Iron in PDB 1ykp: Protocatechuate 3,4-Dioxygenase Y408H Mutant Bound to Dhb

All present enzymatic activity of Protocatechuate 3,4-Dioxygenase Y408H Mutant Bound to Dhb:
1.13.11.3;

The structure of Protocatechuate 3,4-Dioxygenase Y408H Mutant Bound to Dhb, PDB code: 1ykp 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)	30.37 / 2.41
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	196.190, 127.970, 134.180, 90.00, 97.68, 90.00
R / Rfree (%)	14.5 / 21.1

The binding sites of Iron atom in the Protocatechuate 3,4-Dioxygenase Y408H Mutant Bound to Dhb (pdb code 1ykp). 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 Y408H Mutant Bound to Dhb, PDB code: 1ykp:
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 Y408H 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 Y408H Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe600 b:62.6 occ:1.00 O4 A:DHB550 2.0 88.8 1.0 NE2 B:HIS460 2.3 18.1 1.0 NE2 B:HIS462 2.5 16.2 1.0 OH B:TYR447 2.5 33.0 1.0 O B:HOH901 2.5 33.9 1.0 CE1 B:HIS460 3.2 17.0 1.0 CD2 B:HIS460 3.3 13.4 1.0 C4 A:DHB550 3.3 89.0 1.0 CE1 B:HIS462 3.4 13.0 1.0 CD2 B:HIS462 3.4 15.2 1.0 CZ B:TYR447 3.7 28.7 1.0 NE2 B:HIS408 3.9 29.1 1.0 O3 A:DHB550 4.0 88.5 1.0 NH1 B:ARG457 4.0 14.0 1.0 CE2 B:TYR447 4.1 26.9 1.0 C3 A:DHB550 4.1 88.4 1.0 O B:HOH643 4.2 14.2 1.0 O A:HOH606 4.2 15.1 1.0 C5 A:DHB550 4.2 89.5 1.0 ND1 B:HIS460 4.3 14.6 1.0 CG B:HIS460 4.4 13.2 1.0 ND1 B:HIS462 4.5 13.7 1.0 CG B:HIS462 4.5 16.4 1.0 CE1 B:HIS408 4.6 30.7 1.0 CE1 B:TYR447 4.9 28.1 1.0 OE1 B:GLN477 4.9 14.3 1.0 CD2 B:HIS408 5.0 28.7 1.0

Iron binding site 2 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1600 b:54.5 occ:1.00 O4 D:DHB1550 2.0 77.5 1.0 OH D:TYR447 2.3 29.6 1.0 NE2 D:HIS462 2.5 19.1 1.0 O D:HOH1901 2.5 35.4 1.0 NE2 D:HIS460 2.6 16.3 1.0 C4 D:DHB1550 3.1 78.1 1.0 CE1 D:HIS462 3.2 15.4 1.0 CE1 D:HIS460 3.4 15.2 1.0 CD2 D:HIS460 3.6 15.8 1.0 CZ D:TYR447 3.6 27.6 1.0 NE2 D:HIS408 3.7 28.8 1.0 CD2 D:HIS462 3.7 15.3 1.0 C5 D:DHB1550 3.9 78.9 1.0 O3 D:DHB1550 4.0 77.9 1.0 C3 D:DHB1550 4.0 77.8 1.0 NH1 D:ARG457 4.0 20.0 1.0 O C:HOH1606 4.1 15.7 1.0 CE2 D:TYR447 4.2 27.4 1.0 CE1 D:HIS408 4.2 29.3 1.0 ND1 D:HIS462 4.4 16.3 1.0 O D:HOH1643 4.4 17.7 1.0 ND1 D:HIS460 4.6 17.0 1.0 CG D:HIS462 4.6 15.9 1.0 CG D:HIS460 4.7 14.8 1.0 CE1 D:TYR447 4.8 25.1 1.0 CD2 D:HIS408 4.8 30.5 1.0 CD2 C:TYR16 4.8 30.4 1.0 OE1 D:GLN477 4.9 15.6 1.0

Iron binding site 3 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe2600 b:57.4 occ:1.00 O4 F:DHB2550 1.7 0.2 1.0 OH F:TYR447 2.3 30.1 1.0 NE2 F:HIS460 2.3 15.9 1.0 O F:HOH2901 2.3 33.4 1.0 NE2 F:HIS462 2.8 14.2 1.0 CE1 F:HIS460 3.0 15.8 1.0 C4 F:DHB2550 3.0 0.9 1.0 CD2 F:HIS460 3.4 16.9 1.0 CZ F:TYR447 3.6 27.6 1.0 CD2 F:HIS462 3.6 15.8 1.0 CE1 F:HIS462 3.8 14.4 1.0 O3 F:DHB2550 3.8 0.2 1.0 C3 F:DHB2550 3.9 0.3 1.0 C5 F:DHB2550 3.9 0.8 1.0 NE2 F:HIS408 4.0 28.2 1.0 NH1 F:ARG457 4.0 17.7 1.0 ND1 F:HIS460 4.1 16.4 1.0 O F:HOH2643 4.2 25.0 1.0 CE2 F:TYR447 4.2 26.3 1.0 O E:HOH2606 4.3 12.2 1.0 CG F:HIS460 4.4 16.2 1.0 CE1 F:HIS408 4.5 29.2 1.0 OE1 F:GLN477 4.6 15.4 1.0 CE1 F:TYR447 4.7 26.1 1.0 CG F:HIS462 4.8 16.2 1.0 ND1 F:HIS462 4.9 15.5 1.0

