Manganese in PDB 6wdz: Porcine Circovirus 2 Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site

The structure of Porcine Circovirus 2 Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site, PDB code: 6wdz was solved by L.A.Litzau, K.Tompkins, K.Shi, A.Nelson, R.L.Evans Iii, W.R.Gordon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.10 / 2.03
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	99.527, 99.527, 73.695, 90.00, 90.00, 120.00
R / Rfree (%)	22.9 / 28

The binding sites of Manganese atom in the Porcine Circovirus 2 Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site (pdb code 6wdz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Porcine Circovirus 2 Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site, PDB code: 6wdz:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Porcine Circovirus 2 Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Porcine Circovirus 2 Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:28.6 occ:1.00 OE1 D:GLU48 1.8 23.1 1.0 O D:HOH302 2.0 33.5 1.0 NE2 D:HIS57 2.1 29.5 1.0 OE1 D:GLN59 2.2 31.6 1.0 OP1 F:DA306 2.2 22.7 1.0 O3' F:DT305 2.5 29.4 1.0 P F:DA306 2.9 30.4 1.0 CD D:GLU48 3.0 32.0 1.0 CE1 D:HIS57 3.1 33.6 1.0 CD2 D:HIS57 3.1 32.4 1.0 CD D:GLN59 3.1 30.7 1.0 C3' F:DT305 3.7 29.4 1.0 CG D:GLN59 3.7 24.0 1.0 O5' F:DA306 3.7 26.1 1.0 OE2 D:GLU48 3.8 35.5 1.0 CB D:GLU48 3.8 30.6 1.0 CG D:GLU48 4.0 32.8 1.0 C2' F:DT305 4.0 28.4 1.0 CB D:GLN59 4.1 29.7 1.0 C4' F:DT305 4.2 30.1 1.0 NZ D:LYS99 4.2 24.3 1.0 NE2 D:GLN59 4.2 24.4 1.0 OP2 F:DA306 4.2 26.9 1.0 ND1 D:HIS57 4.2 30.8 1.0 CG D:HIS57 4.3 35.8 1.0 OE2 D:GLU100 4.3 27.7 1.0 OE2 G:GLU52 5.0 28.2 1.0

Manganese binding site 2 out of 3 in the Porcine Circovirus 2 Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Porcine Circovirus 2 Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn203 b:35.7 occ:1.00 OE1 G:GLU48 1.9 29.6 1.0 NE2 G:HIS57 2.0 28.2 1.0 O G:HOH315 2.2 33.3 1.0 OP1 I:DA306 2.5 24.8 1.0 OE1 G:GLN59 2.6 32.2 1.0 O3' I:DT305 2.6 38.0 1.0 CE1 G:HIS57 3.0 41.4 1.0 CD2 G:HIS57 3.1 37.9 1.0 CD G:GLU48 3.1 43.4 1.0 P I:DA306 3.1 32.1 1.0 CD G:GLN59 3.5 31.5 1.0 CB G:GLU48 3.7 35.8 1.0 CG G:GLN59 3.7 31.4 1.0 C3' I:DT305 3.8 41.4 1.0 NZ G:LYS99 3.8 43.2 1.0 CB G:GLN59 3.8 31.9 1.0 O5' I:DA306 3.9 43.4 1.0 CG G:GLU48 3.9 47.5 1.0 OE2 G:GLU48 4.1 45.3 1.0 ND1 G:HIS57 4.1 36.4 1.0 C2' I:DT305 4.1 36.5 1.0 C4' I:DT305 4.1 33.9 1.0 CG G:HIS57 4.2 39.1 1.0 CE G:LYS99 4.4 37.2 1.0 OP2 I:DA306 4.4 37.1 1.0 OE2 G:GLU100 4.7 47.2 1.0 NE2 G:GLN59 4.7 33.5 1.0 O G:HOH305 4.9 47.3 1.0 C5' I:DT305 4.9 37.2 1.0

Manganese binding site 3 out of 3 in the Porcine Circovirus 2 Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Porcine Circovirus 2 Rep Domain Complexed with A Single-Stranded Dna 10-Mer Comprising the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:17.1 occ:1.00 OE1 A:GLU48 2.0 15.7 1.0 OE1 A:GLN59 2.1 15.7 1.0 OP1 C:DA306 2.2 16.6 1.0 O A:HOH339 2.2 16.2 1.0 NE2 A:HIS57 2.3 19.2 1.0 O3' C:DT305 2.3 21.3 1.0 P C:DA306 2.9 20.4 1.0 CD A:GLN59 3.1 17.2 1.0 CD2 A:HIS57 3.2 13.3 1.0 CD A:GLU48 3.2 19.9 1.0 CE1 A:HIS57 3.3 17.1 1.0 C3' C:DT305 3.6 20.9 1.0 CG A:GLN59 3.6 15.2 1.0 O5' C:DA306 3.7 17.0 1.0 CB A:GLU48 3.8 14.2 1.0 NZ A:LYS99 3.9 15.0 1.0 C4' C:DT305 4.0 21.6 1.0 CB A:GLN59 4.0 16.5 1.0 CG A:GLU48 4.1 17.2 1.0 OP2 C:DA306 4.1 18.7 1.0 C2' C:DT305 4.1 16.4 1.0 OE2 A:GLU48 4.1 20.2 1.0 NE2 A:GLN59 4.3 15.7 1.0 ND1 A:HIS57 4.3 16.0 1.0 CG A:HIS57 4.4 14.2 1.0 OE2 A:GLU100 4.5 25.4 1.0 CE A:LYS99 4.6 14.5 1.0 C5' C:DT305 4.8 25.3 1.0

K.Tompkins, L.A.Litzau, K.Tompkins, K.Shi, A.Nelson, R.L.Evans Iii, W.R.Gordon. N/A N/A.