Magnesium in PDB 6d8f: Rsago Ternary Complex with Guide Rna and Target Dna Containing T-T Bulge Within the Seed Segment

The structure of Rsago Ternary Complex with Guide Rna and Target Dna Containing T-T Bulge Within the Seed Segment, PDB code: 6d8f 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)	42.30 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.039, 118.312, 117.672, 90.00, 95.48, 90.00
R / Rfree (%)	20.1 / 24

The binding sites of Magnesium atom in the Rsago Ternary Complex with Guide Rna and Target Dna Containing T-T Bulge Within the Seed Segment (pdb code 6d8f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Rsago Ternary Complex with Guide Rna and Target Dna Containing T-T Bulge Within the Seed Segment, PDB code: 6d8f:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Rsago Ternary Complex with Guide Rna and Target Dna Containing T-T Bulge Within the Seed Segment


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 T-T Bulge Within the Seed Segment within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:22.0 occ:1.00 O A:HOH1022 1.9 34.9 1.0 OP3 C:U1 1.9 21.9 1.0 OP1 C:A3 2.0 22.9 1.0 O A:LEU777 2.2 21.2 1.0 OXT A:LEU777 2.3 22.2 1.0 C A:LEU777 2.6 22.9 1.0 P C:U1 3.2 19.1 1.0 HZ3 A:LYS506 3.3 24.4 1.0 P C:A3 3.3 16.9 1.0 HE22 A:GLN478 3.4 21.0 1.0 HH21 A:ARG731 3.4 35.0 1.0 HE A:ARG731 3.5 38.4 1.0 OP1 C:U1 3.6 19.4 1.0 H5' C:U1 3.6 26.2 1.0 HZ1 A:LYS506 3.7 24.4 1.0 O3' C:U2 3.7 22.3 1.0 NZ A:LYS506 3.9 20.5 1.0 OE1 A:GLN478 4.1 19.1 1.0 CA A:LEU777 4.1 22.6 1.0 NE2 A:GLN478 4.1 17.7 1.0 C5' C:U1 4.2 22.0 1.0 O5' C:U1 4.2 23.4 1.0 H5'' C:U1 4.2 26.2 1.0 O A:HOH978 4.2 24.6 1.0 O5' C:A3 4.2 21.2 1.0 OP2 C:U1 4.2 20.3 1.0 O A:HOH970 4.2 20.6 1.0 NH2 A:ARG731 4.2 29.3 1.0 HB3 A:LEU777 4.3 26.7 1.0 NE A:ARG731 4.3 32.1 1.0 OP2 C:A3 4.4 19.8 1.0 HZ2 A:LYS506 4.4 24.4 1.0 HG2 A:ARG731 4.5 34.8 1.0 HA A:LEU777 4.5 26.9 1.0 HB2 A:LEU777 4.5 26.7 1.0 O A:HOH1046 4.5 19.2 1.0 CB A:LEU777 4.5 22.4 1.0 CD A:GLN478 4.6 19.7 1.0 HB1 A:ALA502 4.7 23.8 1.0 HE3 A:LYS506 4.7 23.1 1.0 CZ A:ARG731 4.8 28.8 1.0 HE21 A:GLN478 4.8 21.0 1.0 HH22 A:ARG731 4.9 35.0 1.0 N A:LEU777 5.0 16.4 1.0 CE A:LYS506 5.0 19.4 1.0

Magnesium binding site 2 out of 3 in the Rsago Ternary Complex with Guide Rna and Target Dna Containing T-T Bulge Within the Seed Segment


