Manganese in PDB 4n76: Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+

The structure of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+, PDB code: 4n76 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)	49.37 / 2.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	110.918, 117.420, 160.457, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 26.9

The binding sites of Manganese atom in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+ (pdb code 4n76). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+, PDB code: 4n76:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:50.9 occ:1.00 OP3 E:DT1 2.0 27.7 1.0 OP1 E:DA3 2.1 24.6 1.0 OXT B:VAL685 2.2 27.0 1.0 O B:VAL685 2.4 39.5 1.0 C B:VAL685 2.7 27.8 1.0 P E:DT1 3.4 15.8 1.0 OE1 B:GLN433 3.5 6.9 1.0 P E:DA3 3.5 10.2 1.0 NZ B:LYS457 3.6 3.2 1.0 O3' E:DG2 4.0 14.1 1.0 OP1 E:DT1 4.2 9.9 1.0 O5' E:DT1 4.2 18.5 1.0 NE2 B:GLN433 4.2 4.2 1.0 CA B:VAL685 4.2 15.3 1.0 CD B:GLN433 4.3 2.7 1.0 CE B:LYS457 4.3 5.2 1.0 OP2 E:DT1 4.3 21.1 1.0 OP2 E:DA3 4.5 9.6 1.0 O5' E:DA3 4.5 15.4 1.0 O B:HOH813 4.5 7.6 1.0 C5' E:DA3 4.6 16.6 1.0 CG2 B:VAL685 4.6 13.7 1.0 C5' E:DT1 4.7 21.6 1.0 CB B:VAL685 4.8 16.9 1.0

Manganese binding site 2 out of 4 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn702 b:63.0 occ:0.61 OD2 B:ASP478 2.1 43.1 1.0 OD2 B:ASP546 2.2 43.1 1.0 OP1 F:DT10 2.2 60.0 1.0 MN B:MN703 3.1 81.5 0.9 CG B:ASP478 3.1 33.5 1.0 CG B:ASP546 3.3 36.2 1.0 P F:DT10 3.4 86.9 1.0 OE2 B:GLU512 3.5 39.9 1.0 O B:ALA479 3.5 15.9 1.0 OD1 B:ASP478 3.5 47.9 1.0 O5' F:DT10 3.5 80.9 1.0 C5' F:DT10 3.7 75.0 1.0 N B:ALA479 4.0 10.2 1.0 O B:ASP546 4.1 31.5 1.0 CB B:ASP546 4.1 27.9 1.0 OD1 B:ASP546 4.2 40.8 1.0 OE1 B:GLU512 4.2 61.8 1.0 CD B:GLU512 4.3 54.7 1.0 OP3 F:DT10 4.4 82.4 1.0 OP2 F:DT10 4.4 72.8 1.0 C B:ALA479 4.4 13.7 1.0 CB B:ASP478 4.5 23.2 1.0 CA B:ALA479 4.7 9.7 1.0 C B:ASP546 4.7 20.7 1.0 CA B:ASP478 4.8 28.5 1.0 NZ B:LYS575 4.8 43.8 1.0 C B:ASP478 4.9 23.8 1.0 CB B:ALA479 5.0 11.2 1.0

Manganese binding site 3 out of 4 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn703 b:81.5 occ:0.93 OD2 B:ASP660 2.1 43.9 1.0 OD1 B:ASP478 2.2 47.9 1.0 O5' F:DT10 3.1 80.9 1.0 CG B:ASP478 3.1 33.5 1.0 MN B:MN702 3.1 63.0 0.6 CG B:ASP660 3.3 26.2 1.0 OD2 B:ASP478 3.3 43.1 1.0 OP1 F:DT10 3.4 60.0 1.0 P F:DT10 3.5 86.9 1.0 OP2 F:DT10 3.6 72.8 1.0 OD2 B:ASP546 3.7 43.1 1.0 OD1 B:ASP660 4.0 16.9 1.0 C5' F:DT10 4.1 75.0 1.0 CG B:ASP546 4.1 36.2 1.0 NZ B:LYS575 4.2 43.8 1.0 OP2 F:DA11 4.3 60.9 1.0 OD1 B:ASP546 4.3 40.8 1.0 NZ B:LYS664 4.3 30.6 1.0 CB B:ASP660 4.3 6.8 1.0 O B:ALA479 4.4 15.9 1.0 CB B:ASP478 4.5 23.2 1.0 CA B:ASP660 4.6 1.4 1.0 OP3 F:DT10 5.0 82.4 1.0

Manganese binding site 4 out of 4 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and Cleaved Target Dna with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn101 b:53.2 occ:1.00 OP1 C:DA3 1.8 27.4 1.0 OP3 C:DT1 2.0 26.6 1.0 OXT A:VAL685 2.2 31.6 1.0 O A:VAL685 2.5 39.9 1.0 C A:VAL685 2.7 29.4 1.0 O C:HOH201 2.9 9.8 1.0 P C:DA3 3.3 15.5 1.0 P C:DT1 3.4 14.1 1.0 NZ A:LYS457 3.7 2.2 1.0 OE1 A:GLN433 3.8 19.5 1.0 O3' C:DG2 3.8 17.6 1.0 O5' C:DT1 4.1 19.9 1.0 OP2 C:DA3 4.2 16.1 1.0 OP1 C:DT1 4.2 13.1 1.0 CA A:VAL685 4.3 14.6 1.0 O5' C:DA3 4.3 21.6 1.0 OP2 C:DT1 4.3 17.4 1.0 NE2 A:GLN433 4.4 11.6 1.0 C5' C:DA3 4.4 19.6 1.0 C5' C:DT1 4.5 22.7 1.0 CD A:GLN433 4.5 12.7 1.0 CE A:LYS457 4.6 0.4 1.0 CG2 A:VAL685 4.8 14.9 1.0 CB A:VAL685 4.9 15.1 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