Manganese in PDB 7bvr: Dgpb-Dgpc Complex Apo

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

Resolution Low / High (Å)	46.89 / 2.60
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 (%)	19.4 / 25.3

The binding sites of Manganese atom in the Dgpb-Dgpc Complex Apo (pdb code 7bvr). 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, PDB code: 7bvr:
Jump to Manganese binding site number: 1; 2; 3; 4;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:49.2 occ:1.00 OE2 A:GLU141 2.1 34.0 1.0 O A:HOH504 2.2 35.5 1.0 OD2 A:ASP173 2.3 37.0 1.0 OE2 A:GLU299 2.3 38.4 1.0 ND1 A:HIS263 2.6 36.8 1.0 O A:HOH515 2.6 35.6 1.0 CD A:GLU299 3.0 34.0 1.0 OE1 A:GLU299 3.0 39.8 1.0 CD A:GLU141 3.2 34.6 1.0 CG A:ASP173 3.4 39.2 1.0 CG A:HIS263 3.5 34.3 1.0 CE1 A:HIS263 3.6 36.9 1.0 CB A:HIS263 3.6 31.3 1.0 OE1 A:GLU141 3.7 36.4 1.0 CD2 A:HIS143 3.7 46.1 1.0 CB A:ASP173 4.0 37.5 1.0 NE2 A:HIS143 4.1 45.1 1.0 CE A:LYS265 4.3 41.9 1.0 CG A:GLU141 4.4 36.0 1.0 OD1 A:ASP173 4.4 38.2 1.0 CG A:GLU299 4.5 28.4 1.0 NZ A:LYS265 4.5 44.4 1.0 O2 A:GOL401 4.6 44.8 1.0 NH1 A:ARG114 4.6 30.9 1.0 CD2 A:HIS263 4.6 36.1 1.0 NE2 A:HIS263 4.7 36.5 1.0 CA A:ASP173 4.9 38.3 1.0 CG A:HIS143 5.0 47.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:47.7 occ:1.00 OE2 C:GLU299 2.2 37.7 1.0 OE2 C:GLU141 2.2 39.8 1.0 O C:HOH526 2.4 39.3 1.0 ND1 C:HIS263 2.5 31.6 1.0 OD2 C:ASP173 2.6 43.0 1.0 CD C:GLU299 2.9 41.5 1.0 OE1 C:GLU299 3.0 41.1 1.0 CD C:GLU141 3.4 35.5 1.0 CG C:HIS263 3.4 32.3 1.0 O C:HOH513 3.5 57.4 1.0 CE1 C:HIS263 3.6 30.5 1.0 CB C:HIS263 3.6 28.8 1.0 CG C:ASP173 3.6 38.4 1.0 OE1 C:GLU141 3.9 35.1 1.0 CB C:ASP173 4.0 35.3 1.0 NZ C:LYS265 4.2 55.0 1.0 CD2 C:HIS143 4.3 55.6 1.0 CE C:LYS265 4.3 39.4 1.0 CG C:GLU299 4.4 35.0 1.0 CG C:GLU141 4.5 30.2 1.0 CD2 C:HIS263 4.6 31.2 1.0 NE2 C:HIS263 4.6 29.7 1.0 OD1 C:ASP173 4.7 40.5 1.0 O1 C:GOL401 4.7 46.7 1.0 NH1 C:ARG114 4.9 34.2 1.0 NE2 C:HIS143 4.9 57.8 1.0 CB C:GLU299 5.0 28.6 1.0 O3 C:GOL401 5.0 49.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn402 b:44.3 occ:1.00 OE1 E:GLU141 2.3 32.2 1.0 OE1 E:GLU299 2.4 35.9 1.0 OD1 E:ASP173 2.5 29.6 1.0 O E:HOH521 2.5 43.8 1.0 ND1 E:HIS263 2.6 29.0 1.0 OE2 E:GLU299 3.0 43.5 1.0 CD E:GLU299 3.0 36.6 1.0 CD E:GLU141 3.2 28.7 1.0 CE1 E:HIS263 3.4 23.1 1.0 O1 E:GOL401 3.4 40.0 1.0 OE2 E:GLU141 3.5 37.1 1.0 CG E:ASP173 3.6 26.8 1.0 CG E:HIS263 3.6 25.8 1.0 CD2 E:HIS143 3.9 44.0 1.0 CB E:HIS263 4.0 21.4 1.0 CB E:ASP173 4.2 24.7 1.0 NH1 E:ARG114 4.3 31.1 1.0 CG E:GLU141 4.4 23.6 1.0 C1 E:GOL401 4.4 41.9 1.0 NE2 E:HIS143 4.4 45.0 1.0 CE E:LYS265 4.5 28.6 1.0 CG E:GLU299 4.5 28.6 1.0 OD2 E:ASP173 4.6 34.9 1.0 NE2 E:HIS263 4.6 20.3 1.0 O E:HOH533 4.6 40.1 1.0 CD2 E:HIS263 4.7 21.8 1.0 NZ E:LYS265 4.9 38.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn402 b:48.7 occ:1.00 OE2 G:GLU299 2.3 38.5 1.0 OE2 G:GLU141 2.3 43.2 1.0 O G:HOH504 2.4 40.1 1.0 OD2 G:ASP173 2.5 42.8 1.0 ND1 G:HIS263 2.5 37.0 1.0 O G:HOH507 2.5 47.7 1.0 OE1 G:GLU299 2.9 50.0 1.0 CD G:GLU299 3.0 37.0 1.0 CD G:GLU141 3.3 43.6 1.0 CE1 G:HIS263 3.4 38.0 1.0 CG G:HIS263 3.5 34.8 1.0 CG G:ASP173 3.7 39.4 1.0 OE1 G:GLU141 3.7 45.6 1.0 CB G:HIS263 3.8 36.4 1.0 CD2 G:HIS143 4.0 65.7 1.0 CB G:ASP173 4.3 38.4 1.0 CE G:LYS265 4.3 35.1 1.0 NZ G:LYS265 4.4 43.4 1.0 NE2 G:HIS143 4.4 64.8 1.0 CG G:GLU299 4.4 30.8 1.0 CG G:GLU141 4.5 39.7 1.0 NH1 G:ARG114 4.6 40.9 1.0 NE2 G:HIS263 4.6 32.7 1.0 OD1 G:ASP173 4.7 37.7 1.0 CD2 G:HIS263 4.7 31.1 1.0 O2 G:GOL401 4.8 43.9 1.0 O3 G:GOL401 5.0 47.5 1.0

T.Mori, H.He, I.Abe. Structure of C-Deglycosylation Enzyme To Be Published.