Manganese in PDB 7xrf: Crystal Structaure of Dgpb/C Complex

The structure of Crystal Structaure of Dgpb/C Complex, PDB code: 7xrf was solved by M.Ma, P.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.84 / 2.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.076, 159.704, 176.168, 90, 90, 90
R / Rfree (%)	20.6 / 25.1

The binding sites of Manganese atom in the Crystal Structaure of Dgpb/C Complex (pdb code 7xrf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structaure of Dgpb/C Complex, PDB code: 7xrf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structaure of Dgpb/C Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structaure of Dgpb/C Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:53.8 occ:1.00 OD2 A:ASP173 2.0 63.8 1.0 OE2 A:GLU299 2.0 63.3 1.0 ND1 A:HIS263 2.0 59.6 1.0 OE2 A:GLU141 2.0 63.9 1.0 CD A:GLU299 2.9 54.6 1.0 CE1 A:HIS263 2.9 60.3 1.0 CG A:HIS263 3.1 57.8 1.0 CG A:ASP173 3.2 63.3 1.0 CD A:GLU141 3.2 60.4 1.0 OE1 A:GLU299 3.2 54.5 1.0 CB A:HIS263 3.5 58.4 1.0 OE1 A:GLU141 3.8 63.4 1.0 CB A:ASP173 3.9 53.7 1.0 NE2 A:HIS263 4.1 56.3 1.0 OD1 A:ASP173 4.1 61.6 1.0 CD2 A:HIS263 4.2 54.7 1.0 CG A:GLU299 4.2 51.6 1.0 CG A:GLU141 4.3 56.8 1.0 CE A:LYS265 4.5 62.9 1.0 NZ A:LYS265 4.7 61.0 1.0 CB A:GLU299 4.8 52.9 1.0 NH1 A:ARG114 4.9 62.6 1.0 CA A:HIS263 5.0 54.1 1.0 CA A:ASP173 5.0 53.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structaure of Dgpb/C Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structaure of Dgpb/C Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:54.1 occ:1.00 OE2 C:GLU299 2.0 62.5 1.0 OE2 C:GLU141 2.0 58.1 1.0 ND1 C:HIS263 2.1 59.5 1.0 OD2 C:ASP173 2.1 58.3 1.0 O C:HOH519 2.3 57.6 1.0 O C:HOH532 2.5 63.6 1.0 CE1 C:HIS263 3.0 56.5 1.0 CD C:GLU141 3.0 57.9 1.0 CD C:GLU299 3.0 59.0 1.0 CG C:HIS263 3.1 59.4 1.0 CG C:ASP173 3.2 59.9 1.0 OE1 C:GLU141 3.4 55.5 1.0 OE1 C:GLU299 3.4 61.6 1.0 CB C:HIS263 3.5 54.7 1.0 CB C:ASP173 3.8 57.5 1.0 NE2 C:HIS263 4.1 51.0 1.0 OD1 C:ASP173 4.2 59.2 1.0 CD2 C:HIS263 4.2 54.8 1.0 CG C:GLU141 4.3 56.1 1.0 CG C:GLU299 4.3 56.0 1.0 CE C:LYS265 4.4 59.3 1.0 NZ C:LYS265 4.4 62.2 1.0 CB C:GLU299 4.9 52.9 1.0 CA C:ASP173 4.9 54.2 1.0 NH1 C:ARG114 4.9 58.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structaure of Dgpb/C Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structaure of Dgpb/C Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn401 b:62.6 occ:1.00 OE2 E:GLU299 1.9 62.9 1.0 ND1 E:HIS263 2.1 66.5 1.0 OE2 E:GLU141 2.1 62.2 1.0 OD2 E:ASP173 2.3 65.1 1.0 CD E:GLU299 2.8 61.2 1.0 CE1 E:HIS263 2.9 67.2 1.0 O E:HOH505 2.9 65.1 1.0 OE1 E:GLU299 3.1 65.4 1.0 CG E:HIS263 3.2 64.2 1.0 CD E:GLU141 3.2 62.8 1.0 CG E:ASP173 3.3 61.3 1.0 CB E:HIS263 3.6 61.0 1.0 OE1 E:GLU141 3.7 70.0 1.0 CB E:ASP173 3.9 53.2 1.0 NE2 E:HIS263 4.1 63.5 1.0 NZ E:LYS265 4.1 62.7 1.0 CG E:GLU299 4.2 60.0 1.0 CD2 E:HIS263 4.3 56.8 1.0 OD1 E:ASP173 4.4 62.8 1.0 CG E:GLU141 4.4 55.8 1.0 CE E:LYS265 4.4 64.9 1.0 NH1 E:ARG114 4.8 61.0 1.0 CB E:GLU299 4.9 59.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structaure of Dgpb/C Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structaure of Dgpb/C Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn401 b:57.7 occ:1.00 OE2 G:GLU141 1.9 68.3 1.0 OE2 G:GLU299 2.0 68.0 1.0 ND1 G:HIS263 2.1 63.5 1.0 OD2 G:ASP173 2.2 66.3 1.0 O G:HOH526 2.6 67.0 1.0 CE1 G:HIS263 2.8 63.7 1.0 CD G:GLU299 2.9 63.1 1.0 CD G:GLU141 3.0 62.1 1.0 CG G:HIS263 3.2 61.1 1.0 OE1 G:GLU299 3.2 64.2 1.0 CG G:ASP173 3.4 66.4 1.0 OE1 G:GLU141 3.5 57.7 1.0 CB G:HIS263 3.7 64.0 1.0 CB G:ASP173 4.0 62.3 1.0 NE2 G:HIS263 4.0 61.3 1.0 CG G:GLU141 4.2 57.2 1.0 CG G:GLU299 4.2 65.5 1.0 CD2 G:HIS263 4.2 61.0 1.0 OD1 G:ASP173 4.3 62.9 1.0 CE G:LYS265 4.4 65.4 1.0 NZ G:LYS265 4.6 68.3 1.0 CB G:GLU299 4.8 60.5 1.0 NH1 G:ARG114 4.9 60.8 1.0

P.He, S.Wang, S.Li, S.Liu, S.Zhou, J.Wang, J.Tao, D.Wang, R.Wang, W.Ma. Structural Mechanism of A Dual-Functional Enzyme Dgpa/B/C As Both A C-Glycoside Cleaving Enzyme and An O- to C-Glycoside Isomerase. Acta Pharm Sin B V. 13 246 2023.
ISSN: ESSN 2211-3843
DOI: 10.1016/J.APSB.2022.05.022