Iron in PDB 3a15: Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre)

All present enzymatic activity of Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre):
4.99.1.5;

The structure of Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre), PDB code: 3a15 was solved by H.Sawai, H.Sugimoto, Y.Kato, Y.Asano, Y.Shiro, S.Aono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	97.904, 77.066, 104.831, 90.00, 101.06, 90.00
R / Rfree (%)	16.1 / 19.3

The binding sites of Iron atom in the Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre) (pdb code 3a15). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre), PDB code: 3a15:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre)


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 Substrate-Free Form of Aldoxime Dehydratase (Oxdre) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe354 b:17.1 occ:1.00 FE A:HEM354 0.0 17.1 1.0 NC A:HEM354 2.0 14.1 1.0 NA A:HEM354 2.0 15.5 1.0 NB A:HEM354 2.0 15.9 1.0 ND A:HEM354 2.1 16.3 1.0 NE2 A:HIS299 2.1 18.6 1.0 O A:HOH401 2.9 26.5 1.0 C1C A:HEM354 3.0 15.8 1.0 C4B A:HEM354 3.0 16.8 1.0 C4A A:HEM354 3.0 16.1 1.0 C4C A:HEM354 3.1 15.7 1.0 C1A A:HEM354 3.1 17.5 1.0 C1B A:HEM354 3.1 17.6 1.0 C1D A:HEM354 3.1 15.4 1.0 CE1 A:HIS299 3.1 18.9 1.0 C4D A:HEM354 3.1 17.5 1.0 CD2 A:HIS299 3.2 18.1 1.0 CHC A:HEM354 3.4 16.6 1.0 CHB A:HEM354 3.4 17.6 1.0 CHA A:HEM354 3.4 17.0 1.0 CHD A:HEM354 3.4 15.9 1.0 ND1 A:HIS299 4.2 18.1 1.0 C2C A:HEM354 4.2 14.6 1.0 C3B A:HEM354 4.3 17.1 1.0 CG A:HIS299 4.3 18.3 1.0 C3A A:HEM354 4.3 16.6 1.0 C3C A:HEM354 4.3 15.0 1.0 C2A A:HEM354 4.3 17.9 1.0 C2B A:HEM354 4.3 16.1 1.0 C2D A:HEM354 4.3 14.9 1.0 C3D A:HEM354 4.3 14.9 1.0 OG A:SER219 4.9 20.6 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre)


