Iron in PDB 9qdt: Cytochrome C Peroxidase Yhja

All present enzymatic activity of Cytochrome C Peroxidase Yhja:
1.11.1.5;

The structure of Cytochrome C Peroxidase Yhja, PDB code: 9qdt was solved by O.Einsle, A.Wuest, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.15 / 2.57
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.42, 101.42, 134.68, 90, 90, 90
R / Rfree (%)	17.2 / 22.2

The structure of Cytochrome C Peroxidase Yhja also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Iron atom in the Cytochrome C Peroxidase Yhja (pdb code 9qdt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Cytochrome C Peroxidase Yhja, PDB code: 9qdt:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Cytochrome C Peroxidase Yhja


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome C Peroxidase Yhja within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:34.2 occ:1.00 FE A:HEC501 0.0 34.2 1.0 ND A:HEC501 1.9 42.0 1.0 NA A:HEC501 2.0 40.7 1.0 NB A:HEC501 2.1 40.3 1.0 NC A:HEC501 2.1 45.2 1.0 NE2 A:HIS211 2.1 27.5 1.0 C1D A:HEC501 2.9 39.8 1.0 C4D A:HEC501 2.9 37.2 1.0 C4B A:HEC501 3.0 37.4 1.0 CE1 A:HIS211 3.0 31.3 1.0 C1A A:HEC501 3.0 39.7 1.0 C4A A:HEC501 3.0 36.6 1.0 C4C A:HEC501 3.0 39.9 1.0 C1B A:HEC501 3.0 38.0 1.0 C1C A:HEC501 3.1 39.5 1.0 CD2 A:HIS211 3.2 28.9 1.0 CHD A:HEC501 3.4 36.8 1.0 CHA A:HEC501 3.4 39.9 1.0 CHB A:HEC501 3.4 34.6 1.0 CHC A:HEC501 3.4 37.7 1.0 NE2 A:GLN260 3.8 41.1 1.0 C2D A:HEC501 4.1 34.8 1.0 C3D A:HEC501 4.2 34.7 1.0 ND1 A:HIS211 4.2 28.9 1.0 C3A A:HEC501 4.2 33.6 1.0 CG A:PRO264 4.2 34.1 1.0 C2A A:HEC501 4.2 33.7 1.0 C3C A:HEC501 4.2 38.4 1.0 C2C A:HEC501 4.2 37.6 1.0 C2B A:HEC501 4.3 38.1 1.0 C3B A:HEC501 4.3 34.9 1.0 CG A:HIS211 4.3 30.0 1.0 CD A:GLN260 4.9 37.6 1.0

Iron binding site 2 out of 3 in the Cytochrome C Peroxidase Yhja


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome C Peroxidase Yhja within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:32.2 occ:1.00 FE A:HEC502 0.0 32.2 1.0 CE A:MET429 1.8 40.2 1.0 ND A:HEC502 1.9 32.0 1.0 NE2 A:HIS355 2.0 37.5 1.0 NA A:HEC502 2.0 27.2 1.0 NC A:HEC502 2.0 29.9 1.0 NB A:HEC502 2.1 29.6 1.0 SD A:MET429 2.5 38.7 1.0 CE1 A:HIS355 2.9 34.5 1.0 C4D A:HEC502 2.9 28.8 1.0 C1D A:HEC502 2.9 33.2 1.0 C4C A:HEC502 3.0 29.8 1.0 C1A A:HEC502 3.0 27.6 1.0 CD2 A:HIS355 3.1 39.1 1.0 C1C A:HEC502 3.1 33.6 1.0 C1B A:HEC502 3.1 28.8 1.0 C4A A:HEC502 3.1 27.2 1.0 C4B A:HEC502 3.1 29.7 1.0 CHA A:HEC502 3.3 28.1 1.0 CHD A:HEC502 3.3 29.5 1.0 CHB A:HEC502 3.5 27.4 1.0 CHC A:HEC502 3.5 30.9 1.0 CG A:MET429 3.7 37.6 1.0 ND1 A:HIS355 4.0 36.5 1.0 C3D A:HEC502 4.1 28.6 1.0 C2D A:HEC502 4.1 30.7 1.0 CG A:HIS355 4.1 37.6 1.0 C3C A:HEC502 4.2 31.0 1.0 C2A A:HEC502 4.2 30.2 1.0 C2C A:HEC502 4.2 32.6 1.0 C3A A:HEC502 4.3 29.1 1.0 C2B A:HEC502 4.3 30.3 1.0 C3B A:HEC502 4.3 31.1 1.0 CB A:MET429 4.4 36.0 1.0

Iron binding site 3 out of 3 in the Cytochrome C Peroxidase Yhja


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome C Peroxidase Yhja within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:31.1 occ:1.00 FE A:HEM503 0.0 31.1 1.0 ND A:HEM503 1.9 35.6 1.0 NE2 A:HIS63 2.0 33.3 1.0 NA A:HEM503 2.0 34.6 1.0 NB A:HEM503 2.0 36.9 1.0 NC A:HEM503 2.1 32.8 1.0 SD A:MET125 2.2 30.8 1.0 CE1 A:HIS63 2.8 30.5 1.0 C4D A:HEM503 2.9 35.7 1.0 C1D A:HEM503 2.9 35.1 1.0 C1A A:HEM503 3.0 36.0 1.0 C4B A:HEM503 3.0 35.6 1.0 C4A A:HEM503 3.0 35.6 1.0 C1B A:HEM503 3.0 34.7 1.0 C4C A:HEM503 3.0 33.0 1.0 C1C A:HEM503 3.1 34.9 1.0 CD2 A:HIS63 3.1 33.1 1.0 CHA A:HEM503 3.3 36.8 1.0 CHD A:HEM503 3.4 36.7 1.0 CHB A:HEM503 3.4 34.1 1.0 CG A:MET125 3.4 31.2 1.0 CHC A:HEM503 3.4 34.6 1.0 CE A:MET125 3.4 29.1 1.0 ND1 A:HIS63 4.0 31.0 1.0 C3D A:HEM503 4.1 35.6 1.0 CG A:HIS63 4.1 34.0 1.0 C2A A:HEM503 4.2 37.0 1.0 C3A A:HEM503 4.2 37.7 1.0 C2D A:HEM503 4.2 32.5 1.0 C3C A:HEM503 4.2 33.6 1.0 C2C A:HEM503 4.2 34.2 1.0 C3B A:HEM503 4.2 34.5 1.0 C2B A:HEM503 4.3 34.1 1.0 CB A:MET125 4.3 30.9 1.0

P.Hewitt, J.Seidel, A.Wust, M.Smith, S.J.Maiocco, S.Shternberg, M.Hoffmann, T.Spatzal, S.Gerhardt, O.Einsle, S.J.Elliott. Escherichia Coli Triheme Enzyme Yhja: Structure and Reactivity. Biochemistry 2025.
ISSN: ISSN 0006-2960
PubMed: 40669070
DOI: 10.1021/ACS.BIOCHEM.5C00202