Magnesium in PDB 5awh: Rhodobacter Sphaeroides Argonaute in Complex with Guide Rna/Target Dna Heteroduplex

The structure of Rhodobacter Sphaeroides Argonaute in Complex with Guide Rna/Target Dna Heteroduplex, PDB code: 5awh was solved by T.Miyoshi, K.Ito, R.Murakami, T.Uchiumi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.63 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.186, 118.303, 118.480, 90.00, 95.83, 90.00
R / Rfree (%)	18.4 / 23.3

The binding sites of Magnesium atom in the Rhodobacter Sphaeroides Argonaute in Complex with Guide Rna/Target Dna Heteroduplex (pdb code 5awh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rhodobacter Sphaeroides Argonaute in Complex with Guide Rna/Target Dna Heteroduplex, PDB code: 5awh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rhodobacter Sphaeroides Argonaute in Complex with Guide Rna/Target Dna Heteroduplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rhodobacter Sphaeroides Argonaute in Complex with Guide Rna/Target Dna Heteroduplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:33.8 occ:1.00 OP3 C:U1 1.9 32.1 1.0 OP1 C:A3 2.0 31.6 1.0 O A:HOH851 2.1 32.2 1.0 O C:HOH209 2.2 31.9 1.0 OXT A:LEU777 2.2 29.9 1.0 O A:LEU777 2.2 31.9 1.0 C A:LEU777 2.5 30.2 1.0 P C:U1 3.3 34.1 1.0 P C:A3 3.4 33.5 1.0 OP1 C:U1 3.5 31.5 1.0 O3' C:U2 3.8 32.7 1.0 NH1 A:ARG731 3.9 46.0 1.0 NZ A:LYS506 3.9 36.0 1.0 CA A:LEU777 4.0 31.0 1.0 OE1 A:GLN478 4.1 33.5 1.0 O5' C:U1 4.2 33.7 1.0 C5' C:U1 4.2 33.4 1.0 O A:HOH938 4.2 37.6 1.0 NE2 A:GLN478 4.2 34.8 1.0 O5' C:A3 4.3 36.2 1.0 OP2 C:U1 4.3 32.6 1.0 OP2 C:A3 4.4 32.2 1.0 O A:HOH963 4.5 37.4 1.0 CB A:LEU777 4.5 31.6 1.0 O A:HOH853 4.5 39.2 1.0 CD A:GLN478 4.6 33.6 1.0 CD A:ARG731 4.6 52.0 1.0 CE A:LYS506 4.8 33.1 1.0 O C:HOH221 4.8 45.9 1.0 N A:LEU777 4.8 29.9 1.0 CZ A:ARG731 4.9 45.4 1.0

Magnesium binding site 2 out of 2 in the Rhodobacter Sphaeroides Argonaute in Complex with Guide Rna/Target Dna Heteroduplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rhodobacter Sphaeroides Argonaute in Complex with Guide Rna/Target Dna Heteroduplex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:46.3 occ:1.00 OP1 E:A3 1.9 42.9 1.0 OP3 E:U1 2.0 42.3 1.0 O B:HOH893 2.2 40.3 1.0 O E:HOH206 2.2 35.7 1.0 OXT B:LEU777 2.2 39.4 1.0 O B:LEU777 2.3 44.3 1.0 C B:LEU777 2.6 44.0 1.0 P E:U1 3.2 44.9 1.0 P E:A3 3.2 46.3 1.0 OP2 E:U1 3.5 42.9 1.0 O3' E:U2 3.7 46.5 1.0 NZ B:LYS506 3.8 43.1 1.0 NH1 B:ARG731 3.9 52.8 1.0 NE2 B:GLN478 4.0 45.5 1.0 O5' E:U1 4.1 44.4 1.0 OE1 B:GLN478 4.1 45.4 1.0 O B:HOH831 4.1 44.6 1.0 CA B:LEU777 4.1 41.1 1.0 C5' E:U1 4.1 44.4 1.0 OP2 E:A3 4.2 42.8 1.0 O5' E:A3 4.2 45.9 1.0 OP1 E:U1 4.3 45.6 1.0 CD B:GLN478 4.5 44.1 1.0 O B:HOH841 4.5 46.1 1.0 CB B:LEU777 4.7 41.8 1.0 O B:HOH849 4.7 42.8 1.0 CE B:LYS506 4.9 41.7 1.0 CG B:ARG731 4.9 55.1 1.0 N B:LEU777 5.0 39.7 1.0

T.Miyoshi, K.Ito, R.Murakami, T.Uchiumi. Structural Basis For the Recognition of Guide Rna and Target Dna Heteroduplex By Argonaute. Nat Commun V. 7 11846 2016.
ISSN: ESSN 2041-1723
PubMed: 27325485
DOI: 10.1038/NCOMMS11846