 1.0 HB2 A:LEU777 4.6 41.1 1.0 HB1 A:ALA502 4.7 42.0 1.0 CZ A:ARG731 4.7 39.1 1.0 O A:HOH949 4.7 32.8 1.0 HZ1 A:LYS506 4.8 37.2 1.0 HE21 A:GLN478 4.8 36.2 1.0 HH22 A:ARG731 4.8 48.5 1.0 CE A:LYS506 4.8 27.9 1.0 N A:LEU777 5.0 30.0 1.0

Magnesium binding site 2 out of 2 in the Rsago Ternary Complex with Guide Rna and Target Dna Containing A-A Bulge Within the Seed Segment of the Target Strand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rsago Ternary Complex with Guide Rna and Target Dna Containing A-A Bulge Within the Seed Segment of the Target Strand within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:34.7 occ:1.00 OP1 H:A3 1.8 34.9 1.0 O H:HOH207 2.0 28.8 1.0 O F:HOH950 2.0 29.8 1.0 OP3 H:U1 2.1 28.8 1.0 O F:LEU777 2.2 30.6 1.0 OXT F:LEU777 2.5 37.9 1.0 C F:LEU777 2.7 37.2 1.0 P H:A3 3.1 33.1 1.0 HZ1 F:LYS506 3.1 46.4 1.0 HE22 F:GLN478 3.3 35.4 1.0 HH21 F:ARG731 3.3 46.7 1.0 HE F:ARG731 3.3 46.8 1.0 P H:U1 3.4 30.4 1.0 O3' H:U2 3.6 34.7 1.0 OP1 H:U1 3.6 28.4 1.0 H5' H:U1 3.7 42.2 1.0 NZ F:LYS506 3.9 38.6 1.0 HZ2 F:LYS506 4.0 46.4 1.0 O5' H:A3 4.0 32.7 1.0 H5'' H:U1 4.1 42.2 1.0 OE1 F:GLN478 4.1 33.7 1.0 NE2 F:GLN478 4.1 29.5 1.0 NH2 F:ARG731 4.1 38.9 1.0 NE F:ARG731 4.2 39.0 1.0 CA F:LEU777 4.2 36.8 1.0 C5' H:U1 4.2 35.2 1.0 OP2 H:A3 4.2 26.6 1.0 HB3 F:LEU777 4.2 42.6 1.0 O5' H:U1 4.3 38.9 1.0 O H:HOH204 4.4 35.1 1.0 OP2 H:U1 4.4 31.0 1.0 HG2 F:ARG731 4.4 57.3 1.0 HZ3 F:LYS506 4.5 46.4 1.0 CD F:GLN478 4.5 32.8 1.0 HE3 F:LYS506 4.5 43.9 1.0 HA F:LEU777 4.6 44.2 1.0 CZ F:ARG731 4.6 37.2 1.0 CB F:LEU777 4.7 35.5 1.0 HB2 F:LEU777 4.7 42.6 1.0 HE21 F:GLN478 4.8 35.4 1.0 HH22 F:ARG731 4.8 46.7 1.0 CE F:LYS506 4.8 36.6 1.0 O F:HOH959 4.8 32.2 1.0 HB1 F:ALA502 4.8 41.1 1.0 HO2' H:U2 4.9 34.6 1.0 H5' H:A3 4.9 39.7 1.0 C3' H:U2 5.0 38.1 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