Manganese in PDB 9jhn: Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex

The binding sites of Manganese atom in the Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex (pdb code 9jhn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex, PDB code: 9jhn:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn801 b:49.3 occ:1.00 OP2 C:DT1 1.9 39.5 1.0 OP1 C:DT1 1.9 39.5 1.0 OP1 C:DA3 2.1 39.5 1.0 P C:DT1 2.2 39.5 1.0 OP3 C:DT1 3.3 39.5 1.0 O5' C:DT1 3.4 39.5 1.0 O A:LEU751 3.5 20.1 1.0 P C:DA3 3.5 39.5 1.0 OXT A:LEU751 3.5 20.1 1.0 C5' C:DT1 3.7 39.5 1.0 C A:LEU751 3.9 20.1 1.0 OP2 C:DA3 4.2 39.5 1.0 NE2 A:GLN490 4.2 23.1 1.0 O3' C:DG2 4.2 39.5 1.0 OE1 A:GLN490 4.3 23.1 1.0 O5' C:DA3 4.6 39.5 1.0 CE A:LYS522 4.6 21.8 1.0 NZ A:LYS522 4.6 21.8 1.0 CD A:GLN490 4.7 23.1 1.0 C5' C:DA3 4.8 39.5 1.0 OH A:TYR475 4.8 32.3 1.0 O A:PHE750 4.9 19.8 1.0

Manganese binding site 2 out of 4 in the Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn801 b:30.9 occ:1.00 OD2 A:ASP544 2.0 30.7 1.0 OD1 A:ASP544 2.6 30.7 1.0 OD1 A:ASP730 2.6 29.9 1.0 CG A:ASP544 2.6 30.7 1.0 OP1 E:DT9 2.7 38.4 1.0 CA A:GLY546 3.7 41.2 1.0 CG A:ASP730 3.7 29.9 1.0 P E:DT9 3.8 38.4 1.0 C5' E:DT9 3.9 38.4 1.0 N A:GLY546 3.9 41.2 1.0 CB A:ASP544 4.1 30.7 1.0 O3' E:DC8 4.1 30.8 1.0 O5' E:DT9 4.1 38.4 1.0 C A:VAL545 4.4 33.6 1.0 SG A:CYS733 4.5 28.4 1.0 OD2 A:ASP730 4.5 29.9 1.0 CA A:ASP730 4.6 29.9 1.0 O A:VAL545 4.6 33.6 1.0 CB A:ASP730 4.6 29.9 1.0 CB A:CYS733 4.6 28.4 1.0 N A:VAL545 4.8 33.6 1.0 C A:ASP544 4.9 30.7 1.0

Manganese binding site 3 out of 4 in the Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn801 b:53.5 occ:1.00 OP2 D:DT1 1.9 39.5 1.0 OP1 D:DT1 1.9 39.5 1.0 OP1 D:DA3 2.1 39.5 1.0 P D:DT1 2.2 39.5 1.0 OXT B:LEU751 3.3 20.7 1.0 OP3 D:DT1 3.3 39.5 1.0 O B:LEU751 3.3 20.7 1.0 O5' D:DT1 3.4 39.5 1.0 P D:DA3 3.5 39.5 1.0 C B:LEU751 3.6 20.7 1.0 C5' D:DT1 3.7 39.5 1.0 OP2 D:DA3 4.2 39.5 1.0 O3' D:DG2 4.2 39.5 1.0 NE2 B:GLN490 4.3 24.0 1.0 OE1 B:GLN490 4.3 24.0 1.0 CE B:LYS522 4.5 21.9 1.0 O5' D:DA3 4.6 39.5 1.0 NZ B:LYS522 4.6 21.9 1.0 CD B:GLN490 4.7 24.0 1.0 O B:PHE750 4.7 21.0 1.0 C5' D:DA3 4.8 39.5 1.0

Manganese binding site 4 out of 4 in the Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Cryo-Em Structure of CPAGO_GDNA-TG_BUBBLE_DSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn801 b:32.0 occ:1.00 OD2 B:ASP544 2.0 31.1 1.0 OD1 B:ASP544 2.6 31.1 1.0 CG B:ASP544 2.6 31.1 1.0 OD1 B:ASP730 2.6 30.4 1.0 OP1 F:DT9 2.7 36.8 1.0 CA B:GLY546 3.7 41.6 1.0 CG B:ASP730 3.8 30.4 1.0 P F:DT9 3.8 36.8 1.0 C5' F:DT9 3.9 36.8 1.0 N B:GLY546 3.9 41.6 1.0 CB B:ASP544 4.1 31.1 1.0 O3' F:DC8 4.1 30.4 1.0 O5' F:DT9 4.1 36.8 1.0 C B:VAL545 4.3 34.0 1.0 SG B:CYS733 4.5 28.4 1.0 O B:VAL545 4.6 34.0 1.0 OD2 B:ASP730 4.6 30.4 1.0 CA B:ASP730 4.6 30.4 1.0 CB B:CYS733 4.6 28.4 1.0 CB B:ASP730 4.7 30.4 1.0 N B:VAL545 4.7 34.0 1.0 C B:ASP544 4.9 31.1 1.0

Y.Liu, S.Li, K.Zhang. Dimeric State and Novel Nucleotide-Binding Pocket Drive Cpago-Mediated Dna Cleavage To Be Published.