Magnesium in PDB 4n47: Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 12- Mer Target Dna

The structure of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 12- Mer Target Dna, PDB code: 4n47 was solved by G.Sheng, H.Zhao, J.Wang, Y.Rao, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.33 / 2.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.886, 110.548, 124.039, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 26.4

The binding sites of Magnesium atom in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 12- Mer Target Dna (pdb code 4n47). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 12- Mer Target Dna, PDB code: 4n47:

Magnesium binding site 1 out of 1 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 12- Mer Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 12- Mer Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:75.5 occ:1.00 OXT A:VAL685 1.7 76.2 1.0 O A:VAL685 1.7 92.6 1.0 OP1 C:DA3 1.8 42.8 1.0 OP2 C:DT1 1.9 58.7 1.0 C A:VAL685 2.0 83.3 1.0 P C:DT1 3.2 47.6 1.0 P C:DA3 3.2 43.7 1.0 OP3 C:DT1 3.3 57.8 1.0 CA A:VAL685 3.5 74.3 1.0 OP2 C:DA3 3.9 47.5 1.0 O3' C:DG2 4.0 35.0 1.0 OP1 C:DT1 4.0 39.1 1.0 O5' C:DA3 4.3 32.5 1.0 O5' C:DT1 4.3 33.6 1.0 N A:VAL685 4.3 70.0 1.0 OE1 A:GLN433 4.4 34.1 1.0 CB A:VAL685 4.4 70.3 1.0 NZ A:LYS457 4.4 49.1 1.0 CG2 A:VAL685 4.5 76.1 1.0 C5' C:DT1 4.5 33.2 1.0 NE2 A:GLN433 4.7 34.9 1.0 C5' C:DA3 4.7 32.5 1.0 CE A:LYS457 4.9 34.7 1.0 CD A:GLN433 5.0 82.9 1.0

G.Sheng, H.Zhao, J.Wang, Y.Rao, W.Tian, D.C.Swarts, J.Van Der Oost, D.J.Patel, Y.Wang. Structure-Based Cleavage Mechanism of Thermus Thermophilus Argonaute Dna Guide Strand-Mediated Dna Target Cleavage. Proc.Natl.Acad.Sci.Usa V. 111 652 2014.
ISSN: ISSN 0027-8424
PubMed: 24374628
DOI: 10.1073/PNAS.1321032111