Magnesium in PDB 5gq9: Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target

The structure of Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target, PDB code: 5gq9 was solved by H.Zhao, G.Sheng, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.13 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.831, 116.503, 161.024, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.7

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target (pdb code 5gq9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target, PDB code: 5gq9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target


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 Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:65.6 occ:1.00 OD2 A:ASP546 2.2 63.0 1.0 OD1 A:ASP478 2.3 61.3 1.0 O3' D:DC9 2.4 74.2 1.0 OP1 D:DT10 3.2 67.1 1.0 CG A:ASP478 3.2 56.4 1.0 CG A:ASP546 3.4 55.4 1.0 C3' D:DC9 3.4 62.6 1.0 C4' D:DC9 3.4 64.6 1.0 P D:DT10 3.4 83.9 1.0 OD2 A:ASP478 3.5 58.6 1.0 OE2 A:GLU512 3.5 66.3 1.0 O A:ALA479 3.5 59.3 1.0 OE1 A:GLU512 3.6 64.2 1.0 MG A:MG702 3.9 79.2 1.0 C5' D:DT10 3.9 81.0 1.0 CD A:GLU512 4.0 56.2 1.0 C2' D:DC9 4.1 74.5 1.0 CB A:ASP546 4.1 50.6 1.0 O5' D:DT10 4.2 79.8 1.0 N A:ALA479 4.2 60.3 1.0 C5' D:DC9 4.3 70.4 1.0 OD1 A:ASP546 4.3 58.4 1.0 NZ A:LYS575 4.4 56.5 1.0 O A:ASP546 4.5 60.5 1.0 O4' D:DC9 4.6 72.5 1.0 C A:ALA479 4.6 56.4 1.0 CB A:ASP478 4.6 53.0 1.0 OP2 D:DT10 4.7 67.2 1.0 NH2 A:ARG545 4.8 59.9 1.0 C A:ASP546 4.8 57.5 1.0 CA A:ASP478 4.9 49.5 1.0 C1' D:DC9 4.9 75.8 1.0 CA A:ALA479 5.0 57.2 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target


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 Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:79.2 occ:1.00 OP1 D:DT10 2.0 67.1 1.0 OD1 A:ASP660 2.3 56.8 1.0 OD2 A:ASP478 2.3 58.6 1.0 CG A:ASP478 3.1 56.4 1.0 P D:DT10 3.2 83.9 1.0 CG A:ASP660 3.4 52.8 1.0 O A:ALA479 3.4 59.3 1.0 O5' D:DT10 3.5 79.8 1.0 OD1 A:ASP478 3.5 61.3 1.0 C5' D:DT10 3.5 81.0 1.0 MG A:MG701 3.9 65.6 1.0 CB A:ASP660 4.1 53.7 1.0 O3' D:DC9 4.1 74.2 1.0 OP2 D:DA11 4.2 99.2 1.0 CB A:ASP478 4.2 53.0 1.0 OD2 A:ASP660 4.3 53.8 1.0 CA A:ASP660 4.3 51.6 1.0 CG2 A:VAL663 4.3 49.6 1.0 C A:ALA479 4.4 56.4 1.0 OP2 D:DT10 4.4 67.2 1.0 O A:ASP660 4.5 54.9 1.0 CA A:GLY480 4.6 66.7 1.0 OD2 A:ASP546 4.6 63.0 1.0 C4' D:DT10 4.7 84.6 1.0 O3' D:DT10 4.8 94.7 1.0 C A:ASP660 4.9 50.2 1.0 N A:GLY480 4.9 57.5 1.0 C3' D:DT10 4.9 85.5 1.0 N A:ALA479 4.9 60.3 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target