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 T-T Bulge Within the Seed Segment within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:22.3 occ:1.00 OP1 H:A3 1.9 28.6 1.0 O H:HOH204 1.9 24.4 1.0 O F:HOH953 2.0 19.3 1.0 OP3 H:U1 2.0 21.6 1.0 O F:LEU777 2.2 25.9 1.0 OXT F:LEU777 2.3 22.4 1.0 C F:LEU777 2.6 25.0 1.0 HZ3 F:LYS506 3.2 29.1 1.0 P H:A3 3.2 28.2 1.0 P H:U1 3.3 24.9 1.0 HE F:ARG731 3.3 40.6 1.0 HE22 F:GLN478 3.4 29.1 1.0 HH21 F:ARG731 3.4 43.8 1.0 OP1 H:U1 3.5 25.4 1.0 H5' H:U1 3.6 29.3 1.0 O3' H:U2 3.7 27.3 1.0 HZ1 F:LYS506 3.7 29.1 1.0 NZ F:LYS506 3.9 24.4 1.0 OE1 F:GLN478 3.9 25.4 1.0 CA F:LEU777 4.1 24.6 1.0 NE F:ARG731 4.1 34.0 1.0 O5' H:A3 4.1 27.9 1.0 O5' H:U1 4.2 26.6 1.0 NE2 F:GLN478 4.2 24.4 1.0 HG2 F:ARG731 4.2 46.8 1.0 C5' H:U1 4.2 24.6 1.0 H5'' H:U1 4.2 29.3 1.0 NH2 F:ARG731 4.2 36.6 1.0 OP2 H:A3 4.3 26.2 1.0 O F:HOH944 4.3 28.1 1.0 OP2 H:U1 4.3 23.9 1.0 HB3 F:LEU777 4.3 26.0 1.0 HZ2 F:LYS506 4.5 29.1 1.0 HE3 F:LYS506 4.5 28.6 1.0 HA F:LEU777 4.5 29.3 1.0 O F:HOH1046 4.5 30.0 1.0 CD F:GLN478 4.5 22.8 1.0 HB2 F:LEU777 4.6 26.0 1.0 CB F:LEU777 4.6 21.8 1.0 O F:HOH987 4.7 24.0 1.0 CZ F:ARG731 4.7 37.1 1.0 HB1 F:ALA502 4.7 30.6 1.0 CE F:LYS506 4.8 24.0 1.0 HH22 F:ARG731 4.9 43.8 1.0 HE21 F:GLN478 4.9 29.1 1.0 HO2' H:U2 4.9 33.0 1.0 N F:LEU777 5.0 19.3 1.0

Magnesium binding site 3 out of 3 in the Rsago Ternary Complex with Guide Rna and Target Dna Containing T-T Bulge Within the Seed Segment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rsago Ternary Complex with Guide Rna and Target Dna Containing T-T Bulge Within the Seed Segment within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg101 b:43.3 occ:1.00 O J:HOH219 2.0 42.4 1.0 O J:HOH212 2.0 32.5 1.0 O J:HOH223 2.0 49.5 1.0 OP2 J:DG-4 2.1 32.5 1.0 H3' J:DT-5 3.4 49.3 1.0 P J:DG-4 3.6 30.2 1.0 OP2 J:DT-5 4.1 33.1 1.0 O5' J:DT-5 4.2 30.7 1.0 C3' J:DT-5 4.2 41.2 1.0 O3' J:DT-5 4.3 34.0 1.0 OE2 F:GLU746 4.3 25.4 1.0 O5' J:DG-4 4.5 31.8 1.0 CD F:GLU746 4.5 28.0 1.0 O F:HOH1080 4.5 33.4 1.0 OP1 J:DG-4 4.5 35.1 1.0 P J:DT-5 4.6 30.0 1.0 H8 J:DG-4 4.6 47.6 1.0 OE1 F:GLU746 4.7 29.2 1.0 H5'' J:DT-5 4.7 37.2 1.0 H73 J:DT-5 4.8 36.3 1.0 H6 J:DT-5 4.8 44.2 1.0 HG2 F:GLU746 4.8 26.6 1.0 O F:HOH925 4.9 39.1 1.0 C5' J:DT-5 4.9 31.1 1.0 OP1 J:DT-5 5.0 31.7 1.0 HB3 F:GLU746 5.0 30.4 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