Iron in PDB 7d9f: Spdh Spermidine Dehydrogenase Semet Structure

All present enzymatic activity of Spdh Spermidine Dehydrogenase Semet Structure:
1.5.99.6;

The structure of Spdh Spermidine Dehydrogenase Semet Structure, PDB code: 7d9f was solved by S.Che, Q.Zhang, M.Bartlam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.25 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.197, 85.586, 99.624, 90, 98.33, 90
R / Rfree (%)	15 / 19

The binding sites of Iron atom in the Spdh Spermidine Dehydrogenase Semet Structure (pdb code 7d9f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Spdh Spermidine Dehydrogenase Semet Structure, PDB code: 7d9f:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Spdh Spermidine Dehydrogenase Semet Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Spdh Spermidine Dehydrogenase Semet Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:18.6 occ:1.00 FE A:HEM702 0.0 18.6 1.0 ND A:HEM702 2.0 18.5 1.0 NA A:HEM702 2.0 18.4 1.0 NB A:HEM702 2.0 17.5 1.0 NC A:HEM702 2.1 18.3 1.0 NE2 A:HIS562 2.3 15.1 1.0 NE2 A:HIS54 2.3 19.7 1.0 C4D A:HEM702 3.0 19.5 1.0 C4B A:HEM702 3.0 18.3 1.0 C1A A:HEM702 3.0 19.4 1.0 C4A A:HEM702 3.1 20.2 1.0 C1C A:HEM702 3.1 18.3 1.0 C1B A:HEM702 3.1 21.4 1.0 C1D A:HEM702 3.1 20.1 1.0 C4C A:HEM702 3.1 20.2 1.0 CD2 A:HIS562 3.2 14.8 1.0 CD2 A:HIS54 3.2 19.7 1.0 CE1 A:HIS562 3.3 15.6 1.0 CE1 A:HIS54 3.3 24.6 1.0 CHA A:HEM702 3.4 20.1 1.0 CHC A:HEM702 3.4 17.9 1.0 CHB A:HEM702 3.4 18.7 1.0 CHD A:HEM702 3.5 20.7 1.0 C3B A:HEM702 4.2 19.8 1.0 C3D A:HEM702 4.3 19.7 1.0 C2A A:HEM702 4.3 21.6 1.0 C3A A:HEM702 4.3 17.6 1.0 C2B A:HEM702 4.3 20.5 1.0 C2D A:HEM702 4.3 21.3 1.0 C2C A:HEM702 4.3 16.9 1.0 C3C A:HEM702 4.3 18.9 1.0 CG A:HIS562 4.4 15.3 1.0 ND1 A:HIS562 4.4 18.1 1.0 CG A:HIS54 4.4 21.6 1.0 ND1 A:HIS54 4.4 24.1 1.0 CD A:ARG518 4.5 15.6 1.0 NE1 A:TRP58 4.6 24.8 1.0

Iron binding site 2 out of 2 in the Spdh Spermidine Dehydrogenase Semet Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Spdh Spermidine Dehydrogenase Semet Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe703 b:18.5 occ:1.00 FE B:HEM703 0.0 18.5 1.0 ND B:HEM703 2.0 18.9 1.0 NB B:HEM703 2.0 17.8 1.0 NA B:HEM703 2.1 17.2 1.0 NC B:HEM703 2.1 17.3 1.0 NE2 B:HIS562 2.2 17.3 1.0 NE2 B:HIS54 2.3 20.9 1.0 C4D B:HEM703 3.0 20.4 1.0 C4B B:HEM703 3.0 17.8 1.0 CD2 B:HIS562 3.0 14.3 1.0 C1A B:HEM703 3.1 18.2 1.0 C1C B:HEM703 3.1 19.1 1.0 C4A B:HEM703 3.1 19.9 1.0 C1B B:HEM703 3.1 19.6 1.0 C1D B:HEM703 3.1 20.4 1.0 C4C B:HEM703 3.1 16.9 1.0 CD2 B:HIS54 3.2 19.9 1.0 CE1 B:HIS54 3.3 24.9 1.0 CE1 B:HIS562 3.3 17.0 1.0 CHA B:HEM703 3.4 18.9 1.0 CHC B:HEM703 3.4 18.2 1.0 CHB B:HEM703 3.5 14.3 1.0 CHD B:HEM703 3.5 18.9 1.0 CG B:HIS562 4.3 14.9 1.0 C3B B:HEM703 4.3 18.3 1.0 C3D B:HEM703 4.3 21.9 1.0 C2A B:HEM703 4.3 19.1 1.0 C3A B:HEM703 4.3 20.4 1.0 C2B B:HEM703 4.3 16.0 1.0 C2D B:HEM703 4.3 19.4 1.0 C2C B:HEM703 4.3 18.6 1.0 C3C B:HEM703 4.3 17.6 1.0 ND1 B:HIS562 4.4 16.2 1.0 ND1 B:HIS54 4.4 22.1 1.0 CG B:HIS54 4.4 20.6 1.0 CD B:ARG518 4.5 14.2 1.0 NE1 B:TRP58 4.5 25.8 1.0

S.Che, Y.Liang, Y.Chen, W.Wu, R.Liu, Q.Zhang, M.Bartlam. Structure of Pseudomonas Aeruginosa Spermidine Dehydrogenase: A Polyamine Oxidase with A Novel Heme-Binding Fold. Febs J. 2021.
ISSN: ISSN 1742-464X
PubMed: 34741591
DOI: 10.1111/FEBS.16264