Magnesium 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:

Arsenic

(As)

4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna, PDB code: 6d8p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


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 Containing Guide Rna Paired with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:30.8 occ:1.00 CD A:PRO109 3.0 38.8 1.0 N A:LYS110 3.2 25.2 1.0 CB A:LYS110 3.4 31.1 1.0 N A:PRO109 3.5 42.1 1.0 C A:LEU108 3.6 38.3 1.0 CA A:LEU108 3.8 33.6 1.0 CG A:LYS110 3.8 40.9 1.0 CA A:LYS110 3.8 32.5 1.0 CD1 A:TYR111 4.0 31.4 1.0 CZ A:PHE290 4.2 60.8 1.0 O A:LEU108 4.2 35.5 1.0 C A:PRO109 4.2 23.1 1.0 CG A:PRO109 4.2 41.4 1.0 CE1 A:TYR111 4.3 41.5 1.0 CA A:PRO109 4.3 34.5 1.0 CD A:LYS110 4.4 41.1 1.0 CB A:LEU108 4.5 33.0 1.0 C A:LYS110 4.5 37.1 1.0 O A:ALA107 4.5 39.5 1.0 CG A:LEU108 4.5 36.4 1.0 N A:TYR111 4.6 29.7 1.0 CE2 A:PHE290 4.7 63.7 1.0 CB A:PRO109 4.7 39.4 1.0 N A:LEU108 4.9 29.1 1.0

Magnesium binding site 2 out of 7 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


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 Containing Guide Rna Paired with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:63.9 occ:1.00 NH1 A:ARG279 4.1 66.8 1.0 NH2 A:ARG286 4.1 53.7 1.0 CZ A:ARG286 4.6 54.3 1.0 NH1 A:ARG286 4.9 52.2 1.0

Magnesium binding site 3 out of 7 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg803 b:56.4 occ:1.00 O A:HOH1157 4.8 41.4 1.0 O A:HOH971 4.9 46.6 1.0 OD1 A:ASN629 5.0 34.3 1.0

Magnesium binding site 4 out of 7 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg804 b:26.6 occ:1.00 O A:HOH1040 3.0 29.2 1.0 N A:SER395 3.3 35.0 1.0 N A:LYS396 3.3 22.6 1.0 O A:HOH1232 3.4 56.2 1.0 CG A:LYS396 3.6 45.2 1.0 CZ2 A:TRP343 3.8 22.8 1.0 CB A:LYS396 3.8 38.8 1.0 C A:PHE394 4.0 29.4 1.0 CA A:SER395 4.1 33.9 1.0 CA A:PHE394 4.1 35.4 1.0 C A:SER395 4.2 30.8 1.0 CA A:LYS396 4.2 31.0 1.0 CB A:SER395 4.3 33.4 1.0 CE A:LYS396 4.3 36.7 1.0 O A:GLY393 4.3 30.5 1.0 O A:SER392 4.5 31.0 1.0 CD A:LYS396 4.6 40.6 1.0 OG A:SER347 4.6 49.4 1.0 CE2 A:TRP343 4.6 27.6 1.0 N A:PHE394 4.6 34.9 1.0 CH2 A:TRP343 4.7 21.7 1.0 C A:GLY393 4.7 36.2 1.0 NE1 A:TRP343 4.7 24.1 1.0 OG A:SER395 4.8 51.3 1.0 N A:GLY397 4.8 29.3 1.0 CD2 A:LEU401 5.0 27.5 1.0 CG A:LEU401 5.0 37.0 1.0

