Arsenic in PDB 6d8p: Ternary Rsago Complex Containing Guide Rna Paired with Target Dna

The structure of Ternary Rsago Complex Containing Guide Rna Paired with Target Dna, PDB code: 6d8p 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)	42.34 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.234, 119.216, 117.648, 90.00, 95.62, 90.00
R / Rfree (%)	18.2 / 23.5

The structure of Ternary Rsago Complex Containing Guide Rna Paired with Target Dna also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Arsenic atom in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna (pdb code 6d8p). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna, PDB code: 6d8p:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Ternary Rsago Complex Containing Guide Rna Paired with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:As818 b:0.9 occ:1.00 AS A:CAC818 0.0 0.9 1.0 O2 A:CAC818 1.7 0.6 1.0 O1 A:CAC818 1.7 60.5 1.0 C2 A:CAC818 2.0 0.9 1.0 C1 A:CAC818 2.0 62.5 1.0 CD1 A:LEU22 4.7 22.7 1.0 CG2 A:VAL321 4.7 27.0 1.0 N A:ARG20 4.8 53.2 1.0 CB A:LEU323 4.8 26.1 1.0

Arsenic binding site 2 out of 4 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Ternary Rsago Complex Containing Guide Rna Paired with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:As819 b:0.1 occ:1.00 AS A:CAC819 0.0 0.1 1.0 O1 A:CAC819 1.7 0.8 1.0 O2 A:CAC819 1.7 66.2 1.0 C1 A:CAC819 2.0 0.2 1.0 C2 A:CAC819 2.0 0.5 1.0 OH A:TYR111 3.9 44.9 1.0 SD A:MET287 4.6 34.8 1.0 CZ A:TYR111 4.7 43.5 1.0 CG A:PHE290 4.9 53.1 1.0

Arsenic binding site 3 out of 4 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Ternary Rsago Complex Containing Guide Rna Paired with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:As820 b:0.0 occ:1.00 AS A:CAC820 0.0 0.0 1.0 O1 A:CAC820 1.7 75.6 1.0 O2 A:CAC820 1.7 96.2 1.0 C1 A:CAC820 2.0 89.0 1.0 C2 A:CAC820 2.0 49.0 1.0 NH2 A:ARG384 4.5 26.0 1.0 CD2 A:PHE409 4.6 25.2 1.0 CZ A:ARG384 4.9 35.3 1.0 NH1 A:ARG384 4.9 31.1 1.0 CE2 A:PHE409 5.0 28.1 1.0

Arsenic binding site 4 out of 4 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Ternary Rsago Complex Containing Guide Rna Paired with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:As805 b:0.9 occ:1.00 AS B:CAC805 0.0 0.9 1.0 O2 B:CAC805 1.7 0.3 1.0 O1 B:CAC805 1.7 70.9 1.0 C2 B:CAC805 2.0 0.0 1.0 C1 B:CAC805 2.0 0.4 1.0 NH2 B:ARG384 4.7 43.6 1.0 CD2 B:PHE409 4.8 29.4 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