Iron in PDB 6rte: Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe

All present enzymatic activity of Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe:
1.7.2.1;

The structure of Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe, PDB code: 6rte was solved by T.Kluenemann, A.Preuss, G.Layer, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.21 / 1.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	191.123, 54.957, 131.896, 90.00, 132.42, 90.00
R / Rfree (%)	16.7 / 19.8

The binding sites of Iron atom in the Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe (pdb code 6rte). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe, PDB code: 6rte:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:29.9 occ:1.00 FE A:HEC501 0.0 29.9 1.0 ND A:HEC501 1.9 37.7 1.0 NE2 A:HIS17 2.0 45.8 1.0 NA A:HEC501 2.0 31.2 1.0 NC A:HEC501 2.1 38.1 1.0 NB A:HEC501 2.1 34.4 1.0 SD A:MET55 2.4 38.6 1.0 CE1 A:HIS17 2.7 39.9 1.0 HE1 A:HIS17 2.8 47.9 1.0 C1D A:HEC501 2.9 40.3 1.0 C4D A:HEC501 2.9 38.0 1.0 C1A A:HEC501 3.0 31.4 1.0 C4A A:HEC501 3.0 29.3 1.0 C4C A:HEC501 3.0 40.3 1.0 C1B A:HEC501 3.1 33.6 1.0 C4B A:HEC501 3.1 35.6 1.0 C1C A:HEC501 3.1 38.4 1.0 CD2 A:HIS17 3.1 41.2 1.0 CE A:MET55 3.3 37.2 1.0 HE2 A:MET55 3.3 44.6 1.0 HE1 A:MET55 3.3 44.6 1.0 CHA A:HEC501 3.4 33.7 1.0 CHD A:HEC501 3.4 40.7 1.0 CHB A:HEC501 3.4 31.1 1.0 HD2 A:HIS17 3.5 49.4 1.0 CHC A:HEC501 3.5 36.5 1.0 HG2 A:MET55 3.6 48.2 1.0 CG A:MET55 3.6 40.2 1.0 HB2 A:MET55 3.8 50.9 1.0 ND1 A:HIS17 3.9 39.5 1.0 HD11 A:LEU29 4.1 39.3 1.0 HE3 A:MET55 4.1 44.6 1.0 CG A:HIS17 4.2 40.5 1.0 C2D A:HEC501 4.2 41.8 1.0 C3D A:HEC501 4.2 40.3 1.0 C2A A:HEC501 4.2 28.7 1.0 C3A A:HEC501 4.2 27.2 1.0 HHD A:HEC501 4.2 48.9 1.0 CB A:MET55 4.3 42.4 1.0 HHA A:HEC501 4.3 40.4 1.0 C3C A:HEC501 4.3 38.8 1.0 C2B A:HEC501 4.3 34.0 1.0 C2C A:HEC501 4.3 39.7 1.0 HA A:MET55 4.3 56.7 1.0 C3B A:HEC501 4.3 36.5 1.0 HHB A:HEC501 4.4 37.3 1.0 HHC A:HEC501 4.4 43.8 1.0 HG3 A:MET55 4.4 48.2 1.0 HD2 A:PRO27 4.6 42.4 1.0 HD1 A:HIS17 4.7 47.4 1.0 HE1 A:PHE58 4.8 54.8 1.0 HA3 A:GLY26 4.9 55.7 1.0 CA A:MET55 4.9 47.2 1.0 HB2 A:CYS16 5.0 64.7 1.0 HD21 A:LEU29 5.0 35.8 1.0

Iron binding site 2 out of 2 in the Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:28.6 occ:1.00 FE B:HEC501 0.0 28.6 1.0 ND B:HEC501 1.9 29.1 1.0 NA B:HEC501 2.0 29.6 1.0 NE2 B:HIS17 2.1 36.2 1.0 NC B:HEC501 2.1 32.8 1.0 NB B:HEC501 2.1 31.3 1.0 SD B:MET55 2.4 30.7 1.0 C4D B:HEC501 2.9 26.4 1.0 C1D B:HEC501 2.9 28.0 1.0 CE1 B:HIS17 3.0 28.7 1.0 C1A B:HEC501 3.0 26.0 1.0 C4C B:HEC501 3.0 30.1 1.0 C4A B:HEC501 3.1 26.5 1.0 C4B B:HEC501 3.1 29.0 1.0 C1B B:HEC501 3.1 29.3 1.0 C1C B:HEC501 3.1 32.3 1.0 CD2 B:HIS17 3.1 30.5 1.0 HE1 B:HIS17 3.1 34.5 1.0 CE B:MET55 3.3 31.3 1.0 HE2 B:MET55 3.3 37.5 1.0 HD2 B:HIS17 3.3 36.5 1.0 CHA B:HEC501 3.4 26.1 1.0 CHD B:HEC501 3.4 28.3 1.0 HE1 B:MET55 3.4 37.5 1.0 CHB B:HEC501 3.5 28.0 1.0 CHC B:HEC501 3.5 31.7 1.0 HG2 B:MET55 3.5 39.6 1.0 CG B:MET55 3.5 33.0 1.0 HB2 B:MET55 3.7 40.6 1.0 CB B:MET55 4.1 33.8 1.0 HA B:MET55 4.1 41.4 1.0 ND1 B:HIS17 4.1 28.9 1.0 C2D B:HEC501 4.2 29.8 1.0 C3D B:HEC501 4.2 27.5 1.0 C2A B:HEC501 4.2 25.5 1.0 HE3 B:MET55 4.2 37.5 1.0 C3A B:HEC501 4.2 25.1 1.0 CG B:HIS17 4.2 30.3 1.0 HD11 B:LEU29 4.2 31.0 1.0 HHA B:HEC501 4.3 31.3 1.0 C2C B:HEC501 4.3 35.0 1.0 C3C B:HEC501 4.3 31.3 1.0 HHD B:HEC501 4.3 34.0 1.0 C2B B:HEC501 4.3 29.1 1.0 C3B B:HEC501 4.3 30.8 1.0 HG3 B:MET55 4.4 39.6 1.0 HHB B:HEC501 4.4 33.6 1.0 HHC B:HEC501 4.4 38.0 1.0 HD2 B:PRO27 4.5 33.8 1.0 CA B:MET55 4.7 34.5 1.0 HE1 B:PHE58 4.9 52.0 1.0 HD1 B:HIS17 4.9 34.6 1.0 HD21 B:LEU29 4.9 33.1 1.0 HA3 B:GLY26 5.0 41.9 1.0 HB3 B:MET55 5.0 40.6 1.0 HB2 B:CYS16 5.0 48.5 1.0

T.Klunemann, A.Preuss, J.Adamczack, L.F.M.Rosa, F.Harnisch, G.Layer, W.Blankenfeldt. Crystal Structure of Dihydro-Heme D1DEHYDROGENASE Nirn From Pseudomonas Aeruginosa Reveals Amino Acid Residues Essential For Catalysis. J.Mol.Biol. V. 431 3246 2019.
ISSN: ESSN 1089-8638
PubMed: 31173777
DOI: 10.1016/J.JMB.2019.05.046