Manganese in PDB 7exz: Dgpb-Dgpc Complex Apo 2.5 Angstrom

The structure of Dgpb-Dgpc Complex Apo 2.5 Angstrom, PDB code: 7exz was solved by T.Mori, M.Senda, T.Senda, I.Abe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.89 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.516, 156.721, 158.931, 90, 90, 90
R / Rfree (%)	18.2 / 23.3

The binding sites of Manganese atom in the Dgpb-Dgpc Complex Apo 2.5 Angstrom (pdb code 7exz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dgpb-Dgpc Complex Apo 2.5 Angstrom, PDB code: 7exz:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Dgpb-Dgpc Complex Apo 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dgpb-Dgpc Complex Apo 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:30.1 occ:0.50 OE2 A:GLU141 2.0 36.4 1.0 OE1 A:GLU299 2.1 35.9 1.0 ND1 A:HIS263 2.2 36.7 1.0 O A:HOH515 2.2 39.8 1.0 O A:HOH513 2.3 34.2 1.0 OD2 A:ASP173 2.4 37.0 1.0 CD A:GLU299 3.0 37.2 1.0 CE1 A:HIS263 3.0 38.3 1.0 CD A:GLU141 3.1 36.1 1.0 OE2 A:GLU299 3.2 40.9 1.0 CG A:HIS263 3.3 37.5 1.0 OE1 A:GLU141 3.5 36.0 1.0 CG A:ASP173 3.5 44.6 1.0 CB A:HIS263 3.7 36.7 1.0 CD2 A:HIS143 3.8 45.9 1.0 CB A:ASP173 4.1 44.2 1.0 NE2 A:HIS263 4.2 36.3 1.0 CG A:GLU141 4.3 38.5 1.0 NE2 A:HIS143 4.3 47.8 1.0 CD2 A:HIS263 4.3 36.8 1.0 CE A:LYS265 4.4 41.1 1.0 CG A:GLU299 4.4 35.1 1.0 NZ A:LYS265 4.5 43.0 1.0 O2 A:GOL402 4.5 45.6 1.0 NH1 A:ARG114 4.5 38.6 1.0 OD1 A:ASP173 4.6 44.3 1.0

Manganese binding site 2 out of 4 in the Dgpb-Dgpc Complex Apo 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dgpb-Dgpc Complex Apo 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:24.9 occ:0.50 OE1 C:GLU299 2.0 36.6 1.0 OE2 C:GLU141 2.1 39.4 1.0 ND1 C:HIS263 2.4 33.9 1.0 OD2 C:ASP173 2.4 39.1 1.0 O C:HOH524 2.5 36.8 1.0 O C:HOH535 2.8 45.4 1.0 CD C:GLU299 2.8 37.9 1.0 OE2 C:GLU299 2.9 40.8 1.0 CD C:GLU141 3.1 37.9 1.0 CE1 C:HIS263 3.3 34.4 1.0 CG C:HIS263 3.4 34.7 1.0 CG C:ASP173 3.6 38.8 1.0 OE1 C:GLU141 3.6 36.4 1.0 CB C:HIS263 3.7 35.5 1.0 CD2 C:HIS143 4.1 49.2 1.0 CB C:ASP173 4.2 37.8 1.0 CG C:GLU299 4.2 34.1 1.0 NZ C:LYS265 4.3 45.0 1.0 CE C:LYS265 4.4 39.5 1.0 NE2 C:HIS263 4.4 34.5 1.0 CG C:GLU141 4.4 35.4 1.0 CD2 C:HIS263 4.5 33.1 1.0 OD1 C:ASP173 4.6 42.2 1.0 NE2 C:HIS143 4.6 49.4 1.0 NH1 C:ARG114 4.7 37.2 1.0 O2 C:GOL402 4.9 43.8 1.0 CB C:GLU299 4.9 30.2 1.0

Manganese binding site 3 out of 4 in the Dgpb-Dgpc Complex Apo 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dgpb-Dgpc Complex Apo 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn401 b:20.1 occ:0.50 OE1 E:GLU299 2.0 34.2 1.0 OD2 E:ASP173 2.1 34.1 1.0 OE2 E:GLU141 2.1 34.9 1.0 ND1 E:HIS263 2.3 32.2 1.0 O E:HOH514 2.4 35.8 1.0 O E:HOH522 2.6 33.5 1.0 CD E:GLU299 3.0 35.8 1.0 CD E:GLU141 3.1 33.4 1.0 CE1 E:HIS263 3.1 31.8 1.0 OE2 E:GLU299 3.2 40.2 1.0 CG E:ASP173 3.3 33.0 1.0 CG E:HIS263 3.4 28.8 1.0 OE1 E:GLU141 3.5 35.0 1.0 CB E:HIS263 3.8 28.8 1.0 CD2 E:HIS143 3.9 39.6 1.0 O E:HOH504 4.0 40.6 1.0 CB E:ASP173 4.1 29.1 1.0 OD1 E:ASP173 4.2 34.6 1.0 CE E:LYS265 4.3 34.0 1.0 NE2 E:HIS263 4.3 28.2 1.0 NE2 E:HIS143 4.4 41.1 1.0 CG E:GLU141 4.4 28.8 1.0 CG E:GLU299 4.4 31.4 1.0 CD2 E:HIS263 4.5 26.3 1.0 NH1 E:ARG114 4.7 34.7 1.0 NZ E:LYS265 4.7 37.7 1.0 O E:HOH525 4.8 39.8 1.0 O2 E:GOL402 4.9 45.0 1.0

Manganese binding site 4 out of 4 in the Dgpb-Dgpc Complex Apo 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dgpb-Dgpc Complex Apo 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn401 b:29.8 occ:0.50 O G:HOH502 1.9 39.4 1.0 OE1 G:GLU299 2.0 36.8 1.0 OE2 G:GLU141 2.2 42.1 1.0 ND1 G:HIS263 2.2 38.0 1.0 O G:HOH531 2.3 38.1 1.0 OD2 G:ASP173 2.3 39.7 1.0 CD G:GLU299 2.8 37.9 1.0 OE2 G:GLU299 2.9 40.8 1.0 CE1 G:HIS263 3.1 38.0 1.0 CD G:GLU141 3.2 40.9 1.0 CG G:HIS263 3.3 38.9 1.0 CG G:ASP173 3.6 42.6 1.0 OE1 G:GLU141 3.6 42.6 1.0 CB G:HIS263 3.6 37.9 1.0 CB G:ASP173 4.2 42.9 1.0 CG G:GLU299 4.2 38.9 1.0 NE2 G:HIS263 4.3 35.8 1.0 CE G:LYS265 4.3 39.1 1.0 CD2 G:HIS143 4.3 53.6 1.0 CD2 G:HIS263 4.4 36.2 1.0 NZ G:LYS265 4.4 40.3 1.0 CG G:GLU141 4.5 39.4 1.0 OD1 G:ASP173 4.6 40.0 1.0 O3 G:GOL402 4.6 45.1 1.0 NH1 G:ARG114 4.8 40.6 1.0 NE2 G:HIS143 5.0 54.8 1.0 CB G:GLU299 5.0 39.5 1.0

T.Mori, M.Senda, T.Senda, I.Abe. Dgpb-Dgpc Complex Apo 2.5 Angstrom To Be Published.