Iron in PDB 9dfi: Crystal Structure of Prnb in Complex with Tryptophan

The structure of Crystal Structure of Prnb in Complex with Tryptophan, PDB code: 9dfi 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)	46.50 / 2.02
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.125, 122.533, 66.809, 90, 94.68, 90
R / Rfree (%)	21.8 / 26

The binding sites of Iron atom in the Crystal Structure of Prnb in Complex with Tryptophan (pdb code 9dfi). 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 Tryptophan, PDB code: 9dfi:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Prnb in Complex with Tryptophan


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 Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe504 b:25.0 occ:1.00 FE A:HEM504 0.0 25.0 1.0 NA A:HEM504 2.0 24.9 1.0 NB A:HEM504 2.1 22.1 1.0 ND A:HEM504 2.1 25.2 1.0 NE2 A:HIS299 2.1 26.4 1.0 NC A:HEM504 2.1 24.2 1.0 N A:TRP505 2.4 23.7 1.0 CE1 A:HIS299 2.8 24.9 1.0 C4A A:HEM504 3.0 24.7 1.0 C1B A:HEM504 3.0 20.0 1.0 C1A A:HEM504 3.0 26.7 1.0 C1D A:HEM504 3.0 22.0 1.0 C4D A:HEM504 3.1 26.4 1.0 C4C A:HEM504 3.1 23.8 1.0 C4B A:HEM504 3.1 21.6 1.0 CA A:TRP505 3.1 27.9 1.0 C1C A:HEM504 3.2 21.4 1.0 CD2 A:HIS299 3.3 21.5 1.0 CHB A:HEM504 3.3 20.8 1.0 CHA A:HEM504 3.4 26.2 1.0 CHD A:HEM504 3.4 20.6 1.0 CHC A:HEM504 3.5 23.9 1.0 ND1 A:HIS299 4.0 27.1 1.0 CB A:TRP505 4.2 21.1 1.0 C3A A:HEM504 4.2 28.6 1.0 C2D A:HEM504 4.2 24.0 1.0 C2A A:HEM504 4.2 25.0 1.0 C A:TRP505 4.2 32.7 1.0 C3D A:HEM504 4.3 24.2 1.0 C2B A:HEM504 4.3 28.8 1.0 CG A:HIS299 4.3 25.4 1.0 C3C A:HEM504 4.3 20.0 1.0 C3B A:HEM504 4.3 22.9 1.0 C2C A:HEM504 4.3 18.6 1.0 O A:TRP505 4.5 36.3 1.0 CA A:GLY210 5.0 28.9 1.0 N A:GLY211 5.0 23.4 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Prnb in Complex with Tryptophan


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 Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe506 b:25.3 occ:1.00 FE B:HEM506 0.0 25.3 1.0 NA B:HEM506 2.0 27.7 1.0 ND B:HEM506 2.1 23.6 1.0 NC B:HEM506 2.1 26.3 1.0 NB B:HEM506 2.1 24.3 1.0 NE2 B:HIS299 2.1 25.7 1.0 N B:TRP507 2.4 25.0 1.0 C4A B:HEM506 3.0 24.4 1.0 C4C B:HEM506 3.0 22.0 1.0 C1D B:HEM506 3.0 24.9 1.0 C1A B:HEM506 3.0 26.4 1.0 C4D B:HEM506 3.1 24.9 1.0 C1B B:HEM506 3.1 21.4 1.0 CD2 B:HIS299 3.1 21.4 1.0 CA B:TRP507 3.1 28.1 1.0 CE1 B:HIS299 3.2 29.2 1.0 C1C B:HEM506 3.2 22.1 1.0 C4B B:HEM506 3.2 21.7 1.0 CHB B:HEM506 3.4 23.3 1.0 CHD B:HEM506 3.4 21.9 1.0 CHA B:HEM506 3.4 25.2 1.0 CHC B:HEM506 3.6 23.0 1.0 CB B:TRP507 4.2 25.9 1.0 C B:TRP507 4.2 33.6 1.0 C2D B:HEM506 4.2 28.1 1.0 C2A B:HEM506 4.2 27.8 1.0 C3A B:HEM506 4.2 27.0 1.0 C3D B:HEM506 4.2 27.8 1.0 ND1 B:HIS299 4.3 23.8 1.0 CG B:HIS299 4.3 24.5 1.0 C3C B:HEM506 4.3 21.7 1.0 C2B B:HEM506 4.3 25.8 1.0 C2C B:HEM506 4.3 20.6 1.0 O B:TRP507 4.4 34.0 1.0 C3B B:HEM506 4.4 22.9 1.0 CA B:GLY210 4.9 27.1 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