Iron in PDB 6j63: Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc:
1.13.11.27;

The structure of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc, PDB code: 6j63 was solved by W.C.Yang, G.F.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.19 / 2.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.660, 95.960, 97.930, 90.00, 92.15, 90.00
R / Rfree (%)	27.8 / 30.1

The structure of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Iron atom in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc (pdb code 6j63). 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 Arabidopsis Thaliana Hppd Complexed with Ntbc, PDB code: 6j63:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


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 Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:17.6 occ:1.00 O1 A:NTD502 2.0 20.5 1.0 O7 A:NTD502 2.1 18.1 1.0 OE1 A:GLU394 2.1 15.5 1.0 NE2 A:HIS308 2.2 17.1 1.0 NE2 A:HIS226 2.2 16.6 1.0 C5 A:NTD502 2.7 21.0 1.0 CE1 A:HIS308 2.9 17.1 1.0 CD A:GLU394 3.0 15.6 1.0 C7 A:NTD502 3.1 19.8 1.0 OE2 A:GLU394 3.2 14.3 1.0 CD2 A:HIS226 3.2 16.7 1.0 CE1 A:HIS226 3.2 16.3 1.0 CD2 A:HIS308 3.3 17.1 1.0 C6 A:NTD502 3.3 20.4 1.0 C2 A:NTD502 3.7 20.5 1.0 ND1 A:HIS308 4.1 17.0 1.0 CG A:HIS308 4.3 16.5 1.0 ND1 A:HIS226 4.3 16.3 1.0 CG A:HIS226 4.3 16.9 1.0 CG A:GLU394 4.3 16.2 1.0 O A:PHE419 4.4 19.3 1.0 CG2 A:VAL228 4.5 15.7 1.0 C8 A:NTD502 4.5 20.6 1.0 CB A:ALA310 4.6 17.4 1.0 CD1 A:PHE419 4.6 18.3 1.0 CE2 A:PHE381 4.6 18.5 1.0 CB A:GLU394 4.7 16.3 1.0 C1 A:NTD502 4.7 20.9 1.0 ON1 A:NTD502 4.8 24.6 1.0 CB A:PHE419 4.8 18.9 1.0 CZ A:PHE381 5.0 18.6 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


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 Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:12.3 occ:1.00 O1 B:NTD502 1.9 17.6 1.0 O7 B:NTD502 1.9 19.3 1.0 OE1 B:GLU394 2.0 14.7 1.0 NE2 B:HIS226 2.5 16.4 1.0 NE2 B:HIS308 2.5 16.3 1.0 C5 B:NTD502 2.7 20.0 1.0 CD B:GLU394 2.8 15.6 1.0 OE2 B:GLU394 2.9 15.0 1.0 C7 B:NTD502 2.9 20.5 1.0 CE1 B:HIS308 3.1 16.2 1.0 C6 B:NTD502 3.3 20.3 1.0 CE1 B:HIS226 3.3 16.4 1.0 CD2 B:HIS226 3.6 16.1 1.0 CD2 B:HIS308 3.6 16.4 1.0 C2 B:NTD502 3.8 19.1 1.0 O B:PHE419 4.0 21.6 1.0 ND1 B:HIS308 4.2 16.5 1.0 CG B:GLU394 4.2 16.2 1.0 C8 B:NTD502 4.3 22.9 1.0 CE2 B:PHE381 4.4 18.8 1.0 ND1 B:HIS226 4.5 16.5 1.0 CG B:HIS308 4.5 16.1 1.0 CG B:HIS226 4.6 16.5 1.0 CD1 B:PHE419 4.6 16.6 1.0 CZ B:PHE381 4.6 19.1 1.0 CB B:PHE419 4.7 17.4 1.0 CB B:GLU394 4.7 16.4 1.0 C1 B:NTD502 4.7 20.8 1.0 NE2 B:GLN379 4.7 19.5 1.0 CB B:ALA310 4.8 15.7 1.0 CG2 B:VAL228 4.8 15.6 1.0 ON2 B:NTD502 4.9 33.4 1.0 N B:NTD502 5.0 30.9 1.0 C B:PHE419 5.0 20.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


