Manganese in PDB 7dnn: Crystal Structure of the AGCARB2-C2 Complex with Homoorientin

The structure of Crystal Structure of the AGCARB2-C2 Complex with Homoorientin, PDB code: 7dnn 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)	36.17 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.905, 102.511, 136.09, 90, 90, 90
R / Rfree (%)	19.6 / 24.7

The structure of Crystal Structure of the AGCARB2-C2 Complex with Homoorientin 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 with Homoorientin (pdb code 7dnn). 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 with Homoorientin, PDB code: 7dnn:
Jump to Manganese binding site number: 1; 2;

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


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 with Homoorientin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:39.9 occ:0.50 OE2 A:GLU147 2.1 43.4 1.0 OE2 A:GLU305 2.2 41.8 1.0 OD2 A:ASP179 2.2 43.1 1.0 ND1 A:HIS269 2.3 39.4 1.0 O A:HOH566 2.3 43.1 1.0 NZ A:LYS271 2.7 44.2 1.0 CE1 A:HIS269 3.1 39.5 1.0 CD A:GLU147 3.2 41.5 1.0 CG A:HIS269 3.2 40.1 1.0 CD A:GLU305 3.3 39.6 1.0 CG A:ASP179 3.4 39.3 1.0 CB A:HIS269 3.6 37.8 1.0 OE1 A:GLU305 3.6 43.4 1.0 OE1 A:GLU147 3.7 40.6 1.0 CB A:ASP179 4.0 39.0 1.0 CE A:LYS271 4.1 44.0 1.0 NE2 A:HIS269 4.2 38.9 1.0 CD2 A:HIS149 4.3 43.5 1.0 CD2 A:HIS269 4.3 39.4 1.0 OD1 A:ASP179 4.4 39.8 1.0 CG A:GLU147 4.4 37.8 1.0 O A:HOH551 4.6 42.8 1.0 CG A:GLU305 4.6 37.0 1.0 NH2 A:ARG123 4.6 40.3 1.0 CD A:LYS271 5.0 40.7 1.0

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


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 with Homoorientin within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn401 b:38.8 occ:0.50 OE1 P:GLU147 2.1 44.7 1.0 OE2 P:GLU305 2.2 44.8 1.0 ND1 P:HIS269 2.2 41.8 1.0 OD2 P:ASP179 2.3 43.8 1.0 O P:HOH537 2.6 46.6 1.0 CD P:GLU305 3.1 43.6 1.0 CE1 P:HIS269 3.1 43.1 1.0 CD P:GLU147 3.1 42.8 1.0 CG P:HIS269 3.2 44.1 1.0 OE1 P:GLU305 3.3 46.0 1.0 CG P:ASP179 3.4 40.9 1.0 CB P:HIS269 3.6 41.8 1.0 OE2 P:GLU147 3.6 43.5 1.0 NZ P:LYS271 4.0 41.9 1.0 CB P:ASP179 4.2 39.1 1.0 NE2 P:HIS269 4.2 41.5 1.0 CG P:GLU147 4.3 44.1 1.0 CD2 P:HIS269 4.3 42.3 1.0 OD1 P:ASP179 4.3 41.0 1.0 CE P:LYS271 4.3 45.0 1.0 CG P:GLU305 4.5 43.2 1.0 NH2 P:ARG123 4.9 47.4 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