Iron in PDB 5m26: Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with Methylhydroquinone

The structure of Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with Methylhydroquinone, PDB code: 5m26 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)	30.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.406, 125.231, 91.352, 90.00, 102.55, 90.00
R / Rfree (%)	16 / 20.7

The binding sites of Iron atom in the Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 in Complex with Methylhydroquinone (pdb code 5m26). 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 Methylhydroquinone, PDB code: 5m26:
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 Methylhydroquinone


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 Methylhydroquinone within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:19.0 occ:1.00 OE2 B:GLU264 1.9 25.3 1.0 O1 B:7DV402 1.9 19.3 1.0 NE2 B:HIS305 2.1 14.1 1.0 ND1 B:HIS258 2.1 16.7 1.0 O B:HOH532 2.5 58.8 1.0 CD B:GLU264 2.8 24.7 1.0 CE1 B:HIS305 3.0 14.4 1.0 OE1 B:GLU264 3.1 30.1 1.0 CE1 B:HIS258 3.1 16.3 1.0 CD2 B:HIS305 3.1 14.4 1.0 CG B:HIS258 3.2 15.8 1.0 C1 B:7DV402 3.3 21.6 1.0 CB B:HIS258 3.5 14.6 1.0 CZ B:PHE266 4.0 13.4 1.0 C6 B:7DV402 4.1 20.8 1.0 C7 B:7DV402 4.1 23.1 1.0 ND1 B:HIS305 4.2 14.3 1.0 CG B:GLU264 4.2 21.9 1.0 C2 B:7DV402 4.2 21.9 1.0 NE2 B:HIS258 4.2 16.3 1.0 CG B:HIS305 4.3 13.6 1.0 CD2 B:HIS258 4.3 15.7 1.0 CE1 B:PHE266 4.4 13.3 1.0 CE2 B:PHE78 4.4 24.2 1.0 O B:HIS258 4.8 12.7 1.0 CA B:HIS258 4.9 14.6 1.0 ND2 B:ASN260 5.0 20.7 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 Methylhydroquinone


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 Methylhydroquinone within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:22.1 occ:1.00 OE1 D:GLU264 1.8 35.5 1.0 O1 D:7DV402 1.9 21.7 1.0 NE2 D:HIS305 2.2 17.6 1.0 ND1 D:HIS258 2.2 13.3 1.0 CD D:GLU264 2.7 30.7 1.0 OE2 D:GLU264 3.0 36.1 1.0 CE1 D:HIS305 3.0 17.5 1.0 CG D:HIS258 3.1 12.9 1.0 CE1 D:HIS258 3.1 14.0 1.0 C1 D:7DV402 3.2 21.9 1.0 CD2 D:HIS305 3.2 15.9 1.0 CB D:HIS258 3.4 12.1 1.0 C6 D:7DV402 4.0 22.5 1.0 C7 D:7DV402 4.0 24.3 1.0 C2 D:7DV402 4.0 22.4 1.0 CG D:GLU264 4.1 25.3 1.0 CZ D:PHE266 4.1 14.6 1.0 ND1 D:HIS305 4.2 16.4 1.0 NE2 D:HIS258 4.3 13.8 1.0 CD2 D:HIS258 4.3 13.1 1.0 CE1 D:PHE266 4.3 14.6 1.0 CG D:HIS305 4.3 16.0 1.0 CE2 D:PHE78 4.5 25.2 1.0 O D:HIS258 4.8 11.9 1.0 CA D:HIS258 4.8 12.1 1.0 OE2 D:GLU319 5.0 27.4 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 Methylhydroquinone


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 Methylhydroquinone within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe401 b:23.3 occ:1.00 O1 F:7DV402 1.8 24.1 1.0 OE1 F:GLU264 1.9 31.4 1.0 NE2 F:HIS305 2.1 19.1 1.0 ND1 F:HIS258 2.1 19.8 1.0 CD F:GLU264 2.8 29.3 1.0 CE1 F:HIS305 3.0 19.2 1.0 CE1 F:HIS258 3.1 20.1 1.0 OE2 F:GLU264 3.1 33.6 1.0 C1 F:7DV402 3.1 25.4 1.0 CD2 F:HIS305 3.1 20.0 1.0 CG F:HIS258 3.2 18.4 1.0 CB F:HIS258 3.5 17.8 1.0 C6 F:7DV402 3.9 27.5 1.0 C2 F:7DV402 4.0 26.1 1.0 C7 F:7DV402 4.1 36.1 0.0 CG F:GLU264 4.1 25.7 1.0 CZ F:PHE266 4.1 16.5 1.0 ND1 F:HIS305 4.2 19.6 1.0 NE2 F:HIS258 4.2 20.1 1.0 CG F:HIS305 4.3 19.0 1.0 CD2 F:HIS258 4.3 18.8 1.0 CE2 F:PHE78 4.3 29.7 1.0 CE1 F:PHE266 4.4 16.0 1.0 O F:HIS258 4.8 18.9 1.0 CA F:HIS258 4.9 18.8 1.0 OE1 F:GLU319 4.9 30.5 1.0 ND2 F:ASN260 4.9 23.0 1.0 CZ F:PHE78 5.0 29.6 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 Methylhydroquinone


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 Methylhydroquinone within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe401 b:24.3 occ:1.00 O1 H:7DV402 1.9 24.5 1.0 OE1 H:GLU264 2.0 31.7 1.0 ND1 H:HIS258 2.1 16.5 1.0 NE2 H:HIS305 2.1 16.1 1.0 CD H:GLU264 2.6 30.7 1.0 OE2 H:GLU264 2.7 33.9 1.0 CE1 H:HIS258 3.0 16.6 1.0 CE1 H:HIS305 3.0 17.6 1.0 CG H:HIS258 3.1 15.9 1.0 C1 H:7DV402 3.1 25.6 1.0 CD2 H:HIS305 3.2 17.0 1.0 CB H:HIS258 3.5 15.7 1.0 C6 H:7DV402 3.9 26.9 1.0 CG H:GLU264 4.0 28.0 1.0 C2 H:7DV402 4.1 26.4 1.0 CZ H:PHE266 4.1 20.4 1.0 NE2 H:HIS258 4.1 16.9 1.0 ND1 H:HIS305 4.2 18.1 1.0 C7 H:7DV402 4.2 20.0 0.0 CD2 H:HIS258 4.2 15.9 1.0 CG H:HIS305 4.3 17.3 1.0 CE1 H:PHE266 4.4 20.0 1.0 CE2 H:PHE78 4.5 26.3 1.0 OE2 H:GLU319 4.8 15.0 0.5 O H:HIS258 4.9 16.5 1.0 CA H:HIS258 4.9 15.4 1.0 ND2 H:ASN260 4.9 19.4 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