Iron in PDB 1ykn: Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb

All present enzymatic activity of Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb:
1.13.11.3;

The structure of Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb, PDB code: 1ykn was solved by C.K.Brown, D.H.Ohlendorf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.51 / 2.06
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	195.821, 128.569, 134.356, 90.00, 97.98, 90.00
R / Rfree (%)	14.9 / 19.2

The binding sites of Iron atom in the Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb (pdb code 1ykn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb, PDB code: 1ykn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe600 b:83.1 occ:1.00 NE2 B:HIS462 2.2 15.3 1.0 O4 B:DHB550 2.4 50.6 1.0 NE2 B:HIS460 2.4 12.3 1.0 OH B:TYR447 2.5 17.9 1.0 O B:HOH901 2.7 33.6 1.0 CE1 B:HIS462 2.9 12.7 1.0 CD2 B:HIS460 3.3 12.1 1.0 CD2 B:HIS462 3.4 11.1 1.0 CE1 B:HIS460 3.4 13.1 1.0 C4 B:DHB550 3.5 49.7 1.0 CZ B:TYR447 3.8 15.7 1.0 OE1 B:GLU408 3.8 33.9 1.0 C5 B:DHB550 4.1 50.7 1.0 ND1 B:HIS462 4.1 9.4 1.0 O B:HOH606 4.2 19.9 1.0 CE2 B:TYR447 4.2 17.2 1.0 NH1 B:ARG457 4.3 8.1 1.0 C3 B:DHB550 4.3 50.3 1.0 CG B:HIS462 4.3 11.1 1.0 O3 B:DHB550 4.4 51.9 1.0 CG B:HIS460 4.5 11.2 1.0 ND1 B:HIS460 4.5 12.4 1.0 O B:HOH643 4.5 22.4 1.0 CD B:GLU408 4.5 31.9 1.0 OE2 B:GLU408 4.6 33.2 1.0 OE1 B:GLN477 4.8 16.1 1.0 CE1 B:TYR447 4.8 11.6 1.0

Iron binding site 2 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1600 b:69.8 occ:1.00 NE2 D:HIS460 2.3 14.6 1.0 NE2 D:HIS462 2.4 14.0 1.0 O4 D:DHB1550 2.4 51.5 1.0 OH D:TYR447 2.6 15.8 1.0 O D:HOH1901 2.7 31.3 1.0 CE1 D:HIS462 3.1 10.2 1.0 CE1 D:HIS460 3.2 7.7 1.0 CD2 D:HIS460 3.4 12.1 1.0 C4 D:DHB1550 3.4 51.2 1.0 CD2 D:HIS462 3.5 11.3 1.0 O3 D:DHB1550 3.7 52.1 1.0 CZ D:TYR447 3.7 16.5 1.0 OE1 D:GLU408 3.8 30.1 1.0 C3 D:DHB1550 4.0 51.2 1.0 NH1 D:ARG457 4.2 9.1 1.0 CE2 D:TYR447 4.3 15.8 1.0 O C:HOH1606 4.3 18.2 1.0 ND1 D:HIS462 4.3 10.8 1.0 O D:HOH1643 4.3 12.8 1.0 ND1 D:HIS460 4.3 10.6 1.0 CD D:GLU408 4.4 30.8 1.0 OE2 D:GLU408 4.4 32.2 1.0 C5 D:DHB1550 4.4 53.0 1.0 CG D:HIS460 4.5 11.1 1.0 CG D:HIS462 4.5 10.0 1.0 CE1 D:TYR447 4.8 16.4 1.0 OE1 D:GLN477 5.0 11.3 1.0

Iron binding site 3 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe2600 b:77.4 occ:1.00 O4 F:DHB2550 2.2 60.1 1.0 NE2 F:HIS460 2.3 11.2 1.0 OH F:TYR447 2.3 18.1 1.0 O F:HOH2901 2.5 27.8 1.0 NE2 F:HIS462 2.5 12.3 1.0 CE1 F:HIS460 3.1 11.9 1.0 CD2 F:HIS460 3.4 12.0 1.0 CD2 F:HIS462 3.4 9.7 1.0 C4 F:DHB2550 3.5 57.6 1.0 CE1 F:HIS462 3.5 11.5 1.0 CZ F:TYR447 3.5 18.3 1.0 O3 F:DHB2550 3.8 55.5 1.0 OE1 F:GLU408 3.8 34.3 1.0 CE2 F:TYR447 4.1 16.6 1.0 C3 F:DHB2550 4.1 56.6 1.0 NH1 F:ARG457 4.1 6.8 1.0 O F:HOH2643 4.2 14.8 1.0 ND1 F:HIS460 4.3 13.0 1.0 C5 F:DHB2550 4.4 59.6 1.0 CD F:GLU408 4.5 32.9 1.0 CG F:HIS460 4.5 12.7 1.0 O E:HOH2606 4.5 16.9 1.0 OE2 F:GLU408 4.5 34.9 1.0 CG F:HIS462 4.6 9.7 1.0 ND1 F:HIS462 4.6 13.1 1.0 CE1 F:TYR447 4.7 16.2 1.0 OE1 F:GLN477 4.7 12.5 1.0