Magnesium binding site 5 out of 7 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ternary Rsago Complex Containing Guide Rna Paired with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:23.5 occ:1.00 O A:HOH1116 3.1 29.4 1.0 O A:HOH1249 3.2 37.7 1.0 N A:GLU451 3.3 26.8 1.0 CB A:MET482 3.6 22.5 1.0 CB A:GLU451 3.7 27.5 1.0 CD1 A:PHE450 3.9 25.3 1.0 CA A:PHE450 4.0 20.1 1.0 CA A:GLU451 4.1 19.8 1.0 C A:PHE450 4.1 26.1 1.0 CD A:PRO483 4.2 20.5 1.0 CG A:MET482 4.3 21.1 1.0 CB A:PHE450 4.5 20.3 1.0 CG A:PRO483 4.6 20.7 1.0 CG A:PHE450 4.7 20.7 1.0 CA A:MET482 4.7 20.8 1.0 CE1 A:PHE450 4.8 28.9 1.0 N A:PRO483 4.9 20.8 1.0 O A:HOH1236 4.9 45.7 1.0 N A:ASP452 5.0 25.7 1.0

Magnesium binding site 6 out of 7 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ternary Rsago Complex Containing Guide Rna Paired with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:17.0 occ:1.00 OP1 E:A3 1.9 17.2 1.0 OP3 E:U1 2.0 17.2 1.0 O E:HOH208 2.1 16.6 1.0 O A:HOH973 2.2 17.4 1.0 O A:LEU777 2.3 16.6 1.0 OXT A:LEU777 2.3 17.5 1.0 C A:LEU777 2.6 16.6 1.0 P E:U1 3.2 17.1 1.0 P E:A3 3.3 17.6 1.0 OP1 E:U1 3.4 16.8 1.0 O3' E:U2 3.7 18.4 1.0 NH2 A:ARG731 4.0 24.7 1.0 NZ A:LYS506 4.0 17.1 1.0 C5' E:U1 4.1 17.5 1.0 O5' E:U1 4.1 17.4 1.0 NE2 A:GLN478 4.1 18.0 1.0 CA A:LEU777 4.2 16.4 1.0 O A:HOH1072 4.2 16.1 1.0 O5' E:A3 4.2 17.6 1.0 OE1 A:GLN478 4.2 17.8 1.0 OP2 E:A3 4.3 17.6 1.0 NE A:ARG731 4.3 32.1 1.0 OP2 E:U1 4.3 17.3 1.0 O E:HOH233 4.4 34.5 1.0 O E:HOH211 4.4 17.8 1.0 CD A:GLN478 4.6 18.0 1.0 CZ A:ARG731 4.6 21.3 1.0 O A:HOH999 4.6 16.4 1.0 CB A:LEU777 4.7 16.6 1.0 CE A:LYS506 5.0 17.0 1.0

Magnesium binding site 7 out of 7 in the Ternary Rsago Complex Containing Guide Rna Paired with Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ternary Rsago Complex Containing Guide Rna Paired with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:19.8 occ:1.00 OP1 C:A3 1.9 23.2 1.0 OP3 C:U1 2.0 15.8 1.0 O C:HOH203 2.1 13.7 1.0 O B:HOH972 2.2 13.3 1.0 O B:LEU777 2.2 18.2 1.0 OXT B:LEU777 2.3 22.9 1.0 C B:LEU777 2.6 24.3 1.0 P C:U1 3.2 18.4 1.0 P C:A3 3.3 19.0 1.0 OP1 C:U1 3.4 18.4 1.0 O3' C:U2 3.7 23.9 1.0 NZ B:LYS506 3.9 15.6 1.0 C5' C:U1 4.1 23.9 1.0 O5' C:U1 4.1 22.8 1.0 CA B:LEU777 4.1 15.2 1.0 NH2 B:ARG731 4.2 35.6 1.0 NE2 B:GLN478 4.2 14.3 1.0 O5' C:A3 4.2 21.5 1.0 OE1 B:GLN478 4.2 18.3 1.0 O B:HOH925 4.2 14.6 1.0 OP2 C:U1 4.3 20.7 1.0 NE B:ARG731 4.3 37.6 1.0 OP2 C:A3 4.3 14.8 1.0 O C:HOH212 4.4 21.1 1.0 O B:HOH954 4.5 27.7 1.0 CD B:GLN478 4.6 15.6 1.0 CB B:LEU777 4.7 13.1 1.0 CZ B:ARG731 4.7 33.5 1.0 CE B:LYS506 4.8 13.4 1.0 N B:LEU777 5.0 17.0 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