Manganese in PDB 7dnm: Crystal Structure of the AGCARB2-C2 Complex

The structure of Crystal Structure of the AGCARB2-C2 Complex, PDB code: 7dnm was solved by M.Senda, T.Kumano, S.Watanabe, M.Kobayashi, T.Senda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.18 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.702, 100.575, 136.318, 90, 90, 90
R / Rfree (%)	18 / 22.3

The structure of Crystal Structure of the AGCARB2-C2 Complex also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of the AGCARB2-C2 Complex (pdb code 7dnm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the AGCARB2-C2 Complex, PDB code: 7dnm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the AGCARB2-C2 Complex


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 the AGCARB2-C2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:33.5 occ:0.50 OD2 A:ASP179 2.1 35.5 1.0 O A:HOH756 2.2 42.8 1.0 OE2 A:GLU147 2.2 37.9 1.0 OE1 A:GLU305 2.3 34.6 1.0 ND1 A:HIS269 2.4 31.3 1.0 CG A:ASP179 3.2 35.5 1.0 CG A:HIS269 3.3 31.0 1.0 CE1 A:HIS269 3.3 29.4 1.0 CD A:GLU305 3.3 34.6 1.0 CD A:GLU147 3.4 36.8 1.0 CB A:HIS269 3.5 31.2 1.0 OE2 A:GLU305 3.7 39.5 1.0 OE1 A:GLU147 3.9 40.7 1.0 CD2 A:HIS149 4.0 37.3 1.0 CB A:ASP179 4.0 31.4 1.0 NZ A:LYS271 4.0 36.1 1.0 CE A:LYS271 4.1 37.0 1.0 OD1 A:ASP179 4.1 33.2 1.0 NE2 A:HIS269 4.3 32.5 1.0 CD2 A:HIS269 4.3 31.4 1.0 NE2 A:HIS149 4.5 36.4 1.0 CG A:GLU147 4.6 29.7 1.0 CG A:GLU305 4.6 34.2 1.0 NH2 A:ARG123 4.8 37.6 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the AGCARB2-C2 Complex


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 the AGCARB2-C2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn401 b:25.6 occ:0.50 OE2 P:GLU305 2.0 32.9 1.0 OE2 P:GLU147 2.1 39.2 1.0 OD2 P:ASP179 2.1 32.0 1.0 ND1 P:HIS269 2.3 32.5 1.0 O P:HOH555 2.7 36.4 1.0 CD P:GLU305 3.1 31.5 1.0 CG P:HIS269 3.2 32.9 1.0 CD P:GLU147 3.2 35.0 1.0 CG P:ASP179 3.2 31.9 1.0 CE1 P:HIS269 3.3 34.4 1.0 OE1 P:GLU305 3.4 31.2 1.0 CB P:HIS269 3.5 31.6 1.0 OE1 P:GLU147 3.8 35.8 1.0 CB P:ASP179 3.9 31.1 1.0 NZ P:LYS271 4.0 31.1 1.0 OD1 P:ASP179 4.2 31.0 1.0 CE P:LYS271 4.2 32.9 1.0 CD2 P:HIS269 4.3 29.0 1.0 NE2 P:HIS269 4.3 31.4 1.0 CG P:GLU147 4.4 35.4 1.0 CG P:GLU305 4.4 31.7 1.0 CA P:HIS269 5.0 30.4 1.0

T.Mori, T.Kumano, K.He, T.Awakawa, S.Watanabe, S.Hori, Y.Terashita, Y.Hashimoto, M.Senda, T.Senda, M.Kobayashi, I.Abe. Structural Basis For the Metabolism of Xenobiotic C-Glycosides By Intestinal Bacteria Nat Commun 2021.
ISSN: ESSN 2041-1723