Iron in PDB 7d9h: Spdh Spermidine Dehydrogenase N33 Truncation Structure

All present enzymatic activity of Spdh Spermidine Dehydrogenase N33 Truncation Structure:
1.5.99.6;

The structure of Spdh Spermidine Dehydrogenase N33 Truncation Structure, PDB code: 7d9h 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)	38.74 / 2.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.284, 84.926, 101.081, 90, 98.4, 90
R / Rfree (%)	15.1 / 21.4

The binding sites of Iron atom in the Spdh Spermidine Dehydrogenase N33 Truncation Structure (pdb code 7d9h). 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 N33 Truncation Structure, PDB code: 7d9h:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Spdh Spermidine Dehydrogenase N33 Truncation 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 N33 Truncation Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:32.1 occ:1.00 FE A:HEM702 0.0 32.1 1.0 ND A:HEM702 2.0 29.8 1.0 NC A:HEM702 2.0 33.6 1.0 NA A:HEM702 2.1 30.4 1.0 NB A:HEM702 2.1 29.6 1.0 NE2 A:HIS54 2.3 31.1 1.0 NE2 A:HIS562 2.3 24.1 1.0 C1D A:HEM702 3.0 31.8 1.0 C4C A:HEM702 3.0 30.3 1.0 C4B A:HEM702 3.0 32.2 1.0 C1C A:HEM702 3.0 30.8 1.0 C4D A:HEM702 3.0 30.2 1.0 C1A A:HEM702 3.1 31.0 1.0 C4A A:HEM702 3.1 33.2 1.0 C1B A:HEM702 3.2 28.7 1.0 CD2 A:HIS54 3.2 27.4 1.0 CD2 A:HIS562 3.3 27.1 1.0 CE1 A:HIS562 3.3 27.7 1.0 CE1 A:HIS54 3.3 33.1 1.0 CHC A:HEM702 3.4 30.9 1.0 CHD A:HEM702 3.4 27.0 1.0 CHA A:HEM702 3.4 29.7 1.0 CHB A:HEM702 3.6 30.6 1.0 C2D A:HEM702 4.2 28.2 1.0 C3C A:HEM702 4.2 31.7 1.0 C3D A:HEM702 4.2 29.7 1.0 C2C A:HEM702 4.2 32.9 1.0 C3B A:HEM702 4.3 29.9 1.0 C2A A:HEM702 4.3 29.8 1.0 C3A A:HEM702 4.3 33.1 1.0 C2B A:HEM702 4.4 29.8 1.0 CG A:HIS54 4.4 26.7 1.0 ND1 A:HIS54 4.4 33.7 1.0 ND1 A:HIS562 4.4 27.1 1.0 CG A:HIS562 4.4 28.3 1.0 CD A:ARG518 4.5 28.6 1.0 CZ2 A:TRP58 4.7 37.8 1.0 NE1 A:TRP58 4.8 33.0 1.0 CE2 A:TRP58 5.0 36.0 1.0

Iron binding site 2 out of 2 in the Spdh Spermidine Dehydrogenase N33 Truncation 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 N33 Truncation Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:44.8 occ:1.00 FE B:HEM702 0.0 44.8 1.0 NB B:HEM702 2.0 45.3 1.0 ND B:HEM702 2.1 43.8 1.0 NC B:HEM702 2.1 50.6 1.0 NA B:HEM702 2.1 40.0 1.0 NE2 B:HIS562 2.4 35.0 1.0 NE2 B:HIS54 2.5 43.9 1.0 C4B B:HEM702 3.0 45.2 1.0 C1B B:HEM702 3.1 39.4 1.0 C1D B:HEM702 3.1 45.7 1.0 C4C B:HEM702 3.1 45.7 1.0 C1C B:HEM702 3.1 46.5 1.0 C4D B:HEM702 3.1 43.2 1.0 C4A B:HEM702 3.1 44.9 1.0 C1A B:HEM702 3.2 39.2 1.0 CD2 B:HIS54 3.2 41.8 1.0 CD2 B:HIS562 3.4 35.9 1.0 CHC B:HEM702 3.4 46.8 1.0 CE1 B:HIS562 3.4 35.7 1.0 CHD B:HEM702 3.4 41.8 1.0 CHB B:HEM702 3.5 37.8 1.0 CHA B:HEM702 3.5 42.7 1.0 CE1 B:HIS54 3.6 45.4 1.0 C3B B:HEM702 4.2 47.4 1.0 C2B B:HEM702 4.2 49.4 1.0 C3C B:HEM702 4.3 48.1 1.0 C2D B:HEM702 4.3 48.5 1.0 C3D B:HEM702 4.3 45.4 1.0 C2C B:HEM702 4.3 46.3 1.0 CD B:ARG518 4.4 31.3 1.0 C2A B:HEM702 4.4 45.8 1.0 C3A B:HEM702 4.4 42.3 1.0 NE1 B:TRP58 4.5 48.1 1.0 CG B:HIS54 4.5 45.1 1.0 CG B:HIS562 4.5 31.5 1.0 ND1 B:HIS562 4.5 31.1 1.0 ND1 B:HIS54 4.6 53.4 1.0 CZ2 B:TRP58 5.0 45.3 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