Iron in PDB 6rtd: 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: 6rtd 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)	45.09 / 2.36
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	191.382, 54.590, 132.135, 90.00, 131.94, 90.00
R / Rfree (%)	19.2 / 23.5

The binding sites of Iron atom in the Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe (pdb code 6rtd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe, PDB code: 6rtd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 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:Fe502 b:44.9 occ:1.00 FE A:DHE502 0.0 44.9 1.0 NE2 A:HIS147 2.0 68.6 1.0 NC A:DHE502 2.1 48.3 1.0 NB A:DHE502 2.1 47.4 1.0 NA A:DHE502 2.1 46.1 1.0 ND A:DHE502 2.1 45.8 1.0 NE2 A:HIS323 2.2 1.0 0.4 HE1 A:HIS323 2.6 0.4 0.4 CE1 A:HIS323 2.7 0.1 0.4 CE1 A:HIS147 2.7 65.7 1.0 HE1 A:HIS147 2.8 78.9 1.0 C1C A:DHE502 3.0 47.5 1.0 C1B A:DHE502 3.0 45.0 1.0 C4B A:DHE502 3.1 46.6 1.0 C4C A:DHE502 3.1 47.4 1.0 C4A A:DHE502 3.1 44.7 1.0 C1A A:DHE502 3.1 44.7 1.0 C1D A:DHE502 3.1 44.5 1.0 C4D A:DHE502 3.1 44.3 1.0 CD2 A:HIS147 3.2 66.8 1.0 CHC A:DHE502 3.4 46.5 1.0 CHB A:DHE502 3.4 44.3 1.0 CD2 A:HIS323 3.4 0.2 0.4 CHA A:DHE502 3.4 44.1 1.0 CHD A:DHE502 3.4 45.8 1.0 HD2 A:HIS147 3.5 80.3 1.0 HD2 A:HIS323 3.8 0.4 0.4 ND1 A:HIS147 3.9 64.3 1.0 ND1 A:HIS323 4.0 0.7 0.4 CG A:HIS147 4.2 64.3 1.0 C2A A:DHE502 4.3 44.9 1.0 C2C A:DHE502 4.3 48.8 1.0 C3A A:DHE502 4.3 45.2 1.0 HHC A:DHE502 4.3 55.8 1.0 C2D A:DHE502 4.3 43.5 1.0 C3D A:DHE502 4.3 44.9 1.0 HHB A:DHE502 4.3 53.2 1.0 C2B A:DHE502 4.3 44.1 1.0 CG A:HIS323 4.3 0.2 0.4 HHA A:DHE502 4.4 53.1 1.0 HHD A:DHE502 4.4 55.0 1.0 C3B A:DHE502 4.4 46.1 1.0 C3C A:DHE502 4.4 47.2 1.0 H A:GLY148 4.5 62.2 1.0 HH22 A:ARG164 4.5 66.1 1.0 HD1 A:HIS147 4.7 77.3 1.0 HGB3 A:DHE502 4.8 54.5 1.0 HGC3 A:DHE502 4.9 52.8 1.0 NH2 A:ARG164 5.0 55.0 1.0

