Magnesium in PDB 3hvr: Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site

The structure of Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site, PDB code: 3hvr 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)	37.68 / 3.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.252, 116.903, 170.504, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 27.3

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 with Two MG2+ at the Cleavage Site (pdb code 3hvr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 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 with Two MG2+ at the Cleavage Site, PDB code: 3hvr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site


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 with Two MG2+ at the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg686 b:66.8 occ:1.00 OP1 C:DA3 2.2 54.6 1.0 OP3 C:DT1 2.2 81.2 1.0 OXT A:VAL685 2.3 95.4 1.0 O A:VAL685 2.3 0.4 1.0 C A:VAL685 2.6 98.3 1.0 OE1 A:GLN433 3.2 71.0 1.0 P C:DT1 3.5 83.0 1.0 P C:DA3 3.6 73.5 1.0 NZ A:LYS457 3.9 77.6 1.0 NE2 A:GLN433 3.9 69.4 1.0 CD A:GLN433 4.0 68.0 1.0 OP1 C:DT1 4.1 70.5 1.0 CE A:LYS457 4.1 76.0 1.0 CA A:VAL685 4.1 88.3 1.0 O3' C:DG2 4.2 76.2 1.0 O5' C:DT1 4.3 74.3 1.0 CG2 A:VAL685 4.4 88.0 1.0 O5' C:DA3 4.5 76.0 1.0 OP2 C:DT1 4.6 81.8 1.0 C5' C:DA3 4.6 76.0 1.0 OP2 C:DA3 4.6 73.2 1.0 CB A:VAL685 4.7 85.8 1.0 C5' C:DT1 4.8 78.5 1.0 O A:PHE684 4.9 72.4 1.0 N A:VAL685 5.0 76.1 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site


