Manganese in PDB 7rpw: Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna

All present enzymatic activity of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna:
6.5.1.1;

The binding sites of Manganese atom in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna (pdb code 7rpw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna, PDB code: 7rpw:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn101 b:110.4 occ:1.00 O E:GLY60 1.8 106.9 1.0 O3' X:DG20 1.9 122.2 1.0 C E:GLY60 2.2 106.9 1.0 C4' X:DG20 2.3 122.2 1.0 C3' X:DG20 2.4 122.2 1.0 CA E:GLY60 2.9 106.9 1.0 O E:ILE61 2.9 94.3 1.0 C E:ILE61 3.0 94.3 1.0 N E:ILE61 3.1 94.3 1.0 P X:DC21 3.2 136.5 1.0 OP1 X:DC21 3.2 136.5 1.0 C5' X:DG20 3.3 122.2 1.0 O4' X:DG20 3.4 122.2 1.0 N E:GLY62 3.5 110.6 1.0 CA E:ILE61 3.5 94.3 1.0 C2' X:DG20 3.8 122.2 1.0 C5' X:DC21 3.9 136.5 1.0 O E:LEU59 4.0 89.1 1.0 C1' X:DG20 4.0 122.2 1.0 CA E:GLY62 4.0 110.6 1.0 O5' X:DC21 4.0 136.5 1.0 N E:GLY60 4.0 106.9 1.0 OP2 X:DC21 4.3 136.5 1.0 O5' X:DG20 4.4 122.2 1.0 C E:LEU59 4.4 89.1 1.0 CB E:ILE61 5.0 94.3 1.0

Manganese binding site 2 out of 4 in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn102 b:117.3 occ:1.00 OP1 X:DC21 2.1 136.5 1.0 O5' X:DC21 2.2 136.5 1.0 P X:DC21 2.3 136.5 1.0 OP2 X:DC21 2.6 136.5 1.0 C5' X:DC21 3.2 136.5 1.0 C3' X:DC21 3.8 136.5 1.0 O3' X:DG20 3.9 122.2 1.0 C2' X:DC21 4.0 136.5 1.0 C4' X:DC21 4.0 136.5 1.0 OP2 X:DG22 4.5 152.2 1.0 O E:GLU167 4.7 109.5 1.0 C6 X:DC21 4.7 136.5 1.0 O E:ILE61 4.8 94.3 1.0 O E:LEU59 4.9 89.1 1.0 C3' X:DG20 4.9 122.2 1.0 O4' X:DC21 4.9 136.5 1.0

Manganese binding site 3 out of 4 in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn701 b:115.0 occ:1.00 OP1 X:DG22 1.8 152.2 1.0 OD2 E:ASP52 3.0 79.4 1.0 P X:DG22 3.0 152.2 1.0 OE1 E:GLU58 3.2 119.2 1.0 O5' X:DG22 3.5 152.2 1.0 C5' X:DG22 3.7 152.2 1.0 OP2 X:DG22 3.7 152.2 1.0 CD E:GLU58 4.0 119.2 1.0 CG E:ASP52 4.1 79.4 1.0 CB E:GLU58 4.2 119.2 1.0 O3' X:DC21 4.3 136.5 1.0 NH2 E:ARG281 4.4 115.6 1.0 CG E:GLU58 4.5 119.2 1.0 OE2 E:GLU58 4.8 119.2 1.0 CB E:ASP52 4.8 79.4 1.0 CG E:GLU283 4.8 106.3 1.0

Manganese binding site 4 out of 4 in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn702 b:216.3 occ:1.00 NZ E:LYS260 2.2 197.3 1.0 O5' Y:AMP101 2.2 192.9 1.0 O E:TYR261 2.7 192.7 1.0 O4' Y:AMP101 2.8 192.9 1.0 C5' Y:AMP101 2.8 192.9 1.0 P Y:AMP101 2.9 192.9 1.0 OE2 E:GLU409 3.0 193.3 1.0 O1P Y:AMP101 3.0 192.9 1.0 C8 Y:AMP101 3.0 192.9 1.0 O2P Y:AMP101 3.1 192.9 1.0 C4' Y:AMP101 3.3 192.9 1.0 OE2 E:GLU310 3.4 185.3 1.0 CE E:LYS260 3.6 197.3 1.0 C E:TYR261 3.7 192.7 1.0 C1' Y:AMP101 3.8 192.9 1.0 N9 Y:AMP101 3.8 192.9 1.0 CA E:ASP262 3.8 191.5 1.0 CD E:GLU409 3.9 193.3 1.0 C3' Y:AMP101 4.1 192.9 1.0 CD E:LYS260 4.1 197.3 1.0 N7 Y:AMP101 4.1 192.9 1.0 N E:ASP262 4.1 191.5 1.0 OE1 E:GLU409 4.2 193.3 1.0 C2' Y:AMP101 4.2 192.9 1.0 OP1 Y:DG1 4.4 190.5 1.0 N E:GLY263 4.4 182.5 1.0 C E:ASP262 4.5 191.5 1.0 CD E:GLU310 4.6 185.3 1.0 OD1 E:ASP262 4.7 191.5 1.0 OP2 Y:DG1 4.7 190.5 1.0 O E:GLY263 4.7 182.5 1.0 CB E:ASP262 4.7 191.5 1.0 CG E:ASP262 4.8 191.5 1.0 CA E:TYR261 5.0 192.7 1.0

A.Sverzhinsky, A.E.Tomkinson, J.M.Pascal. Cryo-Em Structures and Biochemical Insights Into Heterotrimeric Pcna Regulation of Dna Ligase To Be Published.