Magnesium in PDB 3hm9: Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand

The structure of Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand, PDB code: 3hm9 was solved by Y.Wang, H.Li, G.Sheng, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.916, 111.916, 175.551, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 28.9

The binding sites of Magnesium atom in the Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand (pdb code 3hm9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand, PDB code: 3hm9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg686 b:60.5 occ:1.00 O A:VAL685 2.0 59.4 1.0 OP1 X:DA3 2.1 54.5 1.0 OP1 X:DT1 2.1 54.9 1.0 OXT A:VAL685 2.4 58.9 1.0 C A:VAL685 2.5 59.0 1.0 P X:DT1 3.2 53.0 1.0 OE1 A:GLN433 3.4 55.8 1.0 NZ A:LYS457 3.4 59.6 1.0 P X:DA3 3.5 51.5 1.0 O5' X:DT1 3.6 53.4 1.0 OP3 X:DT1 3.7 51.8 1.0 O3' X:DG2 3.9 50.6 1.0 NE2 A:GLN433 4.0 54.9 1.0 CA A:VAL685 4.0 59.0 1.0 CD A:GLN433 4.1 55.1 1.0 C5' X:DT1 4.3 54.4 1.0 OP2 X:DA3 4.4 53.3 1.0 OP2 X:DT1 4.4 54.2 1.0 O5' X:DA3 4.5 52.7 1.0 CE A:LYS457 4.6 58.9 1.0 CB A:VAL685 4.7 58.8 1.0 CG2 A:VAL685 4.7 58.9 1.0 C5' X:DA3 4.8 53.4 1.0 N A:VAL685 4.8 59.1 1.0 O A:PHE684 4.9 59.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg687 b:69.0 occ:1.00 OD2 A:ASP546 2.1 65.7 1.0 OD1 A:ASP478 2.3 66.0 1.0 O2' Y:C9 2.6 52.3 1.0 O3' Y:C9 3.1 50.6 1.0 CG A:ASP546 3.2 61.1 1.0 C4' Y:C9 3.3 49.4 1.0 CG A:ASP478 3.5 61.6 1.0 C3' Y:C9 3.5 50.2 1.0 C2' Y:C9 3.6 50.5 1.0 OD2 A:ASP478 4.0 62.2 1.0 OD1 A:ASP546 4.0 61.6 1.0 O A:ALA479 4.1 62.2 1.0 OE1 A:GLU512 4.1 60.8 1.0 O4' Y:C9 4.1 49.3 1.0 CB A:ASP546 4.1 58.1 1.0 C5' Y:C9 4.4 48.6 1.0 N A:ALA479 4.5 61.5 1.0 P Y:U10 4.5 50.5 1.0 C1' Y:C9 4.5 49.8 1.0 OP1 Y:U10 4.6 49.1 1.0 OD1 A:ASP660 4.6 71.4 1.0 CB A:ASP478 4.7 60.4 1.0 NZ A:LYS575 4.8 66.3 1.0 CD A:GLU512 4.9 60.0 1.0 OD2 A:ASP660 5.0 71.2 1.0

Y.Wang, S.Juranek, H.Li, G.Sheng, G.S.Wardle, T.Tuschl, D.J.Patel. Nucleation, Propagation and Cleavage of Target Rnas in Ago Silencing Complexes. Nature V. 461 754 2009.
ISSN: ISSN 0028-0836
PubMed: 19812667
DOI: 10.1038/NATURE08434