Magnesium in PDB 3f73: Alignment of Guide-Target Seed Duplex Within An Argonaute Silencing Complex

The structure of Alignment of Guide-Target Seed Duplex Within An Argonaute Silencing Complex, PDB code: 3f73 was solved by Y.Wang, H.Li, G.Sheng, S.Juranek, T.Tuschl, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.162, 120.527, 109.085, 90.00, 105.30, 90.00
R / Rfree (%)	22.1 / 28.2

The binding sites of Magnesium atom in the Alignment of Guide-Target Seed Duplex Within An Argonaute Silencing Complex (pdb code 3f73). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Alignment of Guide-Target Seed Duplex Within An Argonaute Silencing Complex, PDB code: 3f73:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Alignment of Guide-Target Seed Duplex Within An Argonaute Silencing Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Alignment of Guide-Target Seed Duplex Within An Argonaute Silencing Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg686 b:62.1 occ:1.00 OD1 A:ASP546 2.4 70.2 1.0 OD1 A:ASP478 2.4 62.0 1.0 OD2 A:ASP660 2.6 69.0 1.0 CG A:ASP478 2.9 58.2 1.0 CG A:ASP660 2.9 67.3 1.0 OD1 A:ASP660 3.0 68.5 1.0 OD2 A:ASP478 3.2 59.6 1.0 CG A:ASP546 3.3 69.0 1.0 NH1 A:ARG548 3.3 78.9 1.0 CB A:ASP478 3.9 56.8 1.0 OD2 A:ASP546 4.0 70.2 1.0 CB A:ASP660 4.2 64.1 1.0 CB A:ASP546 4.2 62.4 1.0 CZ A:ARG548 4.3 78.6 1.0 CA A:ASP660 4.4 61.4 1.0 OP1 H:C10 4.5 0.1 1.0 CA A:ASP478 4.6 55.6 1.0 NH2 A:ARG548 4.6 78.3 1.0

Magnesium binding site 2 out of 3 in the Alignment of Guide-Target Seed Duplex Within An Argonaute Silencing Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Alignment of Guide-Target Seed Duplex Within An Argonaute Silencing Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg22 b:39.8 occ:1.00 OP1 C:DA3 2.1 54.5 1.0 OXT A:VAL685 2.5 59.7 1.0 OP1 C:DT1 2.6 77.5 1.0 O A:VAL685 2.8 58.5 1.0 OP3 C:DT1 3.0 77.7 1.0 C A:VAL685 3.0 58.4 1.0 P C:DT1 3.1 77.3 1.0 P C:DA3 3.1 56.6 1.0 O5' C:DT1 3.3 75.4 1.0 OP2 C:DA3 3.4 54.3 1.0 O3' C:DG2 3.7 57.3 1.0 OE1 A:GLN433 3.8 51.0 1.0 NZ A:LYS457 4.1 58.4 1.0 O5' C:DA3 4.4 54.3 1.0 C5' C:DT1 4.4 75.0 1.0 CA A:VAL685 4.5 57.7 1.0 OP2 C:DT1 4.6 78.5 1.0 CE A:LYS457 4.6 58.0 1.0 CD A:GLN433 4.7 52.7 1.0 NE2 A:GLN433 4.7 51.7 1.0 NH2 A:ARG661 4.8 90.1 1.0 C5' C:DA3 4.9 52.1 1.0 CB A:VAL685 5.0 57.9 1.0 C3' C:DG2 5.0 55.8 1.0

Magnesium binding site 3 out of 3 in the Alignment of Guide-Target Seed Duplex Within An Argonaute Silencing Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Alignment of Guide-Target Seed Duplex Within An Argonaute Silencing Complex within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg22 b:47.4 occ:1.00 OP1 X:DA3 2.2 59.2 1.0 O B:VAL685 2.5 66.1 1.0 OXT B:VAL685 2.7 65.9 1.0 OP3 X:DT1 2.7 63.8 1.0 C B:VAL685 2.9 65.5 1.0 OP2 X:DT1 3.3 64.3 1.0 P X:DT1 3.3 64.5 1.0 P X:DA3 3.4 60.1 1.0 O5' X:DT1 3.5 63.3 1.0 NH2 B:ARG661 3.9 89.5 1.0 OP2 X:DA3 3.9 59.1 1.0 NZ B:LYS457 3.9 63.5 1.0 O3' X:DG2 4.0 59.0 1.0 C5' X:DT1 4.4 62.5 1.0 OE1 B:GLN433 4.4 40.8 1.0 CA B:VAL685 4.5 64.1 1.0 O5' X:DA3 4.6 59.0 1.0 CE B:LYS457 4.7 62.8 1.0 OP1 X:DT1 4.8 67.2 1.0 O B:PHE684 4.8 62.9 1.0 CZ B:ARG661 5.0 88.1 1.0 C5' X:DA3 5.0 56.6 1.0

Y.Wang, S.Juranek, H.Li, G.Sheng, T.Tuschl, D.J.Patel. Structure of An Argonaute Silencing Complex with A Seed-Containing Guide Dna and Target Rna Duplex. Nature V. 456 921 2008.
ISSN: ISSN 0028-0836
PubMed: 19092929
DOI: 10.1038/NATURE07666