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 with Two MG2+ at the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg686 b:55.2 occ:1.00 OP1 M:DA3 2.2 77.0 1.0 OP3 M:DT1 2.2 83.2 1.0 OXT B:VAL685 2.3 0.9 1.0 O B:VAL685 2.3 0.0 1.0 C B:VAL685 2.7 0.8 1.0 P M:DT1 3.6 85.3 1.0 P M:DA3 3.6 77.3 1.0 OE1 B:GLN433 3.8 71.0 1.0 NZ B:LYS457 3.8 66.5 1.0 NE2 B:GLN433 4.1 75.3 1.0 O3' M:DG2 4.1 83.4 1.0 OP1 M:DT1 4.2 73.9 1.0 CA B:VAL685 4.2 95.7 1.0 CD B:GLN433 4.4 71.2 1.0 C5' M:DA3 4.4 84.0 1.0 CE B:LYS457 4.4 62.6 1.0 O5' M:DT1 4.4 77.0 1.0 O5' M:DA3 4.4 82.4 1.0 OP2 M:DT1 4.5 90.0 1.0 O B:PHE684 4.5 73.8 1.0 OP2 M:DA3 4.7 79.7 1.0 C5' M:DT1 4.7 80.7 1.0 CB B:VAL685 4.9 91.3 1.0 N B:VAL685 5.0 87.2 1.0 CG2 B:VAL685 5.0 89.4 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg687 b:61.8 occ:1.00 O3' D:C9 2.1 0.9 1.0 OP1 D:U10 2.1 0.7 1.0 OD1 A:ASP478 2.3 99.8 1.0 OD2 A:ASP546 2.3 100.0 1.0 P D:U10 2.7 0.3 1.0 CG A:ASP546 3.2 95.4 1.0 CG A:ASP478 3.3 94.5 1.0 C3' D:C9 3.4 0.9 1.0 C4' D:C9 3.7 0.9 1.0 OD2 A:ASP478 3.8 98.3 1.0 O5' D:U10 3.8 0.9 1.0 C5' D:U10 3.8 0.8 1.0 OP2 D:U10 3.8 0.2 1.0 O A:ASP546 3.9 87.1 1.0 CB A:ASP546 3.9 83.3 1.0 OD1 A:ASP546 3.9 96.7 1.0 MG A:MG688 3.9 68.7 1.0 OE2 A:GLU512 4.0 94.8 1.0 C5' D:C9 4.1 1.0 1.0 OE1 A:GLU512 4.1 0.4 1.0 O2' D:C9 4.2 0.9 1.0 C2' D:C9 4.4 0.8 1.0 C A:ASP546 4.4 81.5 1.0 CD A:GLU512 4.4 0.2 1.0 N A:ALA479 4.5 81.5 1.0 CB A:ASP478 4.6 84.2 1.0 CA A:ASP478 4.8 79.9 1.0 CA A:ASP546 4.9 77.2 1.0 O A:ALA479 4.9 95.8 1.0 O5' D:C9 5.0 0.1 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg688 b:68.7 occ:1.00 OP1 D:U10 2.1 0.7 1.0 OD1 A:ASP660 2.1 97.4 1.0 OD2 A:ASP478 2.3 98.3 1.0 CG A:ASP660 2.9 93.2 1.0 P D:U10 2.9 0.3 1.0 OD2 A:ASP546 3.1 100.0 1.0 OP2 D:U10 3.1 0.2 1.0 OD2 A:ASP660 3.3 95.3 1.0 CG A:ASP478 3.3 94.5 1.0 NZ A:LYS575 3.5 0.2 1.0 OD1 A:ASP478 3.6 99.8 1.0 O5' D:U10 3.8 0.9 1.0 MG A:MG687 3.9 61.8 1.0 CB A:ASP660 4.1 83.4 1.0 CG A:ASP546 4.1 95.4 1.0 O3' D:C9 4.2 0.9 1.0 NZ A:LYS664 4.3 90.5 1.0 OP2 D:A11 4.4 0.6 1.0 CA A:ASP660 4.4 79.7 1.0 CB A:ASP478 4.6 84.2 1.0 CE A:LYS575 4.6 90.2 1.0 C5' D:U10 4.7 0.8 1.0 OD1 A:ASP546 4.8 96.7 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg687 b:95.1 occ:1.00 OD2 B:ASP546 2.1 96.3 1.0 OP1 N:U10 2.1 0.9 1.0 OD1 B:ASP478 2.2 96.2 1.0 O3' N:C9 2.4 0.8 1.0 CG B:ASP546 2.8 99.1 1.0 P N:U10 2.8 0.8 1.0 CG B:ASP478 3.2 93.9 1.0 OD1 B:ASP546 3.5 99.7 1.0 OD2 B:ASP478 3.5 99.1 1.0 C3' N:C9 3.5 0.0 1.0 CB B:ASP546 3.5 89.2 1.0 C4' N:C9 3.6 0.7 1.0 O B:ASP546 3.7 84.6 1.0 OP2 N:U10 3.9 0.9 1.0 MG B:MG688 3.9 0.7 1.0 C5' N:C9 3.9 0.7 1.0 O5' N:U10 4.0 0.3 1.0 OE2 B:GLU512 4.1 96.9 1.0 C B:ASP546 4.1 77.0 1.0 C5' N:U10 4.3 0.3 1.0 O2' N:C9 4.3 0.7 1.0 OE1 B:GLU512 4.4 0.9 1.0 C2' N:C9 4.5 0.1 1.0 CA B:ASP546 4.5 76.8 1.0 N B:ALA479 4.5 84.9 1.0 CB B:ASP478 4.5 77.1 1.0 NZ B:LYS575 4.6 0.3 1.0 CD B:GLU512 4.7 0.2 1.0 N B:GLY547 4.8 70.0 1.0 CA B:ASP478 4.8 74.0 1.0 O5' N:C9 4.8 0.3 1.0 O B:ALA479 4.9 76.5 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of T. Thermophilus Argonaute Complexed with Dna Guide Strand and 19-Nt Rna Target Strand with Two MG2+ at the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg688 b:0.7 occ:1.00 OP2 N:U10 2.1 0.9 1.0 OD1 B:ASP660 2.2 95.8 1.0 OD2 B:ASP478 2.2 99.1 1.0 OP1 N:U10 2.2 0.9 1.0 P N:U10 2.5 0.8 1.0 CG B:ASP660 3.2 88.6 1.0 OD2 B:ASP546 3.2 96.3 1.0 CG B:ASP478 3.3 93.9 1.0 O5' N:U10 3.5 0.3 1.0 NZ B:LYS664 3.6 93.9 1.0 NZ B:LYS575 3.7 0.3 1.0 OD1 B:ASP478 3.7 96.2 1.0 MG B:MG687 3.9 95.1 1.0 O3' N:C9 3.9 0.8 1.0 OD2 B:ASP660 3.9 93.3 1.0 CB B:ASP660 4.2 72.9 1.0 C5' N:U10 4.3 0.3 1.0 OP2 N:A11 4.3 0.7 1.0 CG B:ASP546 4.5 99.1 1.0 CB B:ASP478 4.6 77.1 1.0 CA B:ASP660 4.6 67.7 1.0 O B:ALA479 4.7 76.5 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