Iron binding site 2 out of 4 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 A:Fe503 b:51.2 occ:1.00 FE A:HEC503 0.0 51.2 1.0 ND A:HEC503 1.9 52.0 1.0 NA A:HEC503 2.0 48.4 1.0 NE2 A:HIS17 2.0 92.5 1.0 NC A:HEC503 2.1 51.9 1.0 NB A:HEC503 2.1 49.8 1.0 SD A:MET55 2.3 61.1 1.0 CE1 A:HIS17 2.8 90.9 1.0 HE1 A:HIS17 2.8 0.2 1.0 C4D A:HEC503 2.9 50.6 1.0 C1D A:HEC503 2.9 51.0 1.0 C1A A:HEC503 3.0 46.8 1.0 C4A A:HEC503 3.0 46.4 1.0 C4C A:HEC503 3.0 50.6 1.0 C4B A:HEC503 3.1 48.9 1.0 C1B A:HEC503 3.1 48.7 1.0 C1C A:HEC503 3.1 50.8 1.0 HE2 A:MET55 3.2 70.8 1.0 CE A:MET55 3.2 59.0 1.0 CD2 A:HIS17 3.2 92.9 1.0 HE1 A:MET55 3.3 70.8 1.0 CHA A:HEC503 3.3 48.0 1.0 CHD A:HEC503 3.4 50.4 1.0 CHB A:HEC503 3.4 47.1 1.0 CHC A:HEC503 3.5 50.0 1.0 HD2 A:HIS17 3.5 0.6 1.0 CG A:MET55 3.6 63.8 1.0 HG2 A:MET55 3.6 76.7 1.0 HB2 A:MET55 3.9 81.5 1.0 ND1 A:HIS17 4.0 89.6 1.0 HE3 A:MET55 4.1 70.8 1.0 C2D A:HEC503 4.1 50.3 1.0 C3D A:HEC503 4.1 50.0 1.0 C2A A:HEC503 4.2 43.7 1.0 HD11 A:LEU29 4.2 47.4 1.0 C3A A:HEC503 4.2 44.0 1.0 CG A:HIS17 4.2 90.1 1.0 HHD A:HEC503 4.2 60.5 1.0 HHA A:HEC503 4.2 57.6 1.0 CB A:MET55 4.3 67.8 1.0 C3C A:HEC503 4.3 48.9 1.0 HA A:MET55 4.3 87.6 1.0 C2B A:HEC503 4.3 47.1 1.0 C2C A:HEC503 4.3 49.8 1.0 HHB A:HEC503 4.3 56.6 1.0 C3B A:HEC503 4.3 46.3 1.0 HG3 A:MET55 4.4 76.7 1.0 HHC A:HEC503 4.4 60.1 1.0 HD2 A:PRO27 4.5 56.3 1.0 HD1 A:HIS17 4.7 0.6 1.0 CA A:MET55 4.9 72.9 1.0 HE1 A:PHE58 4.9 85.1 1.0 HA3 A:GLY26 5.0 64.7 1.0

Iron binding site 3 out of 4 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 3 of Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:48.6 occ:1.00 FE B:DHE501 0.0 48.6 1.0 NE2 B:HIS147 1.9 60.0 1.0 NC B:DHE501 2.1 44.4 1.0 NB B:DHE501 2.1 45.2 1.0 NA B:DHE501 2.1 43.0 1.0 ND B:DHE501 2.1 43.5 1.0 NE2 B:HIS323 2.2 0.6 0.6 CE1 B:HIS147 2.7 57.4 1.0 HE1 B:HIS147 2.8 68.9 1.0 CE1 B:HIS323 2.9 0.8 0.6 HE1 B:HIS323 2.9 0.9 0.6 C1C B:DHE501 3.0 41.7 1.0 C1B B:DHE501 3.1 42.9 1.0 C4B B:DHE501 3.1 42.3 1.0 C4A B:DHE501 3.1 41.6 1.0 C4C B:DHE501 3.1 41.8 1.0 C1D B:DHE501 3.1 40.9 1.0 CD2 B:HIS147 3.1 57.9 1.0 C1A B:DHE501 3.1 40.5 1.0 C4D B:DHE501 3.1 40.6 1.0 CD2 B:HIS323 3.3 0.6 0.6 CHC B:DHE501 3.4 40.6 1.0 HD2 B:HIS147 3.4 69.6 1.0 CHB B:DHE501 3.4 41.8 1.0 CHD B:DHE501 3.4 40.0 1.0 CHA B:DHE501 3.4 39.6 1.0 HD2 B:HIS323 3.6 0.6 0.6 ND1 B:HIS147 3.9 57.0 1.0 CG B:HIS147 4.1 56.8 1.0 ND1 B:HIS323 4.1 0.7 0.6 HH22 B:ARG164 4.2 59.6 1.0 C3A B:DHE501 4.3 40.7 1.0 C2A B:DHE501 