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 Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:54.7 occ:1.00 OP3 C:DC1 1.9 61.7 1.0 OP1 C:DA3 2.0 59.4 1.0 OXT A:VAL685 2.2 55.7 1.0 O A:VAL685 2.3 61.3 1.0 C A:VAL685 2.6 55.2 1.0 P C:DC1 3.1 54.4 1.0 OP2 C:DC1 3.1 59.9 1.0 P C:DA3 3.3 51.5 1.0 OE1 A:GLN433 3.7 56.6 1.0 NZ A:LYS457 3.7 53.1 1.0 O3' C:DG2 3.9 52.1 1.0 OP1 C:DC1 3.9 52.6 1.0 OP2 C:DA3 4.1 68.7 1.0 CA A:VAL685 4.1 48.6 1.0 NE2 A:GLN433 4.1 53.3 1.0 O5' C:DC1 4.3 62.0 1.0 CD A:GLN433 4.3 52.4 1.0 C5' C:DC1 4.4 59.0 1.0 O5' C:DA3 4.5 52.6 1.0 CE A:LYS457 4.6 49.0 1.0 CG2 A:VAL685 4.8 49.6 1.0 C5' C:DA3 4.8 52.2 1.0 CB A:VAL685 4.8 50.7 1.0 N A:VAL685 4.9 52.3 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:51.0 occ:1.00 OP1 E:DA3 2.0 58.0 1.0 OP3 E:DC1 2.1 54.4 1.0 OXT B:VAL685 2.1 52.0 1.0 O B:VAL685 2.3 52.3 1.0 C B:VAL685 2.5 52.8 1.0 P E:DA3 3.4 48.7 1.0 OE1 B:GLN433 3.5 54.7 1.0 P E:DC1 3.5 55.2 1.0 NZ B:LYS457 3.7 50.0 1.0 O3' E:DG2 3.8 47.2 1.0 CA B:VAL685 4.0 49.1 1.0 OP2 E:DC1 4.1 57.3 1.0 NE2 B:GLN433 4.1 48.5 1.0 CD B:GLN433 4.2 52.0 1.0 OP1 E:DC1 4.3 49.2 1.0 OP2 E:DA3 4.3 55.6 1.0 O5' E:DC1 4.5 54.8 1.0 O5' E:DA3 4.5 51.6 1.0 CE B:LYS457 4.6 47.2 1.0 CG2 B:VAL685 4.6 46.1 1.0 CB B:VAL685 4.6 48.2 1.0 C5' E:DA3 4.7 49.6 1.0 C5' E:DC1 4.8 50.5 1.0 N B:VAL685 4.8 49.1 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:67.3 occ:1.00 OD1 B:ASP478 2.3 57.5 1.0 OD2 B:ASP546 2.3 61.7 1.0 O3' F:DC9 2.3 74.1 1.0 OP1 F:DT10 2.7 60.3 1.0 P F:DT10 3.1 76.3 1.0 CG B:ASP478 3.3 56.8 1.0 C3' F:DC9 3.4 63.2 1.0 CG B:ASP546 3.4 61.1 1.0 C4' F:DC9 3.5 63.7 1.0 O B:ALA479 3.5 67.0 1.0 OD2 B:ASP478 3.7 59.9 1.0 OE2 B:GLU512 3.7 73.7 1.0 OE1 B:GLU512 3.8 75.4 1.0 C5' F:DT10 4.0 70.5 1.0 O5' F:DT10 4.0 71.9 1.0 CB B:ASP546 4.1 49.0 1.0 N B:ALA479 4.1 47.9 1.0 CD B:GLU512 4.2 68.9 1.0 C2' F:DC9 4.2 67.2 1.0 C5' F:DC9 4.3 59.7 1.0 MG B:MG703 4.3 67.6 1.0 O B:ASP546 4.4 54.3 1.0 OP2 F:DT10 4.4 72.0 1.0 OD1 B:ASP546 4.4 70.1 1.0 C B:ALA479 4.5 60.2 1.0 CB B:ASP478 4.7 46.6 1.0 C B:ASP546 4.7 57.9 1.0 O4' F:DC9 4.7 63.6 1.0 CA B:ASP478 4.8 50.5 1.0 NH2 B:ARG545 4.8 54.3 1.0 CA B:ALA479 4.9 52.6 1.0 NZ B:LYS575 4.9 53.0 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:67.6 occ:1.00 OP1 F:DT10 1.7 60.3 1.0 OD1 B:ASP660 2.0 58.1 1.0 P F:DT10 2.5 76.3 1.0 O5' F:DT10 2.8 71.9 1.0 OD2 B:ASP478 2.8 59.9 1.0 OP2 F:DT10 3.2 72.0 1.0 CG B:ASP660 3.2 46.6 1.0 C5' F:DT10 3.6 70.5 1.0 NZ B:LYS664 3.7 72.1 1.0 CG B:ASP478 3.9 56.8 1.0 O3' F:DC9 3.9 74.1 1.0 OP2 F:DA11 4.0 86.8 1.0 CB B:ASP660 4.1 44.4 1.0 OD2 B:ASP660 4.1 55.0 1.0 OD1 B:ASP478 4.2 57.5 1.0 MG B:MG702 4.3 67.3 1.0 OD2 B:ASP546 4.5 61.7 1.0 C3' F:DT10 4.6 71.3 1.0 O B:ALA479 4.6 67.0 1.0 C4' F:DT10 4.6 69.9 1.0 CA B:ASP660 4.7 48.8 1.0 CD B:LYS664 4.8 74.7 1.0 CE B:LYS664 4.9 76.7 1.0 O3' F:DT10 4.9 81.2 1.0

H.Zhao, G.Sheng, Y.Wang. Crystal Structure of Thermus Thermophilus Argonaute in Complex with G1C Sidna and Dna Target To Be Published.