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 Substrate-Free Form of Aldoxime Dehydratase (Oxdre) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe354 b:17.5 occ:1.00 FE B:HEM354 0.0 17.5 1.0 NC B:HEM354 2.0 16.2 1.0 NB B:HEM354 2.0 16.9 1.0 ND B:HEM354 2.0 16.7 1.0 NE2 B:HIS299 2.0 18.3 1.0 NA B:HEM354 2.1 15.7 1.0 O B:HOH401 2.2 21.1 1.0 C1C B:HEM354 3.0 16.3 1.0 C4C B:HEM354 3.0 15.5 1.0 CE1 B:HIS299 3.0 18.4 1.0 C4B B:HEM354 3.0 16.5 1.0 CD2 B:HIS299 3.0 17.8 1.0 C1B B:HEM354 3.0 18.7 1.0 C4A B:HEM354 3.1 16.4 1.0 C1D B:HEM354 3.1 17.5 1.0 C4D B:HEM354 3.1 15.1 1.0 C1A B:HEM354 3.1 15.3 1.0 CHC B:HEM354 3.4 15.9 1.0 CHB B:HEM354 3.4 17.6 1.0 CHD B:HEM354 3.4 15.8 1.0 CHA B:HEM354 3.5 15.4 1.0 ND1 B:HIS299 4.1 18.0 1.0 CG B:HIS299 4.2 17.0 1.0 C2C B:HEM354 4.2 15.2 1.0 C3C B:HEM354 4.2 16.1 1.0 C3B B:HEM354 4.3 18.3 1.0 C2B B:HEM354 4.3 17.9 1.0 C3A B:HEM354 4.3 14.7 1.0 C3D B:HEM354 4.3 15.3 1.0 C2D B:HEM354 4.3 15.3 1.0 C2A B:HEM354 4.3 15.9 1.0 OG B:SER219 4.7 20.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe354 b:23.6 occ:1.00 FE C:HEM354 0.0 23.6 1.0 NE2 C:HIS299 2.0 24.0 1.0 NC C:HEM354 2.0 21.8 1.0 ND C:HEM354 2.0 22.5 1.0 NB C:HEM354 2.1 22.6 1.0 NA C:HEM354 2.1 23.0 1.0 O C:HOH401 2.2 27.1 1.0 CE1 C:HIS299 2.9 23.9 1.0 C4C C:HEM354 3.0 20.7 1.0 C1D C:HEM354 3.0 21.4 1.0 C1C C:HEM354 3.0 20.4 1.0 C4D C:HEM354 3.1 21.3 1.0 C4B C:HEM354 3.1 21.0 1.0 C1A C:HEM354 3.1 22.7 1.0 C1B C:HEM354 3.1 21.3 1.0 CD2 C:HIS299 3.1 25.5 1.0 C4A C:HEM354 3.1 22.3 1.0 CHD C:HEM354 3.4 20.7 1.0 CHA C:HEM354 3.4 22.3 1.0 CHC C:HEM354 3.4 21.5 1.0 CHB C:HEM354 3.5 22.6 1.0 ND1 C:HIS299 4.0 26.6 1.0 CG C:HIS299 4.2 26.0 1.0 C2C C:HEM354 4.3 21.4 1.0 C3C C:HEM354 4.3 21.4 1.0 C2D C:HEM354 4.3 20.8 1.0 C3D C:HEM354 4.3 21.9 1.0 C3B C:HEM354 4.3 21.4 1.0 C2B C:HEM354 4.3 22.1 1.0 C2A C:HEM354 4.3 23.0 1.0 C3A C:HEM354 4.3 23.2 1.0 OG C:SER219 5.0 26.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (Oxdre) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe354 b:23.6 occ:1.00 FE D:HEM354 0.0 23.6 1.0 NC D:HEM354 2.0 22.3 1.0 NE2 D:HIS299 2.0 25.9 1.0 NA D:HEM354 2.0 23.4 1.0 ND D:HEM354 2.0 22.7 1.0 NB D:HEM354 2.1 23.7 1.0 O D:HOH401 2.1 26.6 1.0 CE1 D:HIS299 2.9 27.3 1.0 C1C D:HEM354 3.0 26.3 1.0 C4C D:HEM354 3.0 24.5 1.0 C1D D:HEM354 3.0 22.9 1.0 C4A D:HEM354 3.0 23.4 1.0 C1A D:HEM354 3.1 22.6 1.0 C4B D:HEM354 3.1 24.7 1.0 C4D D:HEM354 3.1 23.0 1.0 CD2 D:HIS299 3.1 25.6 1.0 C1B D:HEM354 3.1 24.1 1.0 CHD D:HEM354 3.4 23.2 1.0 CHC D:HEM354 3.4 24.2 1.0 CHA D:HEM354 3.4 23.7 1.0 CHB D:HEM354 3.4 24.1 1.0 ND1 D:HIS299 4.1 26.6 1.0 CG D:HIS299 4.2 25.8 1.0 C2C D:HEM354 4.2 26.0 1.0 C3C D:HEM354 4.2 25.2 1.0 C3A D:HEM354 4.3 23.8 1.0 C2D D:HEM354 4.3 21.8 1.0 C2A D:HEM354 4.3 23.6 1.0 C3D D:HEM354 4.3 23.8 1.0 C3B D:HEM354 4.3 23.5 1.0 C2B D:HEM354 4.3 24.5 1.0 OG D:SER219 4.8 30.1 1.0

H.Sawai, H.Sugimoto, Y.Kato, Y.Asano, Y.Shiro, S.Aono. X-Ray Crystal Structure of Michaelis Complex of Aldoxime Dehydratase J.Biol.Chem. V. 284 32089 2009.
ISSN: ISSN 0021-9258
PubMed: 19740758
DOI: 10.1074/JBC.M109.018762