Iron in PDB 1b4u: Protocatechuate 4,5-Dioxygenase (Ligab) in Complex with Protocatechuate (Pca)

All present enzymatic activity of Protocatechuate 4,5-Dioxygenase (Ligab) in Complex with Protocatechuate (Pca):
1.13.11.8;

The structure of Protocatechuate 4,5-Dioxygenase (Ligab) in Complex with Protocatechuate (Pca), PDB code: 1b4u was solved by K.Sugimoto, T.Senda, Y.Mitsui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.400, 66.500, 119.800, 90.00, 92.50, 90.00
R / Rfree (%)	16.1 / 22

The binding sites of Iron atom in the Protocatechuate 4,5-Dioxygenase (Ligab) in Complex with Protocatechuate (Pca) (pdb code 1b4u). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Protocatechuate 4,5-Dioxygenase (Ligab) in Complex with Protocatechuate (Pca), PDB code: 1b4u:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Protocatechuate 4,5-Dioxygenase (Ligab) in Complex with Protocatechuate (Pca)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Protocatechuate 4,5-Dioxygenase (Ligab) in Complex with Protocatechuate (Pca) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:19.6 occ:1.00 OE2 B:GLU242 2.1 21.7 1.0 NE2 B:HIS12 2.2 15.2 1.0 O4 B:DHB503 2.2 18.6 1.0 NE2 B:HIS61 2.3 19.8 1.0 O3 B:DHB503 2.4 23.3 1.0 CD B:GLU242 2.9 20.4 1.0 OE1 B:GLU242 3.0 18.9 1.0 CD2 B:HIS12 3.1 13.8 1.0 C4 B:DHB503 3.1 21.6 1.0 C3 B:DHB503 3.2 22.6 1.0 CD2 B:HIS61 3.2 15.2 1.0 CE1 B:HIS12 3.3 13.3 1.0 CE1 B:HIS61 3.3 19.4 1.0 NE2 B:HIS127 3.9 15.8 1.0 OH A:TYR90 4.1 45.4 1.0 ND2 B:ASN59 4.1 19.2 1.0 CG B:GLU242 4.3 17.6 1.0 CG B:HIS61 4.3 17.5 1.0 CG B:HIS12 4.3 14.7 1.0 ND1 B:HIS12 4.3 13.8 1.0 ND1 B:HIS61 4.4 15.4 1.0 C5 B:DHB503 4.4 21.1 1.0 OD1 B:ASN59 4.4 20.9 1.0 NE2 B:HIS195 4.5 22.4 1.0 O B:HOH506 4.5 15.8 1.0 C2 B:DHB503 4.5 20.8 1.0 CE1 A:TYR90 4.6 39.5 1.0 CD2 B:HIS127 4.7 16.9 1.0 CG B:ASN59 4.7 18.9 1.0 CZ A:TYR90 4.8 39.8 1.0 CE1 B:HIS127 4.9 14.7 1.0

Iron binding site 2 out of 2 in the Protocatechuate 4,5-Dioxygenase (Ligab) in Complex with Protocatechuate (Pca)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Protocatechuate 4,5-Dioxygenase (Ligab) in Complex with Protocatechuate (Pca) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:23.0 occ:1.00 O4 D:DHB504 2.1 26.0 1.0 OE2 D:GLU242 2.2 25.3 1.0 NE2 D:HIS61 2.2 19.8 1.0 NE2 D:HIS12 2.2 17.8 1.0 O3 D:DHB504 2.5 24.1 1.0 C4 D:DHB504 2.9 26.2 1.0 CD D:GLU242 3.0 24.8 1.0 C3 D:DHB504 3.1 27.8 1.0 CD2 D:HIS12 3.1 18.1 1.0 CD2 D:HIS61 3.1 18.4 1.0 OE1 D:GLU242 3.2 23.1 1.0 CE1 D:HIS61 3.2 22.2 1.0 CE1 D:HIS12 3.3 19.5 1.0 NE2 D:HIS127 3.8 20.5 1.0 OH C:TYR90 3.9 43.3 1.0 ND2 D:ASN59 4.1 22.3 1.0 C5 D:DHB504 4.2 26.4 1.0 CG D:HIS61 4.3 19.6 1.0 ND1 D:HIS61 4.3 20.7 1.0 CG D:HIS12 4.3 20.6 1.0 CG D:GLU242 4.4 22.8 1.0 OD1 D:ASN59 4.4 24.6 1.0 ND1 D:HIS12 4.4 20.6 1.0 C2 D:DHB504 4.5 25.7 1.0 O D:HOH517 4.6 29.7 1.0 CD2 D:HIS127 4.7 19.6 1.0 CZ C:TYR90 4.7 40.5 1.0 NE2 D:HIS195 4.7 23.4 1.0 CG D:ASN59 4.7 24.0 1.0 CE1 D:HIS127 4.8 21.3 1.0 CE1 C:TYR90 4.9 40.6 1.0

K.Sugimoto, T.Senda, H.Aoshima, E.Masai, M.Fukuda, Y.Mitsui. Crystal Structure of An Aromatic Ring Opening Dioxygenase Ligab, A Protocatechuate 4,5-Dioxygenase, Under Aerobic Conditions. Structure Fold.Des. V. 7 953 1999.
ISSN: ISSN 0969-2126
PubMed: 10467151
DOI: 10.1016/S0969-2126(99)80122-1