Iron in PDB 3w08: Crystal Structure of Aldoxime Dehydratase

The structure of Crystal Structure of Aldoxime Dehydratase, PDB code: 3w08 was solved by H.Hashimoto, J.Nomura, Y.Hashimoto, K.I.Oinuma, K.Wada, A.Hishiki, K.Hara, M.Kobayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	152.946, 84.458, 76.360, 90.00, 114.32, 90.00
R / Rfree (%)	15.7 / 18.9

The binding sites of Iron atom in the Crystal Structure of Aldoxime Dehydratase (pdb code 3w08). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Aldoxime Dehydratase, PDB code: 3w08:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Aldoxime Dehydratase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Aldoxime Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:26.1 occ:1.00 FE A:HEM501 0.0 26.1 1.0 NE2 A:HIS299 1.9 21.5 1.0 NC A:HEM501 2.0 25.9 1.0 NA A:HEM501 2.0 26.9 1.0 ND A:HEM501 2.0 24.9 1.0 NB A:HEM501 2.1 27.9 1.0 CE1 A:HIS299 2.9 22.6 1.0 CD2 A:HIS299 3.0 23.8 1.0 C1C A:HEM501 3.0 28.0 1.0 C4B A:HEM501 3.0 29.2 1.0 C4C A:HEM501 3.0 26.1 1.0 C4D A:HEM501 3.0 25.5 1.0 C1D A:HEM501 3.0 25.2 1.0 C4A A:HEM501 3.0 29.4 1.0 C1A A:HEM501 3.1 28.1 1.0 C1B A:HEM501 3.1 30.1 1.0 CHC A:HEM501 3.3 31.7 1.0 CHD A:HEM501 3.4 26.2 1.0 CHA A:HEM501 3.4 26.7 1.0 CHB A:HEM501 3.4 30.6 1.0 ND1 A:HIS299 4.0 21.4 1.0 CG A:HIS299 4.1 23.1 1.0 C3C A:HEM501 4.2 25.1 1.0 C2C A:HEM501 4.2 26.0 1.0 C3B A:HEM501 4.3 31.1 1.0 C3D A:HEM501 4.3 22.8 1.0 C3A A:HEM501 4.3 28.8 1.0 C2D A:HEM501 4.3 24.2 1.0 C2A A:HEM501 4.3 27.2 1.0 C2B A:HEM501 4.3 29.8 1.0 OG A:SER219 4.8 25.1 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Aldoxime Dehydratase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Aldoxime Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:28.5 occ:1.00 FE B:HEM501 0.0 28.5 1.0 NE2 B:HIS299 1.9 23.1 1.0 NC B:HEM501 2.0 29.4 1.0 NA B:HEM501 2.0 28.9 1.0 ND B:HEM501 2.1 27.1 1.0 NB B:HEM501 2.1 30.5 1.0 CE1 B:HIS299 2.8 24.2 1.0 CD2 B:HIS299 3.0 23.8 1.0 C4B B:HEM501 3.0 31.1 1.0 C4C B:HEM501 3.0 28.3 1.0 C1C B:HEM501 3.0 29.8 1.0 C1D B:HEM501 3.0 26.4 1.0 C4D B:HEM501 3.0 27.0 1.0 C1A B:HEM501 3.1 29.9 1.0 C4A B:HEM501 3.1 31.6 1.0 C1B B:HEM501 3.1 32.8 1.0 CHC B:HEM501 3.4 31.9 1.0 CHD B:HEM501 3.4 28.2 1.0 CHA B:HEM501 3.4 28.7 1.0 CHB B:HEM501 3.4 33.3 1.0 ND1 B:HIS299 4.0 22.7 1.0 CG B:HIS299 4.0 24.2 1.0 C3C B:HEM501 4.2 29.0 1.0 C2C B:HEM501 4.3 27.9 1.0 C3A B:HEM501 4.3 31.6 1.0 C3B B:HEM501 4.3 33.7 1.0 C2A B:HEM501 4.3 29.6 1.0 C3D B:HEM501 4.3 24.5 1.0 C2D B:HEM501 4.3 24.7 1.0 C2B B:HEM501 4.4 32.6 1.0 OG B:SER219 4.8 27.3 1.0

J.Nomura, H.Hashimoto, T.Ohta, Y.Hashimoto, K.Wada, Y.Naruta, K.I.Oinuma, M.Kobayashi. Crystal Structure of Aldoxime Dehydratase and Its Catalytic Mechanism Involved in Carbon-Nitrogen Triple-Bond Synthesis. Proc.Natl.Acad.Sci.Usa 2013.
ISSN: ESSN 1091-6490
PubMed: 23382199
DOI: 10.1073/PNAS.1200338110