Manganese in PDB 8xpa: Crystal Structure of D(Acgmccgt/Acggcgt)

The structure of Crystal Structure of D(Acgmccgt/Acggcgt), PDB code: 8xpa was solved by M.H.Hou, S.M.Lin, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.28 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.432, 46.243, 47.061, 90, 110.92, 90
R / Rfree (%)	22.1 / 25.2

The structure of Crystal Structure of D(Acgmccgt/Acggcgt) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Crystal Structure of D(Acgmccgt/Acggcgt) (pdb code 8xpa). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of D(Acgmccgt/Acggcgt), PDB code: 8xpa:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of D(Acgmccgt/Acggcgt)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of D(Acgmccgt/Acggcgt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:31.9 occ:0.81 O G:HOH107 2.0 35.0 1.0 O A:HOH215 2.1 39.0 1.0 O A:HOH207 2.1 37.9 1.0 O A:HOH206 2.2 32.0 1.0 OP2 G:DC5 2.4 44.3 1.0 N7 A:DG3 2.4 35.2 1.0 C8 A:DG3 3.2 36.3 1.0 C5 A:DG3 3.5 33.1 1.0 P G:DC5 3.7 46.4 1.0 O5' G:DC5 3.7 43.0 1.0 O6 A:DG3 3.9 35.3 1.0 O A:HOH205 3.9 42.1 1.0 C6 A:DG3 4.1 35.0 1.0 O A:HOH216 4.1 37.0 1.0 O A:HOH213 4.1 35.9 1.0 O B:HOH102 4.2 33.2 1.0 O6 A:DG4 4.2 32.6 1.0 O G:HOH101 4.2 41.3 1.0 N9 A:DG3 4.4 35.0 1.0 C3' G:5CM4 4.4 43.2 0.1 C3' G:5CM4 4.5 42.2 0.9 O3' G:5CM4 4.5 49.6 0.1 OP1 G:DC5 4.6 47.9 1.0 O3' G:5CM4 4.6 49.6 0.9 C2' G:5CM4 4.6 46.3 0.9 C4 A:DG3 4.6 32.0 1.0 C2' G:5CM4 4.6 46.2 0.1 O G:HOH109 4.6 46.4 1.0 O A:HOH212 4.7 34.9 1.0 C5' G:DC5 4.9 43.7 1.0 C2' A:DC2 4.9 31.4 1.0 C6 A:DC2 4.9 28.2 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of D(Acgmccgt/Acggcgt)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of D(Acgmccgt/Acggcgt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:32.2 occ:0.64 OP2 A:DG3 2.0 40.0 1.0 O A:HOH213 2.1 35.9 1.0 O G:HOH103 2.2 29.7 1.0 O A:HOH216 2.2 37.0 1.0 O G:HOH105 2.3 34.8 1.0 O A:HOH209 2.4 42.7 1.0 P A:DG3 3.4 36.5 1.0 O G:HOH107 4.0 35.0 1.0 OP1 A:DG3 4.2 36.6 1.0 O A:HOH215 4.2 39.0 1.0 O5' A:DG3 4.3 35.8 1.0 O3' A:DC2 4.4 36.6 1.0 C5 G:DC5 4.4 41.0 1.0 C6 G:DC5 4.4 44.2 1.0 C3' A:DC2 4.4 36.6 1.0 O G:HOH104 4.5 34.6 1.0 C5' G:DC5 4.6 43.7 1.0 N7 G:DG6 4.6 37.8 1.0 O6 G:DG6 4.7 38.0 1.0 O5' G:DC5 4.9 43.0 1.0 C2' A:DC2 4.9 31.4 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of D(Acgmccgt/Acggcgt)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of D(Acgmccgt/Acggcgt) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn101 b:31.2 occ:0.78 O E:HOH110 2.0 40.1 1.0 O E:HOH112 2.0 32.4 1.0 OP2 E:DC5 2.2 42.8 1.0 O E:HOH106 2.3 38.1 1.0 O D:HOH203 2.3 32.7 1.0 N7 D:DG3 2.5 34.1 1.0 C8 D:DG3 3.2 38.4 1.0 P E:DC5 3.5 49.4 1.0 C5 D:DG3 3.6 31.5 1.0 O5' E:DC5 3.7 41.9 1.0 O D:HOH205 4.0 35.9 1.0 O E:HOH107 4.0 41.4 1.0 O6 D:DG3 4.1 37.0 1.0 O D:HOH218 4.1 40.2 1.0 O D:HOH213 4.1 38.4 1.0 C6 D:DG3 4.2 36.2 1.0 O C:HOH103 4.2 36.4 1.0 O6 D:DG4 4.3 29.7 1.0 C3' E:5CM4 4.4 43.2 0.4 N9 D:DG3 4.4 36.6 1.0 O D:HOH215 4.5 38.3 1.0 O3' E:5CM4 4.5 47.4 0.4 C3' E:5CM4 4.5 42.9 0.6 OP1 E:DC5 4.5 50.0 1.0 O3' E:5CM4 4.5 47.5 0.6 O E:HOH114 4.5 51.3 1.0 C4 D:DG3 4.6 33.8 1.0 C2' E:5CM4 4.7 43.4 0.4 C5' E:DC5 4.8 45.1 1.0 C2' D:DC2 4.8 31.8 1.0 C6 D:DC2 4.9 29.2 1.0 C2' E:5CM4 4.9 43.7 0.6

M.H.Hou, S.M.Lin. Crystal Structure of D(Acgmccgt/Acggcgt) To Be Published.