Magnesium in PDB 3dlh: Crystal Structure of the Guide-Strand-Containing Argonaute Protein Silencing Complex

The structure of Crystal Structure of the Guide-Strand-Containing Argonaute Protein Silencing Complex, PDB code: 3dlh was solved by Y.Wang, G.Sheng, 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 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.744, 114.629, 175.689, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 28.4

The binding sites of Magnesium atom in the Crystal Structure of the Guide-Strand-Containing Argonaute Protein Silencing Complex (pdb code 3dlh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Guide-Strand-Containing Argonaute Protein Silencing Complex, PDB code: 3dlh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Guide-Strand-Containing Argonaute Protein Silencing Complex


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 the Guide-Strand-Containing Argonaute Protein Silencing Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg686 b:31.0 occ:1.00 OP1 X:DA3 2.1 45.3 1.0 OP1 X:DT1 2.3 64.8 1.0 OXT A:VAL685 2.5 45.1 1.0 O A:VAL685 2.7 43.3 1.0 C A:VAL685 2.9 42.3 1.0 P X:DA3 3.3 49.2 1.0 NZ A:LYS457 3.5 35.0 1.0 OE1 A:GLN433 3.5 47.8 1.0 P X:DT1 3.6 65.1 1.0 O3' X:DG2 3.6 50.4 1.0 O5' X:DT1 3.8 64.0 1.0 NE2 A:GLN433 4.1 49.0 1.0 OP3 X:DT1 4.2 66.7 1.0 OP2 X:DA3 4.2 49.4 1.0 CD A:GLN433 4.3 47.5 1.0 CA A:VAL685 4.4 40.3 1.0 C5' X:DT1 4.4 64.7 1.0 O5' X:DA3 4.5 47.9 1.0 CG2 A:VAL685 4.7 38.9 1.0 C5' X:DA3 4.7 45.5 1.0 CE A:LYS457 4.8 37.7 1.0 OP2 X:DT1 4.8 64.7 1.0 CB A:VAL685 4.8 38.6 1.0 C3' X:DG2 4.8 49.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Guide-Strand-Containing Argonaute Protein Silencing Complex


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 the Guide-Strand-Containing Argonaute Protein Silencing Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg687 b:57.9 occ:1.00 O A:GLY459 2.8 58.2 1.0 OE1 A:GLN342 2.9 94.1 1.0 NE2 A:GLN342 3.3 93.9 1.0 CD A:GLN342 3.5 93.8 1.0 CB A:GLU680 3.7 53.5 1.0 C A:GLY459 3.8 58.4 1.0 CG A:GLU680 4.0 57.1 1.0 O A:HOH702 4.0 37.4 1.0 CA A:GLY459 4.1 56.2 1.0 OD2 A:ASP678 4.3 62.9 1.0 OE1 A:GLU680 4.3 60.0 1.0 CD A:GLU680 4.7 59.8 1.0 O A:ALA458 4.8 52.8 1.0 CG A:GLN342 5.0 92.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Guide-Strand-Containing Argonaute Protein Silencing Complex


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 the Guide-Strand-Containing Argonaute Protein Silencing Complex within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg2 b:26.8 occ:1.00 OP1 Y:DA103 2.1 58.4 1.0 OXT B:VAL685 2.3 53.1 1.0 OP2 Y:DT101 2.4 59.2 1.0 O B:VAL685 2.6 53.2 1.0 C B:VAL685 2.8 53.1 1.0 OP3 Y:DT101 3.2 58.3 1.0 P Y:DT101 3.3 58.3 1.0 P Y:DA103 3.4 59.3 1.0 OP2 Y:DA103 4.0 60.4 1.0 O5' Y:DT101 4.0 59.1 1.0 NZ B:LYS457 4.0 52.3 1.0 CA B:VAL685 4.3 52.1 1.0 O5' Y:DA103 4.3 58.2 1.0 O3' Y:DG102 4.4 59.9 1.0 OE1 B:GLN433 4.4 48.7 1.0 OP1 Y:DT101 4.6 59.3 1.0 C5' Y:DT101 4.9 61.3 1.0 CE B:LYS457 4.9 50.7 1.0

Y.Wang, G.Sheng, S.Juranek, T.Tuschl, D.J.Patel. Structure of the Guide-Strand-Containing Argonaute Silencing Complex. Nature V. 456 209 2008.
ISSN: ISSN 0028-0836
PubMed: 18754009
DOI: 10.1038/NATURE07315