Manganese in PDB 9jh9: Cryo-Em Structure of CPAGO_GDNA-TG_SSDNA Dimeric Ternary Complex

The binding sites of Manganese atom in the Cryo-Em Structure of CPAGO_GDNA-TG_SSDNA Dimeric Ternary Complex (pdb code 9jh9). 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_SSDNA Dimeric Ternary Complex, PDB code: 9jh9:
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_SSDNA 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_SSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn801 b:88.3 occ:1.00 OP1 C:DA3 1.9 69.4 1.0 OP1 C:DT1 1.9 71.0 1.0 OP2 C:DT1 1.9 71.0 1.0 P C:DT1 2.2 71.0 1.0 O A:LEU751 2.3 64.2 1.0 OXT A:LEU751 2.7 64.2 1.0 C A:LEU751 2.8 64.2 1.0 O5' C:DT1 3.3 71.0 1.0 P C:DA3 3.3 69.4 1.0 OP3 C:DT1 3.4 71.0 1.0 C5' C:DT1 3.8 71.0 1.0 NE2 A:GLN490 3.9 65.7 1.0 OE1 A:GLN490 4.1 65.7 1.0 O3' C:DG2 4.1 71.9 1.0 OP2 C:DA3 4.1 69.4 1.0 O5' C:DA3 4.3 69.4 1.0 CA A:LEU751 4.3 64.2 1.0 CD A:GLN490 4.4 65.7 1.0 C5' C:DA3 4.5 69.4 1.0 CE A:LYS522 4.5 68.6 1.0 NZ A:LYS522 4.6 68.6 1.0 N A:LEU751 4.8 64.2 1.0

Manganese binding site 2 out of 4 in the Cryo-Em Structure of CPAGO_GDNA-TG_SSDNA 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_SSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn801 b:75.0 occ:1.00 OD2 A:ASP544 1.8 68.6 1.0 OP1 E:DT9 1.8 74.0 1.0 CG A:ASP544 2.6 68.6 1.0 OD1 A:ASP544 2.7 68.6 1.0 P E:DT9 3.0 74.0 1.0 OD1 A:ASP730 3.1 65.0 1.0 O3' E:DC8 3.4 74.5 1.0 O5' E:DT9 3.5 74.0 1.0 C5' E:DT9 3.7 74.0 1.0 CB A:ASP544 4.0 68.6 1.0 CG A:ASP730 4.2 65.0 1.0 CA A:GLY546 4.3 79.5 1.0 OP2 E:DT9 4.3 74.0 1.0 N A:GLY546 4.5 79.5 1.0 CB A:ASP730 4.6 65.0 1.0 C3' E:DC8 4.7 74.5 1.0 CA A:ASP730 4.7 65.0 1.0 NZ A:LYS642 4.8 63.0 1.0 C A:VAL545 4.8 73.9 1.0 C4' E:DC8 4.9 74.5 1.0 C5' E:DC8 4.9 74.5 1.0 O A:VAL545 4.9 73.9 1.0 CB A:ALA614 5.0 59.5 1.0

Manganese binding site 3 out of 4 in the Cryo-Em Structure of CPAGO_GDNA-TG_SSDNA 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_SSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn801 b:87.7 occ:1.00 OP1 D:DA3 1.9 69.4 1.0 OP1 D:DT1 1.9 71.6 1.0 OP2 D:DT1 1.9 71.6 1.0 P D:DT1 2.2 71.6 1.0 O B:LEU751 2.3 63.8 1.0 OXT B:LEU751 2.8 63.8 1.0 C B:LEU751 2.9 63.8 1.0 O5' D:DT1 3.3 71.6 1.0 P D:DA3 3.3 69.4 1.0 OP3 D:DT1 3.4 71.6 1.0 C5' D:DT1 3.8 71.6 1.0 NE2 B:GLN490 4.1 66.2 1.0 O3' D:DG2 4.1 71.9 1.0 OP2 D:DA3 4.1 69.4 1.0 OE1 B:GLN490 4.1 66.2 1.0 O5' D:DA3 4.3 69.4 1.0 CA B:LEU751 4.3 63.8 1.0 C5' D:DA3 4.5 69.4 1.0 CE B:LYS522 4.5 68.8 1.0 NZ B:LYS522 4.5 68.8 1.0 CD B:GLN490 4.5 66.2 1.0 N B:LEU751 4.8 63.8 1.0

Manganese binding site 4 out of 4 in the Cryo-Em Structure of CPAGO_GDNA-TG_SSDNA 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_SSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn801 b:73.6 occ:1.00 OD2 B:ASP544 1.8 67.5 1.0 OP1 F:DT9 1.8 73.4 1.0 CG B:ASP544 2.6 67.5 1.0 OD1 B:ASP544 2.7 67.5 1.0 P F:DT9 3.0 73.4 1.0 OD1 B:ASP730 3.1 64.1 1.0 O3' F:DC8 3.4 73.8 1.0 O5' F:DT9 3.5 73.4 1.0 C5' F:DT9 3.7 73.4 1.0 CB B:ASP544 4.0 67.5 1.0 CG B:ASP730 4.2 64.1 1.0 CA B:GLY546 4.3 79.0 1.0 OP2 F:DT9 4.3 73.4 1.0 N B:GLY546 4.5 79.0 1.0 CB B:ASP730 4.6 64.1 1.0 C3' F:DC8 4.7 73.8 1.0 CA B:ASP730 4.7 64.1 1.0 NZ B:LYS642 4.8 62.4 1.0 C B:VAL545 4.8 73.3 1.0 C5' F:DC8 4.9 73.8 1.0 C4' F:DC8 4.9 73.8 1.0 O B:VAL545 4.9 73.3 1.0 CB B:ALA614 5.0 58.7 1.0

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