Iron in PDB 5m21: Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 with 4-Hydroxybenzoate Bound

The structure of Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 with 4-Hydroxybenzoate Bound, PDB code: 5m21 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)	29.80 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.782, 124.869, 92.371, 90.00, 105.15, 90.00
R / Rfree (%)	17.9 / 24.2

The binding sites of Iron atom in the Crystal Structure of Hydroquinone 1,2-Dioxygenase From Sphingomonas Sp. TTNP3 with 4-Hydroxybenzoate Bound (pdb code 5m21). 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 with 4-Hydroxybenzoate Bound, PDB code: 5m21:
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 with 4-Hydroxybenzoate Bound


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 with 4-Hydroxybenzoate Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:28.4 occ:1.00 O1' B:PHB402 2.0 27.7 1.0 ND1 B:HIS258 2.1 22.5 1.0 NE2 B:HIS305 2.2 20.0 1.0 OE2 B:GLU264 2.2 36.6 1.0 O2' B:PHB402 2.3 37.0 1.0 C1' B:PHB402 2.5 28.0 1.0 OE1 B:GLU264 2.6 37.0 1.0 CD B:GLU264 2.7 31.6 1.0 CE1 B:HIS305 3.1 20.4 1.0 CE1 B:HIS258 3.1 20.8 1.0 CG B:HIS258 3.1 17.8 1.0 CD2 B:HIS305 3.3 19.4 1.0 CB B:HIS258 3.5 16.6 1.0 C1 B:PHB402 4.0 28.1 1.0 CG B:GLU264 4.0 29.3 1.0 CZ B:PHE266 4.1 20.9 1.0 NE2 B:HIS258 4.2 19.0 1.0 CD2 B:HIS258 4.2 18.9 1.0 ND1 B:HIS305 4.2 21.4 1.0 CG B:HIS305 4.4 19.2 1.0 CE1 B:PHE266 4.4 19.6 1.0 CE2 B:PHE78 4.6 34.6 1.0 ND2 B:ASN260 4.6 17.8 1.0 O B:HIS258 4.7 16.3 1.0 C2 B:PHB402 4.8 26.7 1.0 CA B:HIS258 4.8 16.8 1.0 CB B:ASN260 4.9 18.8 1.0 C6 B:PHB402 4.9 26.1 1.0 OE1 B:GLU319 4.9 37.8 1.0

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


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 with 4-Hydroxybenzoate Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:32.5 occ:1.00 O2' D:PHB402 1.8 44.6 1.0 OE1 D:GLU264 1.8 39.4 1.0 O1' D:PHB402 2.1 46.8 1.0 NE2 D:HIS305 2.2 19.6 1.0 C1' D:PHB402 2.2 32.1 1.0 ND1 D:HIS258 2.2 17.6 1.0 CD D:GLU264 2.8 33.7 1.0 CE1 D:HIS305 2.9 20.1 1.0 OE2 D:GLU264 3.0 36.1 1.0 CE1 D:HIS258 3.1 18.2 1.0 CG D:HIS258 3.2 16.5 1.0 CD2 D:HIS305 3.3 19.2 1.0 CB D:HIS258 3.5 15.3 1.0 C1 D:PHB402 3.7 29.2 1.0 CZ D:PHE266 4.1 20.7 1.0 CG D:GLU264 4.1 31.6 1.0 ND1 D:HIS305 4.1 18.7 1.0 NE2 D:HIS258 4.2 20.8 1.0 CD2 D:HIS258 4.3 18.0 1.0 CG D:HIS305 4.3 19.0 1.0 CE1 D:PHE266 4.4 20.0 1.0 C6 D:PHB402 4.5 27.5 1.0 CE2 D:PHE78 4.6 24.6 1.0 C2 D:PHB402 4.6 28.1 1.0 ND2 D:ASN260 4.7 25.0 1.0 OE2 D:GLU319 4.9 39.1 1.0 O D:HIS258 4.9 13.7 1.0 CA D:HIS258 4.9 16.1 1.0 CB D:ASN260 4.9 23.9 1.0 CZ D:PHE78 5.0 25.4 1.0

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


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 with 4-Hydroxybenzoate Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe401 b:35.2 occ:1.00 O2' F:PHB402 1.8 55.4 1.0 O1' F:PHB402 2.0 58.1 1.0 NE2 F:HIS305 2.1 26.3 1.0 ND1 F:HIS258 2.2 24.9 1.0 C1' F:PHB402 2.2 42.1 1.0 OE1 F:GLU264 2.4 39.8 1.0 CE1 F:HIS305 2.9 26.3 1.0 CD F:GLU264 2.9 33.7 1.0 OE2 F:GLU264 3.0 39.0 1.0 CE1 F:HIS258 3.1 24.6 1.0 CG F:HIS258 3.1 24.9 1.0 CD2 F:HIS305 3.3 24.5 1.0 CB F:HIS258 3.5 21.9 1.0 C1 F:PHB402 3.7 36.3 1.0 CZ F:PHE266 4.1 17.8 1.0 ND1 F:HIS305 4.1 26.9 1.0 NE2 F:HIS258 4.2 25.4 1.0 CD2 F:HIS258 4.3 26.6 1.0 CG F:HIS305 4.3 23.6 1.0 CG F:GLU264 4.3 34.9 1.0 C2 F:PHB402 4.5 32.8 1.0 CE1 F:PHE266 4.5 20.0 1.0 CE2 F:PHE78 4.5 32.1 1.0 C6 F:PHB402 4.6 33.6 1.0 ND2 F:ASN260 4.8 31.7 1.0 CA F:HIS258 4.8 21.9 1.0 O F:HIS258 4.9 19.7 1.0 CZ F:PHE78 5.0 29.3 1.0 OE2 F:GLU319 5.0 44.0 1.0

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


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 with 4-Hydroxybenzoate Bound within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe401 b:35.4 occ:1.00 O1' H:PHB402 1.7 36.8 1.0 ND1 H:HIS258 2.0 19.8 1.0 OE1 H:GLU264 2.2 43.0 1.0 NE2 H:HIS305 2.3 24.2 1.0 C1' H:PHB402 2.3 34.6 1.0 O2' H:PHB402 2.5 40.8 1.0 OE2 H:GLU264 2.7 39.0 1.0 CD H:GLU264 2.7 40.9 1.0 CE1 H:HIS258 2.9 19.6 1.0 CG H:HIS258 3.1 18.3 1.0 CD2 H:HIS305 3.3 23.2 1.0 CE1 H:HIS305 3.3 24.4 1.0 CB H:HIS258 3.5 18.4 1.0 C1 H:PHB402 3.8 33.0 1.0 NE2 H:HIS258 4.0 19.6 1.0 CG H:GLU264 4.1 37.0 1.0 CD2 H:HIS258 4.2 18.9 1.0 CZ H:PHE266 4.2 35.9 1.0 CG H:HIS305 4.4 25.5 1.0 ND1 H:HIS305 4.4 26.8 1.0 C6 H:PHB402 4.5 30.9 1.0 CE1 H:PHE266 4.5 36.7 1.0 ND2 H:ASN260 4.5 27.2 1.0 CE2 H:PHE78 4.6 32.0 1.0 C2 H:PHB402 4.8 33.4 1.0 CB H:ASN260 4.9 26.2 1.0 CZ H:PHE78 4.9 32.3 1.0 CA H:HIS258 4.9 19.5 1.0 O H:HIS258 4.9 20.6 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