4.3 40.7 1.0 HHC B:DHE501 4.3 48.8 1.0 C2D B:DHE501 4.3 38.8 1.0 C3D B:DHE501 4.3 40.5 1.0 C2C B:DHE501 4.3 42.4 1.0 HHB B:DHE501 4.3 50.2 1.0 C2B B:DHE501 4.3 42.6 1.0 CG B:HIS323 4.4 0.4 0.6 HHD B:DHE501 4.4 48.1 1.0 HHA B:DHE501 4.4 47.6 1.0 C3B B:DHE501 4.4 42.9 1.0 C3C B:DHE501 4.4 42.7 1.0 HH21 B:ARG164 4.5 59.6 1.0 H B:GLY148 4.6 56.9 1.0 NH2 B:ARG164 4.6 49.6 1.0 HD1 B:HIS147 4.7 68.5 1.0 HGB3 B:DHE501 4.7 52.8 1.0 HE1 B:PHE370 4.9 47.6 1.0 HGC3 B:DHE501 4.9 51.3 1.0 O2B B:DHE501 4.9 42.8 1.0

Iron binding site 4 out of 4 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 4 of Dihydro-Heme D1 Dehydrogenase Nirn in Complex with Dhe within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:42.2 occ:1.00 FE B:HEC502 0.0 42.2 1.0 ND B:HEC502 1.9 42.7 1.0 NA B:HEC502 2.0 42.1 1.0 NE2 B:HIS17 2.0 78.6 1.0 NC B:HEC502 2.1 45.3 1.0 NB B:HEC502 2.1 41.6 1.0 SD B:MET55 2.3 57.8 1.0 CE1 B:HIS17 2.8 77.3 1.0 HE1 B:HIS17 2.8 92.8 1.0 C4D B:HEC502 2.9 42.4 1.0 C1D B:HEC502 2.9 42.9 1.0 C1A B:HEC502 2.9 41.8 1.0 C4C B:HEC502 3.0 44.7 1.0 C4A B:HEC502 3.0 41.0 1.0 C4B B:HEC502 3.1 40.2 1.0 C1B B:HEC502 3.1 40.2 1.0 C1C B:HEC502 3.1 44.8 1.0 CD2 B:HIS17 3.2 79.4 1.0 HE1 B:MET55 3.2 70.0 1.0 CE B:MET55 3.2 58.2 1.0 CHA B:HEC502 3.3 42.0 1.0 CHD B:HEC502 3.4 43.8 1.0 HE2 B:MET55 3.4 70.0 1.0 CHB B:HEC502 3.5 40.3 1.0 CHC B:HEC502 3.5 42.2 1.0 HD2 B:HIS17 3.5 95.4 1.0 CG B:MET55 3.7 58.7 1.0 HG2 B:MET55 3.8 70.5 1.0 HB2 B:MET55 4.0 69.5 1.0 ND1 B:HIS17 4.0 77.3 1.0 HE3 B:MET55 4.1 70.0 1.0 HA B:MET55 4.1 69.5 1.0 C2D B:HEC502 4.1 42.9 1.0 C3D B:HEC502 4.1 42.2 1.0 C2A B:HEC502 4.2 40.8 1.0 C3A B:HEC502 4.2 40.3 1.0 CG B:HIS17 4.2 77.5 1.0 HHD B:HEC502 4.2 52.7 1.0 HD11 B:LEU29 4.2 46.2 1.0 HHA B:HEC502 4.2 50.4 1.0 C3C B:HEC502 4.3 42.7 1.0 C2B B:HEC502 4.3 38.9 1.0 C2C B:HEC502 4.3 44.2 1.0 HHB B:HEC502 4.3 48.5 1.0 CB B:MET55 4.3 57.8 1.0 C3B B:HEC502 4.3 37.5 1.0 HHC B:HEC502 4.4 50.8 1.0 HG3 B:MET55 4.4 70.5 1.0 HD2 B:PRO27 4.5 52.0 1.0 HD1 B:HIS17 4.7 92.9 1.0 CA B:MET55 4.8 57.8 1.0 HE1 B:PHE58 4.9 76.4 1.0 HD21 B:LEU29 5.0 45.1 1.0 HA3 B:GLY26 5.0 57.3 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