Manganese in PDB 9jhl: Cryo-Em Structure of CPAGO_GDNA-TG_DSDNA Dimeric Ternary Complex

The binding sites of Manganese atom in the Cryo-Em Structure of CPAGO_GDNA-TG_DSDNA Dimeric Ternary Complex (pdb code 9jhl). 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_DSDNA Dimeric Ternary Complex, PDB code: 9jhl:
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_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_DSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:12.2 occ:1.00 OD2 A:ASP544 1.9 7.8 1.0 OP1 E:DT9 2.1 13.4 1.0 OD1 A:ASP730 2.1 9.0 1.0 CG A:ASP544 2.8 7.8 1.0 OD1 A:ASP544 3.1 7.8 1.0 CG A:ASP730 3.3 9.0 1.0 P E:DT9 3.4 13.4 1.0 OD2 A:ASP730 3.9 9.0 1.0 O3' E:DC8 3.9 16.8 1.0 O5' E:DT9 4.1 13.4 1.0 CB A:ASP544 4.2 7.8 1.0 C5' E:DT9 4.2 13.4 1.0 CB A:ASP730 4.4 9.0 1.0 CA A:GLY546 4.5 19.1 1.0 CA A:ASP730 4.5 9.0 1.0 OP2 E:DT9 4.6 13.4 1.0 O A:VAL545 4.7 10.4 1.0 N A:GLY546 4.8 19.1 1.0 C A:VAL545 4.9 10.4 1.0 CB A:ALA614 4.9 6.3 1.0 N A:ASP730 5.0 9.0 1.0

Manganese binding site 2 out of 4 in the Cryo-Em Structure of CPAGO_GDNA-TG_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_DSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn801 b:13.5 occ:1.00 O A:LEU751 1.9 6.0 1.0 OP1 C:DA3 1.9 16.8 1.0 OP1 C:DT1 2.0 7.8 1.0 OXT A:LEU751 2.5 6.0 1.0 C A:LEU751 2.5 6.0 1.0 P C:DT1 3.2 7.8 1.0 P C:DA3 3.4 16.8 1.0 OP2 C:DT1 3.7 7.8 1.0 CA A:LEU751 3.9 6.0 1.0 O3' C:DG2 4.1 13.8 1.0 O5' C:DA3 4.2 16.8 1.0 O5' C:DT1 4.2 7.8 1.0 C5' C:DA3 4.2 16.8 1.0 OP3 C:DT1 4.2 7.8 1.0 C5' C:DT1 4.3 7.8 1.0 OE1 A:GLN490 4.3 5.8 1.0 NE2 A:GLN490 4.4 5.8 1.0 OP2 C:DA3 4.4 16.8 1.0 N A:LEU751 4.4 6.0 1.0 CE A:LYS522 4.5 5.3 1.0 NZ A:LYS522 4.7 5.3 1.0 CD A:GLN490 4.8 5.8 1.0

Manganese binding site 3 out of 4 in the Cryo-Em Structure of CPAGO_GDNA-TG_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_DSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn801 b:12.5 occ:1.00 OD2 B:ASP544 1.9 7.7 1.0 OP1 F:DT9 2.1 11.9 1.0 OD1 B:ASP730 2.1 8.9 1.0 CG B:ASP544 2.8 7.7 1.0 OD1 B:ASP544 3.1 7.7 1.0 CG B:ASP730 3.3 8.9 1.0 P F:DT9 3.4 11.9 1.0 OD2 B:ASP730 3.8 8.9 1.0 O3' F:DC8 3.9 16.8 1.0 O5' F:DT9 4.1 11.9 1.0 CB B:ASP544 4.2 7.7 1.0 C5' F:DT9 4.2 11.9 1.0 CB B:ASP730 4.4 8.9 1.0 CA B:ASP730 4.5 8.9 1.0 CA B:GLY546 4.6 19.2 1.0 OP2 F:DT9 4.6 11.9 1.0 O B:VAL545 4.7 10.3 1.0 N B:GLY546 4.8 19.2 1.0 C B:VAL545 4.9 10.3 1.0 CB B:ALA614 4.9 6.3 1.0 N B:ASP730 4.9 8.9 1.0

Manganese binding site 4 out of 4 in the Cryo-Em Structure of CPAGO_GDNA-TG_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_DSDNA Dimeric Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn801 b:14.1 occ:1.00 OP1 D:DA3 1.9 16.8 1.0 O B:LEU751 2.0 5.6 1.0 OP1 D:DT1 2.0 8.0 1.0 OXT B:LEU751 2.6 5.6 1.0 C B:LEU751 2.6 5.6 1.0 P D:DT1 3.2 8.0 1.0 P D:DA3 3.4 16.8 1.0 OP2 D:DT1 3.7 8.0 1.0 CA B:LEU751 4.0 5.6 1.0 O3' D:DG2 4.1 16.8 1.0 O5' D:DA3 4.2 16.8 1.0 O5' D:DT1 4.2 8.0 1.0 C5' D:DA3 4.2 16.8 1.0 OP3 D:DT1 4.2 8.0 1.0 C5' D:DT1 4.3 8.0 1.0 OE1 B:GLN490 4.3 6.1 1.0 NE2 B:GLN490 4.4 6.1 1.0 OP2 D:DA3 4.4 16.8 1.0 N B:LEU751 4.5 5.6 1.0 CE B:LYS522 4.5 5.2 1.0 NZ B:LYS522 4.7 5.2 1.0 CD B:GLN490 4.8 6.1 1.0

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