Iodine 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:

Manganese

(Mn)

2 atoms

The binding sites of Iodine atom in the Crystal Structure of the AGCARB2-C2 Complex (pdb code 7dnm). 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, PDB code: 7dnm:
Jump to Iodine binding site number: 1; 2;

Iodine 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 Iodine with other atoms in the I binding site number 1 of Crystal Structure of the AGCARB2-C2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I602 b:36.8 occ:0.50 O B:HOH210 3.2 38.8 1.0 ND2 A:ASN85 3.3 34.1 1.0 CG A:ASN49 3.5 35.4 1.0 ND2 A:ASN49 3.6 33.4 1.0 CB A:ASN49 3.6 29.2 1.0 CE1 B:TYR29 4.0 34.0 1.0 OD1 A:ASN49 4.1 39.8 1.0 NH1 A:ARG123 4.1 35.2 1.0 CD B:ARG30 4.1 29.0 1.0 CB B:ARG30 4.3 28.0 1.0 CG A:ASN85 4.3 36.0 1.0 CG A:GLN52 4.3 30.3 1.0 O A:HOH737 4.3 26.5 1.0 OD1 A:ASN85 4.4 37.5 1.0 CZ A:ARG123 4.5 38.1 1.0 CB A:ALA51 4.5 27.6 1.0 CG B:ARG30 4.5 30.3 1.0 CD A:GLN52 4.5 33.0 1.0 OE1 A:GLN52 4.5 33.0 1.0 CD1 B:TYR29 4.7 31.1 1.0 NH2 A:ARG123 4.7 37.6 1.0 OH B:TYR29 4.9 36.0 1.0 CZ B:TYR29 4.9 33.5 1.0

Iodine 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 Iodine with other atoms in the I binding site number 2 of Crystal Structure of the AGCARB2-C2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:I402 b:44.3 occ:0.50 O P:HOH506 3.0 42.6 1.0 O P:HOH556 3.4 38.8 1.0 CB Q:ARG30 3.8 35.0 1.0 ND2 P:ASN49 3.8 35.3 1.0 CG Q:ARG30 3.9 37.2 1.0 CD P:GLN52 4.0 35.8 1.0 CG P:GLN52 4.0 35.5 1.0 OE1 P:GLN52 4.2 37.1 1.0 CE1 P:TYR17 4.2 34.4 1.0 CD1 P:TYR17 4.2 32.9 1.0 CG P:ASN49 4.3 36.5 1.0 CD Q:ARG30 4.3 37.7 1.0 NE2 P:GLN52 4.4 33.0 1.0 CB Q:TYR29 4.5 36.4 1.0 CB P:ASN49 4.5 32.6 1.0 CA Q:ARG30 4.8 35.3 1.0 N Q:ARG30 4.8 34.6 1.0 C Q:TYR29 4.9 36.0 1.0 OD1 P:ASN49 5.0 35.9 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