Iron in PDB 7d9g: Spdh Spermidine Dehydrogenase Native Structure

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

The structure of Spdh Spermidine Dehydrogenase Native Structure, PDB code: 7d9g 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)	49.78 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.399, 85.731, 100.654, 90, 98.45, 90
R / Rfree (%)	18.3 / 24.7

The binding sites of Iron atom in the Spdh Spermidine Dehydrogenase Native Structure (pdb code 7d9g). 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 Native Structure, PDB code: 7d9g:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Spdh Spermidine Dehydrogenase Native 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 Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:30.0 occ:1.00 FE A:HEM702 0.0 30.0 1.0 ND A:HEM702 1.9 28.3 1.0 NA A:HEM702 2.0 27.9 1.0 NC A:HEM702 2.1 28.5 1.0 NB A:HEM702 2.1 29.1 1.0 NE2 A:HIS562 2.2 22.2 1.0 NE2 A:HIS54 2.4 22.9 1.0 C4D A:HEM702 2.9 29.4 1.0 C1D A:HEM702 2.9 27.1 1.0 C1A A:HEM702 3.0 28.6 1.0 C4C A:HEM702 3.0 28.9 1.0 C4A A:HEM702 3.0 29.4 1.0 C1B A:HEM702 3.1 29.4 1.0 C4B A:HEM702 3.1 30.2 1.0 C1C A:HEM702 3.1 27.3 1.0 CE1 A:HIS562 3.1 22.6 1.0 CD2 A:HIS562 3.2 22.0 1.0 CE1 A:HIS54 3.3 22.9 1.0 CD2 A:HIS54 3.3 23.4 1.0 CHA A:HEM702 3.3 29.3 1.0 CHD A:HEM702 3.4 25.4 1.0 CHB A:HEM702 3.5 31.0 1.0 CHC A:HEM702 3.5 28.1 1.0 C3D A:HEM702 4.1 27.1 1.0 C2D A:HEM702 4.1 28.2 1.0 C2A A:HEM702 4.2 29.1 1.0 C3A A:HEM702 4.2 31.1 1.0 C3C A:HEM702 4.2 28.0 1.0 C2C A:HEM702 4.3 29.2 1.0 ND1 A:HIS562 4.3 22.8 1.0 C2B A:HEM702 4.3 30.8 1.0 C3B A:HEM702 4.3 29.1 1.0 CG A:HIS562 4.4 22.2 1.0 ND1 A:HIS54 4.4 22.9 1.0 CG A:HIS54 4.5 23.3 1.0 CD A:ARG518 4.5 27.5 1.0 CZ2 A:TRP58 4.8 37.5 1.0 NE1 A:TRP58 4.9 38.0 1.0

Iron binding site 2 out of 2 in the Spdh Spermidine Dehydrogenase Native 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 Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:36.8 occ:1.00 FE B:HEM702 0.0 36.8 1.0 ND B:HEM702 1.9 38.5 1.0 NA B:HEM702 2.0 35.5 1.0 NC B:HEM702 2.1 36.6 1.0 NB B:HEM702 2.1 32.1 1.0 NE2 B:HIS562 2.2 23.8 1.0 NE2 B:HIS54 2.3 30.1 1.0 C4D B:HEM702 2.9 37.7 1.0 C1D B:HEM702 2.9 35.9 1.0 C1A B:HEM702 3.0 36.2 1.0 C4C B:HEM702 3.0 34.2 1.0 C4A B:HEM702 3.0 36.6 1.0 C1B B:HEM702 3.1 32.4 1.0 C4B B:HEM702 3.1 33.1 1.0 CE1 B:HIS562 3.1 24.1 1.0 C1C B:HEM702 3.1 34.6 1.0 CD2 B:HIS54 3.2 30.1 1.0 CD2 B:HIS562 3.3 23.5 1.0 CE1 B:HIS54 3.3 30.2 1.0 CHA B:HEM702 3.3 38.0 1.0 CHD B:HEM702 3.4 32.5 1.0 CHB B:HEM702 3.5 32.8 1.0 CHC B:HEM702 3.5 33.5 1.0 C2D B:HEM702 4.1 36.8 1.0 C3D B:HEM702 4.1 37.2 1.0 C2A B:HEM702 4.2 37.6 1.0 C3A B:HEM702 4.2 37.3 1.0 C3C B:HEM702 4.2 32.0 1.0 C2C B:HEM702 4.3 32.2 1.0 ND1 B:HIS562 4.3 24.2 1.0 C2B B:HEM702 4.3 32.9 1.0 C3B B:HEM702 4.3 31.3 1.0 CG B:HIS54 4.3 30.0 1.0 CD B:ARG518 4.4 24.4 1.0 ND1 B:HIS54 4.4 30.2 1.0 CG B:HIS562 4.4 23.8 1.0 NE1 B:TRP58 4.4 50.1 1.0 CZ2 B:TRP58 5.0 50.0 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