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 Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:16.1 occ:1.00 OE1 C:GLU394 2.0 18.2 1.0 O1 C:NTD502 2.0 18.0 1.0 O7 C:NTD502 2.1 22.6 1.0 NE2 C:HIS226 2.2 18.6 1.0 NE2 C:HIS308 2.4 17.6 1.0 C5 C:NTD502 2.7 22.1 1.0 CD C:GLU394 2.9 18.4 1.0 OE2 C:GLU394 3.0 17.2 1.0 CE1 C:HIS226 3.1 18.7 1.0 CE1 C:HIS308 3.1 17.8 1.0 CD2 C:HIS226 3.3 18.0 1.0 C7 C:NTD502 3.3 22.8 1.0 CD2 C:HIS308 3.4 18.1 1.0 C6 C:NTD502 3.5 22.5 1.0 C2 C:NTD502 3.7 20.9 1.0 ND1 C:HIS226 4.2 18.9 1.0 ND1 C:HIS308 4.2 18.1 1.0 O C:PHE419 4.2 19.9 1.0 CG C:GLU394 4.3 18.0 1.0 CG C:HIS226 4.3 18.2 1.0 CG C:HIS308 4.4 17.5 1.0 C8 C:NTD502 4.5 24.6 1.0 CB C:ALA310 4.6 16.5 1.0 CD1 C:PHE419 4.6 19.9 1.0 CE1 C:PHE381 4.6 23.4 1.0 CB C:GLU394 4.6 18.2 1.0 C1 C:NTD502 4.6 21.5 1.0 CG2 C:VAL228 4.7 17.1 1.0 CB C:PHE419 4.8 21.1 1.0 CZ C:PHE381 4.9 24.0 1.0 NE2 C:GLN379 4.9 22.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


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 Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:14.9 occ:1.00 O7 D:NTD502 2.0 21.4 1.0 OE2 D:GLU394 2.1 20.5 1.0 NE2 D:HIS226 2.3 20.6 1.0 NE2 D:HIS308 2.3 17.1 1.0 O1 D:NTD502 2.5 34.6 1.0 CE1 D:HIS308 2.9 17.1 1.0 CD D:GLU394 3.0 19.3 1.0 C5 D:NTD502 3.1 30.7 1.0 C7 D:NTD502 3.2 24.9 1.0 CE1 D:HIS226 3.2 20.3 1.0 OE1 D:GLU394 3.3 17.9 1.0 CD2 D:HIS226 3.3 20.3 1.0 CD2 D:HIS308 3.5 17.5 1.0 C6 D:NTD502 3.6 26.6 1.0 ND1 D:HIS308 4.1 17.4 1.0 C2 D:NTD502 4.2 30.3 1.0 O D:PHE419 4.2 23.8 1.0 ND1 D:HIS226 4.3 19.5 1.0 CG D:GLU394 4.3 18.9 1.0 CG D:HIS308 4.4 17.3 1.0 CG D:HIS226 4.4 19.7 1.0 C8 D:NTD502 4.5 24.2 1.0 CG2 D:VAL228 4.6 17.4 1.0 CD1 D:PHE419 4.6 22.9 1.0 CE2 D:PHE381 4.7 22.5 1.0 CB D:PHE419 4.7 23.4 1.0 CB D:ALA310 4.8 17.0 1.0 ON1 D:NTD502 4.8 34.8 1.0 CZ D:PHE381 4.9 23.0 1.0

H.Y.Lin, J.F.Yang, D.W.Wang, G.F.Hao, J.Q.Dong, Y.X.Wang, W.C.Yang, J.W.Wu, C.G.Zhan, G.F.Yang. Molecular Insights Into the Mechanism of 4-Hydroxyphenylpyruvate Dioxygenase Inhibition: Enzyme Kinetics, X-Ray Crystallography and Computational Simulations. Febs J. V. 286 975 2019.
ISSN: ISSN 1742-4658
PubMed: 30632699
DOI: 10.1111/FEBS.14747