Iron in PDB 5m4o: Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol

The structure of Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol, PDB code: 5m4o was solved by M.Ferraroni, S.Da Vela, A.Scozzafava, B.Kolvenbach, P.F.X.Corvini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.70 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.992, 125.982, 92.331, 90.00, 105.14, 90.00
R / Rfree (%)	18.8 / 24.9

The binding sites of Iron atom in the Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol (pdb code 5m4o). 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 Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol, PDB code: 5m4o:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol


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 Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:25.3 occ:1.00 O3 B:NPO402 2.0 33.9 1.0 OE2 B:GLU264 2.0 38.8 1.0 ND1 B:HIS258 2.1 28.3 1.0 NE2 B:HIS305 2.1 25.4 1.0 O2 B:NPO402 2.4 37.2 1.0 N1 B:NPO402 2.5 32.9 1.0 CD B:GLU264 2.8 36.5 1.0 CE1 B:HIS305 2.9 25.7 1.0 OE1 B:GLU264 3.0 40.0 1.0 CE1 B:HIS258 3.0 28.6 1.0 CG B:HIS258 3.1 27.2 1.0 CD2 B:HIS305 3.3 25.5 1.0 CB B:HIS258 3.4 24.8 1.0 C1 B:NPO402 3.9 31.6 1.0 ND1 B:HIS305 4.1 24.9 1.0 NE2 B:HIS258 4.1 28.2 1.0 CG B:GLU264 4.1 33.6 1.0 CZ B:PHE266 4.2 25.8 1.0 CD2 B:HIS258 4.2 27.8 1.0 CG B:HIS305 4.3 25.4 1.0 CE1 B:PHE266 4.5 25.6 1.0 CE2 B:PHE78 4.5 32.7 1.0 O B:HIS258 4.7 22.8 1.0 C6 B:NPO402 4.7 29.7 1.0 ND2 B:ASN260 4.8 25.6 1.0 CA B:HIS258 4.8 24.6 1.0 C2 B:NPO402 4.8 30.2 1.0 C B:HIS258 5.0 23.8 1.0 OE2 B:GLU319 5.0 37.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol


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 Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:37.5 occ:1.00 OE1 D:GLU264 1.5 45.4 1.0 O3 D:NPO402 1.8 37.7 1.0 NE2 D:HIS305 2.1 28.9 1.0 ND1 D:HIS258 2.1 32.9 1.0 N1 D:NPO402 2.4 33.6 1.0 O2 D:NPO402 2.5 38.3 1.0 CD D:GLU264 2.6 46.4 1.0 CE1 D:HIS305 2.8 28.9 1.0 O D:HOH526 2.8 41.4 1.0 CE1 D:HIS258 3.0 34.0 1.0 CG D:HIS258 3.2 31.8 1.0 OE2 D:GLU264 3.2 48.2 1.0 CD2 D:HIS305 3.3 27.5 1.0 CB D:HIS258 3.5 29.7 1.0 C1 D:NPO402 3.7 33.4 1.0 CG D:GLU264 3.8 43.4 1.0 CZ D:PHE266 3.9 33.0 1.0 ND1 D:HIS305 4.0 28.9 1.0 NE2 D:HIS258 4.2 34.2 1.0 CD2 D:HIS258 4.3 32.5 1.0 CG D:HIS305 4.3 28.5 1.0 C6 D:NPO402 4.4 33.2 1.0 CE2 D:PHE78 4.6 32.3 1.0 CE1 D:PHE266 4.7 32.9 1.0 C2 D:NPO402 4.7 31.8 1.0 O D:HIS258 4.7 26.7 1.0 ND2 D:ASN260 4.7 49.4 1.0 CE2 D:PHE266 4.8 34.2 1.0 CA D:HIS258 4.9 29.6 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol


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 Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe401 b:32.5 occ:1.00 NE2 F:HIS305 2.0 30.3 1.0 O2 F:NPO402 2.0 43.3 1.0 O3 F:NPO402 2.0 42.1 1.0 ND1 F:HIS258 2.1 34.6 1.0 OE1 F:GLU264 2.2 49.1 1.0 N1 F:NPO402 2.4 36.9 1.0 CD F:GLU264 2.9 46.6 1.0 CE1 F:HIS305 2.9 31.7 1.0 CE1 F:HIS258 3.0 36.4 1.0 OE2 F:GLU264 3.1 50.5 1.0 CD2 F:HIS305 3.1 31.0 1.0 CG F:HIS258 3.1 34.7 1.0 O F:HOH576 3.4 80.2 1.0 CB F:HIS258 3.5 33.0 1.0 C1 F:NPO402 3.7 34.9 1.0 ND1 F:HIS305 4.1 32.6 1.0 NE2 F:HIS258 4.1 36.9 1.0 CG F:HIS305 4.2 30.6 1.0 CD2 F:HIS258 4.2 35.8 1.0 CZ F:PHE266 4.2 24.8 1.0 CG F:GLU264 4.3 43.8 1.0 C2 F:NPO402 4.6 32.7 1.0 C6 F:NPO402 4.6 32.8 1.0 CE2 F:PHE78 4.6 33.4 1.0 CE1 F:PHE266 4.6 25.5 1.0 ND2 F:ASN260 4.7 38.5 1.0 O F:HIS258 4.7 29.7 1.0 CA F:HIS258 4.9 31.7 1.0 CB F:ASN260 5.0 40.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol


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 Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with 4-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe401 b:42.1 occ:1.00 O2 H:NPO402 1.7 48.5 1.0 OE1 H:GLU264 1.9 55.1 1.0 ND1 H:HIS258 1.9 33.8 1.0 NE2 H:HIS305 2.1 37.3 1.0 N1 H:NPO402 2.5 45.0 1.0 O3 H:NPO402 2.6 47.8 1.0 CD H:GLU264 2.7 54.2 1.0 CE1 H:HIS258 2.8 34.1 1.0 CE1 H:HIS305 2.9 38.5 1.0 OE2 H:GLU264 2.9 53.0 1.0 CG H:HIS258 3.0 34.4 1.0 CD2 H:HIS305 3.3 35.2 1.0 CB H:HIS258 3.5 34.3 1.0 C1 H:NPO402 3.8 41.7 1.0 NE2 H:HIS258 4.0 35.3 1.0 ND1 H:HIS305 4.1 38.1 1.0 CD2 H:HIS258 4.1 33.9 1.0 CG H:GLU264 4.1 51.8 1.0 CZ H:PHE266 4.2 40.8 1.0 CG H:HIS305 4.3 35.0 1.0 C2 H:NPO402 4.5 39.9 1.0 O H:HIS258 4.5 33.6 1.0 CE1 H:PHE266 4.6 38.9 1.0 CE2 H:PHE78 4.6 36.7 1.0 ND2 H:ASN260 4.7 49.3 1.0 CA H:HIS258 4.8 35.0 1.0 C6 H:NPO402 4.8 39.2 1.0 C H:HIS258 4.9 34.4 1.0 CB H:ASN260 4.9 46.5 1.0

M.Ferraroni, S.Da Vela, B.A.Kolvenbach, P.F.Corvini, A.Scozzafava. The Crystal Structures of Native Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 and of Substrate and Inhibitor Complexes. Biochim. Biophys. Acta V.1865 520 2017.
ISSN: ISSN 0006-3002
PubMed: 28232026
DOI: 10.1016/J.BBAPAP.2017.02.013