Magnesium in PDB 4n41: Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 15- Mer Target Dna

The structure of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 15- Mer Target Dna, PDB code: 4n41 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)	45.52 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.513, 101.699, 153.019, 90.00, 93.52, 90.00
R / Rfree (%)	22.3 / 25.9

The binding sites of Magnesium atom in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 15- Mer Target Dna (pdb code 4n41). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 15- Mer Target Dna, PDB code: 4n41:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 15- 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 15- Mer Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:68.1 occ:1.00 O B:HOH808 2.1 66.0 1.0 OD2 B:ASP660 2.2 71.1 1.0 OD1 B:ASP478 2.3 72.9 1.0 OD2 B:ASP478 2.5 60.3 1.0 OP1 F:DT6 2.6 71.7 1.0 CG B:ASP478 2.8 65.4 1.0 CG B:ASP660 3.3 73.2 1.0 O B:ALA479 3.7 78.3 1.0 P F:DT6 3.9 68.2 1.0 OD1 B:ASP660 4.0 83.8 1.0 C5' F:DT6 4.3 76.6 1.0 N B:GLY481 4.3 72.6 1.0 CB B:ASP660 4.3 67.9 1.0 CB B:ASP478 4.3 67.9 1.0 CA B:ASP660 4.3 69.7 1.0 O3' F:DC5 4.3 68.2 1.0 O5' F:DT6 4.5 74.9 1.0 CA B:GLY481 4.7 76.7 1.0 C B:GLY480 4.7 73.0 1.0 C B:ALA479 4.9 72.4 1.0 NZ B:LYS575 5.0 70.0 1.0

Magnesium binding site 2 out of 3 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 15- Mer Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 15- Mer Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:32.4 occ:1.00 OP3 C:DT1 1.9 36.8 1.0 OP1 C:DA3 2.0 39.9 1.0 O A:HOH735 2.0 32.9 1.0 O C:HOH205 2.0 34.9 1.0 OXT A:VAL685 2.3 37.3 1.0 O A:VAL685 2.3 36.4 1.0 C A:VAL685 2.6 45.8 1.0 P C:DA3 3.3 37.3 1.0 P C:DT1 3.3 33.7 1.0 OP2 C:DT1 3.7 30.1 1.0 O3' C:DG2 3.8 34.9 1.0 OE1 A:GLN433 3.9 35.4 1.0 NZ A:LYS457 3.9 36.4 1.0 OP2 C:DA3 3.9 36.9 1.0 CA A:VAL685 4.2 36.7 1.0 NE2 A:GLN433 4.2 38.3 1.0 O A:HOH710 4.3 33.2 1.0 OP1 C:DT1 4.3 37.5 1.0 O5' C:DT1 4.3 39.0 1.0 O A:HOH821 4.4 51.8 1.0 O5' C:DA3 4.4 36.8 1.0 CD A:GLN433 4.5 35.5 1.0 C5' C:DT1 4.5 38.6 1.0 CE A:LYS457 4.6 36.9 1.0 O A:HOH755 4.6 41.8 1.0 C5' C:DA3 4.7 34.6 1.0 CB A:VAL685 4.8 34.0 1.0 CG2 A:VAL685 4.9 33.0 1.0 O C:HOH213 4.9 56.4 1.0 N A:VAL685 4.9 31.4 1.0

Magnesium binding site 3 out of 3 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 15- Mer Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 15- Mer Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:71.6 occ:1.00 OP3 E:DT1 2.0 69.3 1.0 OXT B:VAL685 2.0 68.9 1.0 OP1 E:DA3 2.0 60.1 1.0 O E:HOH203 2.1 63.0 1.0 O B:VAL685 2.2 69.2 1.0 C B:VAL685 2.4 68.2 1.0 P E:DT1 3.2 74.8 1.0 P E:DA3 3.4 64.2 1.0 OP2 E:DT1 3.6 77.5 1.0 CA B:VAL685 4.0 66.2 1.0 OP1 E:DT1 4.0 83.9 1.0 OP2 E:DA3 4.1 67.7 1.0 NZ B:LYS457 4.1 77.4 1.0 O3' E:DG2 4.2 66.7 1.0 OE1 B:GLN433 4.4 70.7 1.0 O5' E:DT1 4.4 76.3 1.0 O5' E:DA3 4.5 58.0 1.0 C5' E:DT1 4.6 75.3 1.0 NE2 B:GLN433 4.7 73.9 1.0 CE B:LYS457 4.7 71.1 1.0 N B:VAL685 4.7 71.4 1.0 CB B:VAL685 4.7 68.9 1.0 CG2 B:VAL685 4.8 66.1 1.0 O B:PHE684 4.9 71.0 1.0 NH2 B:ARG661 4.9 76.8 1.0 CD B:GLN433 5.0 75.5 1.0 C5' E:DA3 5.0 61.0 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