Iron in PDB 9dfl: Crystal Structure of Prnb in Complex with 3-Indolepropionic Acid

The structure of Crystal Structure of Prnb in Complex with 3-Indolepropionic Acid, PDB code: 9dfl was solved by B.Li, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.75 / 2.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	142.246, 122.605, 66.821, 90, 94.51, 90
R / Rfree (%)	20.1 / 25.8

The binding sites of Iron atom in the Crystal Structure of Prnb in Complex with 3-Indolepropionic Acid (pdb code 9dfl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Prnb in Complex with 3-Indolepropionic Acid, PDB code: 9dfl:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Prnb in Complex with 3-Indolepropionic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Prnb in Complex with 3-Indolepropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:24.8 occ:1.00 FE A:HEM401 0.0 24.8 1.0 NA A:HEM401 2.1 23.9 1.0 NC A:HEM401 2.1 25.3 1.0 NB A:HEM401 2.1 28.6 1.0 ND A:HEM401 2.1 19.0 1.0 NE2 A:HIS299 2.2 21.1 1.0 C4A A:HEM401 3.0 27.3 1.0 C1B A:HEM401 3.0 24.1 1.0 C4C A:HEM401 3.1 19.2 1.0 C1D A:HEM401 3.1 18.8 1.0 C1C A:HEM401 3.1 23.5 1.0 CE1 A:HIS299 3.1 23.0 1.0 C4B A:HEM401 3.1 27.5 1.0 C1A A:HEM401 3.1 21.8 1.0 C4D A:HEM401 3.2 21.5 1.0 CD2 A:HIS299 3.2 18.1 1.0 CHB A:HEM401 3.3 23.7 1.0 CHD A:HEM401 3.4 18.2 1.0 O1 A:IOP402 3.4 32.4 1.0 CHC A:HEM401 3.5 24.6 1.0 CHA A:HEM401 3.6 18.6 1.0 C1' A:IOP402 4.1 30.0 1.0 C3A A:HEM401 4.2 27.9 1.0 ND1 A:HIS299 4.3 19.5 1.0 C2B A:HEM401 4.3 33.8 1.0 C3C A:HEM401 4.3 19.5 1.0 C2D A:HEM401 4.3 22.9 1.0 C2C A:HEM401 4.3 20.9 1.0 C3' A:IOP402 4.3 25.3 1.0 C2A A:HEM401 4.3 18.9 1.0 C3B A:HEM401 4.3 25.3 1.0 CG A:HIS299 4.3 19.5 1.0 C3D A:HEM401 4.3 27.3 1.0 C2' A:IOP402 4.4 23.4 1.0 CA A:GLY210 4.5 21.9 1.0 N A:GLY211 4.9 19.4 1.0 O2 A:IOP402 4.9 33.3 1.0 C A:GLY210 5.0 22.1 1.0 N A:GLY210 5.0 21.5 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Prnb in Complex with 3-Indolepropionic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Prnb in Complex with 3-Indolepropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:21.0 occ:1.00 FE B:HEM401 0.0 21.0 1.0 NA B:HEM401 2.0 22.5 1.0 NC B:HEM401 2.0 23.1 1.0 NB B:HEM401 2.1 25.5 1.0 ND B:HEM401 2.1 19.3 1.0 NE2 B:HIS299 2.1 22.2 1.0 CE1 B:HIS299 3.0 22.3 1.0 C4A B:HEM401 3.0 23.5 1.0 C4C B:HEM401 3.0 19.3 1.0 C1D B:HEM401 3.0 18.3 1.0 C1B B:HEM401 3.1 22.0 1.0 C1C B:HEM401 3.1 22.2 1.0 C1A B:HEM401 3.1 24.5 1.0 C4B B:HEM401 3.1 25.7 1.0 C4D B:HEM401 3.1 24.0 1.0 CD2 B:HIS299 3.2 19.4 1.0 CHD B:HEM401 3.4 18.8 1.0 CHB B:HEM401 3.4 20.1 1.0 CHC B:HEM401 3.5 23.6 1.0 CHA B:HEM401 3.5 22.1 1.0 O2 B:IOP402 3.6 33.3 1.0 ND1 B:HIS299 4.2 20.8 1.0 C1' B:IOP402 4.2 32.8 1.0 C2D B:HEM401 4.3 21.0 1.0 C3C B:HEM401 4.3 16.5 1.0 C3A B:HEM401 4.3 25.0 1.0 C2C B:HEM401 4.3 18.7 1.0 C2B B:HEM401 4.3 25.1 1.0 CG B:HIS299 4.3 21.1 1.0 C2A B:HEM401 4.3 21.6 1.0 C3D B:HEM401 4.3 23.5 1.0 C3B B:HEM401 4.3 25.1 1.0 C3' B:IOP402 4.3 22.1 1.0 CA B:GLY210 4.5 18.7 1.0 C2' B:IOP402 4.6 27.2 1.0 N B:GLY210 4.9 19.3 1.0 N B:GLY211 4.9 19.6 1.0 O1 B:IOP402 4.9 36.2 1.0 C B:GLY210 5.0 19.8 1.0

B.Li, R.Usai, J.Campbell, Y.Wang. Elucidating Ligand Interactions and Small-Molecule Activation in the Pyrrolnitrin Biosynthetic Enzyme Prnb. J.Biol.Chem. V. 301 08123 2025.
ISSN: ESSN 1083-351X
PubMed: 39725034
DOI: 10.1016/J.JBC.2024.108123