Iodine 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:

Manganese

(Mn)

2 atoms

The binding sites of Iodine 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 Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of the AGCARB2-C2 Complex with Homoorientin, PDB code: 7dnn:
Jump to Iodine binding site number: 1; 2;

Iodine 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 Iodine with other atoms in the I 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:I403 b:55.0 occ:0.50 ND2 A:ASN85 2.8 40.8 1.0 O A:HOH504 3.0 37.5 1.0 OD1 A:ASN85 3.5 41.1 1.0 CG A:ASN85 3.6 41.0 1.0 CB A:ASN49 3.6 36.1 1.0 CG A:ASN49 3.7 36.7 1.0 NH1 A:ARG123 3.8 38.0 1.0 CG B:ARG30 3.8 38.8 1.0 O A:HOH535 3.8 35.2 1.0 CE1 B:TYR29 3.9 36.8 1.0 CD B:ARG30 3.9 36.4 1.0 CB A:ALA51 4.0 36.0 1.0 OH B:TYR29 4.1 38.6 1.0 ND2 A:ASN49 4.1 36.8 1.0 OD1 A:ASN49 4.1 41.4 1.0 CZ B:TYR29 4.5 40.7 1.0 CZ A:ARG123 4.5 40.6 1.0 O A:THR84 4.9 36.8 1.0 CG A:GLN52 4.9 35.0 1.0 CD1 B:TYR29 4.9 36.8 1.0 NE B:ARG30 4.9 33.2 1.0 CB A:ASN85 5.0 35.3 1.0 CA A:ALA51 5.0 37.6 1.0 CA A:ASN49 5.0 34.6 1.0

Iodine 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 Iodine with other atoms in the I 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:I402 b:66.8 occ:0.50 OD1 P:ASN85 3.1 54.0 1.0 O Q:HOH201 3.2 45.9 1.0 CB P:ASN49 3.5 48.4 1.0 CG P:ASN49 3.5 49.7 1.0 CE2 Q:TYR29 3.6 46.0 1.0 NH1 P:ARG123 3.8 48.9 1.0 OH Q:TYR29 3.8 57.4 1.0 OD1 P:ASN49 3.8 50.8 1.0 ND2 P:ASN85 3.9 53.4 1.0 CG P:ASN85 3.9 54.3 1.0 ND2 P:ASN49 4.0 48.3 1.0 O P:HOH517 4.1 47.1 1.0 CZ Q:TYR29 4.1 54.1 1.0 CD Q:ARG30 4.1 48.6 1.0 CZ P:ARG123 4.5 47.8 1.0 CB Q:ARG30 4.5 47.1 1.0 CB P:ALA51 4.5 51.5 1.0 CD2 Q:TYR29 4.7 51.5 1.0 CG Q:ARG30 4.7 48.7 1.0 NH2 P:ARG123 4.7 47.4 1.0 CG P:GLN52 4.7 50.8 1.0 CA P:ASN49 4.9 48.4 1.0 OE1 P:GLN52 4.9 49.0 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