Iron in PDB 5m22: Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3

The structure of Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3, PDB code: 5m22 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 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.329, 126.090, 92.967, 90.00, 105.02, 90.00
R / Rfree (%)	17.8 / 25.4

The binding sites of Iron atom in the Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 (pdb code 5m22). 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, PDB code: 5m22:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:24.9 occ:1.00 OE2 B:GLU264 1.7 27.9 1.0 ND1 B:HIS258 2.0 24.1 1.0 NE2 B:HIS305 2.1 21.4 1.0 O B:HOH614 2.3 5.8 1.0 CD B:GLU264 2.7 25.7 1.0 CE1 B:HIS258 3.0 23.3 1.0 CE1 B:HIS305 3.0 20.4 1.0 OE1 B:GLU264 3.0 27.2 1.0 CG B:HIS258 3.1 24.0 1.0 CD2 B:HIS305 3.2 20.7 1.0 CB B:HIS258 3.5 22.6 1.0 O B:HOH624 4.1 32.8 1.0 NE2 B:HIS258 4.1 21.5 1.0 CG B:GLU264 4.1 23.9 1.0 CZ B:PHE266 4.1 21.2 1.0 ND1 B:HIS305 4.2 19.7 1.0 CD2 B:HIS258 4.2 23.3 1.0 CG B:HIS305 4.3 20.3 1.0 CE2 B:PHE78 4.3 27.1 1.0 CE1 B:PHE266 4.4 22.9 1.0 O B:HIS258 4.8 23.2 1.0 O B:HOH625 4.8 30.6 1.0 ND2 B:ASN260 4.8 23.4 1.0 CZ B:PHE78 4.9 25.5 1.0 CA B:HIS258 4.9 23.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:26.8 occ:1.00 OE1 D:GLU264 1.6 24.7 1.0 NE2 D:HIS305 2.0 25.9 1.0 ND1 D:HIS258 2.1 25.8 1.0 O D:HOH612 2.2 4.1 1.0 CD D:GLU264 2.7 29.0 1.0 CE1 D:HIS305 2.8 26.2 1.0 CG D:HIS258 3.0 26.2 1.0 CE1 D:HIS258 3.1 27.3 1.0 CD2 D:HIS305 3.1 26.0 1.0 OE2 D:GLU264 3.1 27.7 1.0 CB D:HIS258 3.3 25.9 1.0 CZ D:PHE266 3.8 23.7 1.0 ND1 D:HIS305 4.0 25.2 1.0 CG D:GLU264 4.0 29.1 1.0 NE2 D:HIS258 4.2 26.6 1.0 CD2 D:HIS258 4.2 26.1 1.0 CG D:HIS305 4.2 26.0 1.0 CE2 D:PHE78 4.3 26.6 1.0 CE1 D:PHE266 4.3 23.9 1.0 O D:HOH624 4.4 32.1 1.0 CZ D:PHE78 4.8 24.8 1.0 CA D:HIS258 4.8 24.6 1.0 CE2 D:PHE266 5.0 24.0 1.0 O D:HIS258 5.0 23.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe401 b:24.3 occ:1.00 OE1 F:GLU264 1.7 36.3 1.0 ND1 F:HIS258 1.9 20.5 1.0 NE2 F:HIS305 2.1 30.5 1.0 O F:HOH604 2.3 9.7 1.0 CD F:GLU264 2.8 36.3 1.0 CE1 F:HIS258 2.8 20.7 1.0 CG F:HIS258 2.9 21.6 1.0 CE1 F:HIS305 3.0 28.7 1.0 CD2 F:HIS305 3.1 30.4 1.0 OE2 F:GLU264 3.1 38.9 1.0 CB F:HIS258 3.4 22.2 1.0 NE2 F:HIS258 3.9 19.3 1.0 CZ F:PHE266 4.0 20.7 1.0 CD2 F:HIS258 4.0 20.5 1.0 CG F:GLU264 4.1 35.7 1.0 ND1 F:HIS305 4.1 28.5 1.0 CG F:HIS305 4.2 29.2 1.0 CE2 F:PHE78 4.3 29.3 1.0 CE1 F:PHE266 4.5 19.8 1.0 O F:HOH606 4.6 29.9 1.0 CZ F:PHE78 4.7 27.4 1.0 CA F:HIS258 4.8 24.1 1.0 O F:HIS258 4.9 20.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe401 b:25.9 occ:1.00 OE1 H:GLU264 1.5 37.3 1.0 ND1 H:HIS258 2.0 23.1 1.0 NE2 H:HIS305 2.1 25.9 1.0 O H:HOH614 2.3 21.9 1.0 CD H:GLU264 2.6 40.0 1.0 CE1 H:HIS258 2.9 23.1 1.0 CG H:HIS258 3.0 23.4 1.0 OE2 H:GLU264 3.1 42.8 1.0 CE1 H:HIS305 3.1 26.2 1.0 CD2 H:HIS305 3.2 26.8 1.0 CB H:HIS258 3.4 23.5 1.0 CG H:GLU264 3.9 38.3 1.0 CE2 H:PHE78 4.1 29.3 1.0 NE2 H:HIS258 4.1 23.4 1.0 CD2 H:HIS258 4.1 23.6 1.0 CZ H:PHE266 4.1 27.3 1.0 ND1 H:HIS305 4.2 27.7 1.0 CG H:HIS305 4.3 27.4 1.0 CE1 H:PHE266 4.5 27.0 1.0 CZ H:PHE78 4.6 27.7 1.0 O H:HIS258 4.6 24.4 1.0 CA H:HIS258 4.7 25.2 1.0 ND2 H:ASN260 4.9 33.1 1.0 C H:HIS258 4.9 25.0 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