Iodine in PDB 6tmc: Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases

The structure of Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases, PDB code: 6tmc was solved by H.-K.S.Leiros, T.Christopeit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.26 / 1.40
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	45.805, 63.925, 90.748, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 16.8

The structure of Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Iodine atom in the Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases (pdb code 6tmc). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases, PDB code: 6tmc:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:68.8 occ:0.51 I A:IOD405 0.0 68.8 0.5 H151 A:NL5401 2.9 40.0 0.8 HG3 A:ARG228 2.9 26.9 0.3 I A:IOD405 3.0 29.9 0.5 HG3 A:ARG228 3.2 27.0 0.7 O A:HOH679 3.2 30.7 1.0 O A:HOH683 3.3 47.8 1.0 HD2 A:ARG228 3.4 23.3 0.7 HD3 A:ARG228 3.6 28.3 0.3 C15 A:NL5401 3.6 33.3 0.8 CG A:ARG228 3.7 22.4 0.3 HB2 A:ARG228 3.8 26.4 0.7 HB2 A:ARG228 3.8 26.8 0.3 H141 A:NL5401 3.8 30.5 0.8 HE2 A:TYR67 3.8 19.8 1.0 CG A:ARG228 3.9 22.5 0.7 O A:HOH681 3.9 35.9 1.0 CD A:ARG228 4.0 19.4 0.7 CD A:ARG228 4.0 23.6 0.3 C14 A:NL5401 4.1 25.4 0.8 HD2 A:TYR67 4.1 17.8 1.0 HA A:ARG228 4.1 29.2 0.7 HA A:ARG228 4.2 28.7 0.3 CB A:ARG228 4.2 22.4 0.3 CB A:ARG228 4.3 22.0 0.7 NE A:ARG228 4.3 28.7 0.3 HE A:ARG228 4.3 34.4 0.3 NE A:ARG228 4.4 17.2 0.7 HG2 A:ARG228 4.5 26.9 0.3 CE2 A:TYR67 4.5 16.5 1.0 HE A:ARG228 4.7 20.7 0.7 C16 A:NL5401 4.7 32.5 0.8 CD2 A:TYR67 4.7 14.9 1.0 HG2 A:ARG228 4.7 27.0 0.7 CA A:ARG228 4.7 24.3 0.7 CA A:ARG228 4.7 23.9 0.3 H161 A:NL5401 4.8 39.0 0.8 HD3 A:ARG228 4.9 23.3 0.7 OE2 A:GLU225 4.9 28.3 1.0 HD2 A:ARG228 5.0 28.3 0.3

Iodine binding site 2 out of 2 in the Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:29.9 occ:0.49 I A:IOD405 0.0 29.9 0.5 H151 A:NL5401 2.7 40.0 0.8 OE2 A:GLU225 3.0 28.3 1.0 I A:IOD405 3.0 68.8 0.5 H161 A:NL5401 3.1 39.0 0.8 HD2 A:ARG228 3.3 23.3 0.7 C15 A:NL5401 3.4 33.3 0.8 HB3 A:HIS263 3.4 20.9 1.0 HB2 A:HIS263 3.5 20.9 1.0 HG2 A:GLU225 3.5 25.6 1.0 C16 A:NL5401 3.6 32.5 0.8 HE A:ARG228 3.7 34.4 0.3 HH21 A:ARG228 3.7 18.3 0.3 O A:HOH679 3.8 30.7 1.0 HB2 A:ARG228 3.8 26.4 0.7 NE A:ARG228 3.9 28.7 0.3 HB2 A:ARG228 3.9 26.8 0.3 NH2 A:ARG228 3.9 15.3 0.3 HD2 A:PRO68 3.9 19.3 1.0 CB A:HIS263 3.9 17.4 1.0 CZ A:ARG228 4.0 26.0 0.3 CD A:GLU225 4.0 26.5 1.0 O A:HIS263 4.0 19.6 1.0 HD2 A:TYR67 4.1 17.8 1.0 HA3 A:GLY264 4.2 22.2 1.0 CG A:GLU225 4.2 21.3 1.0 HG2 A:PRO68 4.3 20.3 1.0 C A:HIS263 4.3 18.4 1.0 CD A:ARG228 4.3 19.4 0.7 HH22 A:ARG228 4.3 18.3 0.3 HH11 A:ARG228 4.3 22.0 0.7 HD3 A:ARG228 4.4 28.3 0.3 HG3 A:ARG228 4.6 26.9 0.3 CD A:ARG228 4.6 23.6 0.3 CD A:PRO68 4.6 16.1 1.0 C14 A:NL5401 4.7 25.4 0.8 N A:GLY264 4.7 16.4 1.0 HD3 A:ARG228 4.7 23.3 0.7 NH1 A:ARG228 4.7 20.7 0.3 HG3 A:ARG228 4.7 27.0 0.7 CB A:ARG228 4.7 22.0 0.7 CB A:ARG228 4.8 22.4 0.3 CG A:PRO68 4.8 16.9 1.0 CA A:HIS263 4.8 15.9 1.0 HG3 A:PRO68 4.8 20.3 1.0 CA A:GLY264 4.8 18.5 1.0 HG3 A:GLU225 4.8 25.6 1.0 HA2 A:GLY264 4.8 22.2 1.0 CG A:ARG228 4.9 22.5 0.7 NH1 A:ARG228 4.9 18.4 0.7 CG A:ARG228 4.9 22.4 0.3 HD3 A:PRO68 4.9 19.3 1.0 HB3 A:GLU225 4.9 23.5 1.0 H141 A:NL5401 5.0 30.5 0.8 C17 A:NL5401 5.0 26.9 0.8 CD2 A:TYR67 5.0 14.9 1.0

Z.Muhammad, S.Skagseth, M.Boomgaren, S.Akhter, C.Frohlich, A.Ismael, T.Christopeit, A.Bayer, H.S.Leiros. Structural Studies of Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases. Bioorg.Med.Chem. V. 28 15598 2020.
ISSN: ESSN 1464-3391
PubMed: 32631568
DOI: 10.1016/J.BMC.2020.115598