Iron binding site 4 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe3600 b:82.8 occ:1.00 NE2 H:HIS462 2.2 11.5 1.0 O4 H:DHB3550 2.3 54.7 1.0 O H:HOH3901 2.4 32.8 1.0 NE2 H:HIS460 2.4 10.3 1.0 OH H:TYR447 2.5 16.3 1.0 CE1 H:HIS462 3.1 9.2 1.0 CE1 H:HIS460 3.3 8.8 1.0 CD2 H:HIS462 3.3 6.8 1.0 CD2 H:HIS460 3.4 11.3 1.0 C4 H:DHB3550 3.4 54.8 1.0 CZ H:TYR447 3.7 16.7 1.0 O3 H:DHB3550 3.8 55.8 1.0 C3 H:DHB3550 4.0 54.9 1.0 NH1 H:ARG457 4.2 7.2 1.0 ND1 H:HIS462 4.2 8.2 1.0 C5 H:DHB3550 4.3 56.7 1.0 CE2 H:TYR447 4.3 14.8 1.0 O G:HOH3606 4.4 14.6 1.0 CG H:HIS462 4.4 9.4 1.0 OE1 H:GLU408 4.4 31.9 1.0 ND1 H:HIS460 4.4 10.8 1.0 OE2 H:GLU408 4.5 32.4 1.0 O H:HOH3643 4.5 16.6 1.0 CG H:HIS460 4.5 11.5 1.0 OE1 H:GLN477 4.6 14.1 1.0 CD H:GLU408 4.7 30.6 1.0 CE1 H:TYR447 4.8 15.1 1.0 CD H:GLN477 5.0 13.8 1.0

Iron binding site 5 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe4600 b:80.5 occ:1.00 O J:HOH4901 2.3 31.4 1.0 NE2 J:HIS462 2.3 14.2 1.0 O4 J:DHB4550 2.4 52.0 1.0 OH J:TYR447 2.5 16.8 1.0 NE2 J:HIS460 2.6 13.8 1.0 CE1 J:HIS462 3.3 14.7 1.0 CD2 J:HIS462 3.3 11.9 1.0 OE1 J:GLU408 3.5 33.1 1.0 CE1 J:HIS460 3.5 12.7 1.0 C4 J:DHB4550 3.5 51.5 1.0 CD2 J:HIS460 3.5 9.4 1.0 CZ J:TYR447 3.7 16.6 1.0 CD J:GLU408 4.1 32.5 1.0 CE2 J:TYR447 4.1 16.6 1.0 O3 J:DHB4550 4.2 53.4 1.0 OE2 J:GLU408 4.2 33.1 1.0 O I:HOH4606 4.3 19.6 1.0 O J:HOH4643 4.3 13.0 1.0 C3 J:DHB4550 4.3 52.6 1.0 C5 J:DHB4550 4.4 52.1 1.0 ND1 J:HIS462 4.4 13.7 1.0 CG J:HIS462 4.4 12.9 1.0 NH1 J:ARG457 4.5 9.0 1.0 ND1 J:HIS460 4.6 13.4 1.0 CG J:HIS460 4.7 11.4 1.0 CE1 J:TYR447 4.9 14.0 1.0 OE1 J:GLN477 5.0 13.6 1.0

Iron binding site 6 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe5600 b:75.3 occ:1.00 NE2 L:HIS460 2.2 11.8 1.0 NE2 L:HIS462 2.3 16.6 1.0 O4 L:DHB5550 2.4 60.6 1.0 O L:HOH5901 2.4 35.1 1.0 OH L:TYR447 2.6 18.7 1.0 CE1 L:HIS460 3.2 9.0 1.0 CE1 L:HIS462 3.2 14.6 1.0 CD2 L:HIS462 3.2 13.6 1.0 CD2 L:HIS460 3.2 9.9 1.0 C4 L:DHB5550 3.5 57.6 1.0 OE1 L:GLU408 3.9 31.8 1.0 CZ L:TYR447 3.9 17.5 1.0 O3 L:DHB5550 4.0 55.7 1.0 C3 L:DHB5550 4.2 57.2 1.0 NH1 L:ARG457 4.2 8.3 1.0 ND1 L:HIS462 4.3 15.1 1.0 ND1 L:HIS460 4.3 11.8 1.0 CG L:HIS462 4.3 13.9 1.0 O L:HOH5643 4.3 13.7 1.0 CG L:HIS460 4.4 10.9 1.0 O K:HOH5606 4.4 16.6 1.0 CE2 L:TYR447 4.5 17.5 1.0 C5 L:DHB5550 4.5 58.7 1.0 OE1 L:GLN477 4.5 15.1 1.0 CD L:GLU408 4.6 31.4 1.0 OE2 L:GLU408 4.8 32.8 1.0 CE1 L:TYR447 5.0 13.3 1.0

M.P.Valley, C.K.Brown, D.L.Burk, M.W.Vetting, D.H.Ohlendorf, J.D.Lipscomb. Roles of the Equatorial Tyrosyl Iron Ligand of Protocatechuate 3,4-Dioxygenase in Catalysis Biochemistry V. 44 11024 2005.
ISSN: ISSN 0006-2960
PubMed: 16101286
DOI: 10.1021/BI050902I