Iron binding site 4 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe3600 b:63.4 occ:1.00 O4 H:DHB3550 1.9 0.3 1.0 NE2 H:HIS460 2.3 15.3 1.0 O H:HOH3901 2.4 39.4 1.0 OH H:TYR447 2.4 30.8 1.0 NE2 H:HIS462 2.7 13.7 1.0 CE1 H:HIS460 3.1 16.0 1.0 C4 H:DHB3550 3.2 0.3 1.0 CD2 H:HIS460 3.4 14.4 1.0 CD2 H:HIS462 3.6 13.2 1.0 CZ H:TYR447 3.6 28.3 1.0 CE1 H:HIS462 3.7 9.8 1.0 O3 H:DHB3550 3.7 0.3 1.0 NE2 H:HIS408 3.9 27.9 1.0 C3 H:DHB3550 3.9 0.4 1.0 CE2 H:TYR447 4.1 26.6 1.0 C5 H:DHB3550 4.2 0.2 1.0 ND1 H:HIS460 4.3 17.1 1.0 O H:HOH3643 4.3 21.7 1.0 CE1 H:HIS408 4.3 29.0 1.0 NH1 H:ARG457 4.4 13.4 1.0 O G:HOH3606 4.4 17.8 1.0 CG H:HIS460 4.5 15.6 1.0 CE1 H:TYR447 4.7 27.3 1.0 CG H:HIS462 4.7 13.8 1.0 ND1 H:HIS462 4.7 12.9 1.0 OE1 H:GLN477 4.9 15.6 1.0 CD2 H:HIS408 4.9 29.1 1.0

Iron binding site 5 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe4600 b:67.7 occ:1.00 O J:HOH4901 2.2 36.5 1.0 O4 J:DHB4550 2.4 0.5 1.0 OH J:TYR447 2.4 32.1 1.0 NE2 J:HIS462 2.4 17.1 1.0 NE2 J:HIS460 2.4 20.3 1.0 CD2 J:HIS462 3.3 14.1 1.0 CE1 J:HIS460 3.3 19.5 1.0 CE1 J:HIS462 3.4 14.2 1.0 CD2 J:HIS460 3.5 17.6 1.0 C4 J:DHB4550 3.6 0.9 1.0 CZ J:TYR447 3.7 29.7 1.0 NE2 J:HIS408 3.8 31.1 1.0 O3 J:DHB4550 3.9 0.9 1.0 O I:HOH4606 4.0 24.2 1.0 O J:HOH4643 4.1 17.8 1.0 CE2 J:TYR447 4.2 28.2 1.0 C3 J:DHB4550 4.2 0.0 1.0 NH1 J:ARG457 4.3 21.4 1.0 ND1 J:HIS462 4.4 15.4 1.0 CG J:HIS462 4.5 15.2 1.0 ND1 J:HIS460 4.5 19.3 1.0 C5 J:DHB4550 4.5 0.9 1.0 CE1 J:HIS408 4.5 32.0 1.0 CG J:HIS460 4.6 17.1 1.0 CD2 J:HIS408 4.6 31.6 1.0 OE1 J:GLN477 4.8 19.4 1.0 CE1 J:TYR447 4.9 27.1 1.0

Iron binding site 6 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant Bound to Dhb within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe5600 b:63.9 occ:1.00 O4 L:DHB5550 1.8 88.1 1.0 OH L:TYR447 2.3 33.7 1.0 NE2 L:HIS460 2.4 19.5 1.0 O L:HOH5901 2.5 36.8 1.0 NE2 L:HIS462 2.6 21.0 1.0 C4 L:DHB5550 3.0 87.9 1.0 CE1 L:HIS460 3.2 18.0 1.0 CE1 L:HIS462 3.5 18.0 1.0 CD2 L:HIS460 3.5 16.5 1.0 O3 L:DHB5550 3.5 87.7 1.0 CZ L:TYR447 3.6 29.3 1.0 CD2 L:HIS462 3.7 16.3 1.0 C3 L:DHB5550 3.7 87.5 1.0 NE2 L:HIS408 3.9 29.1 1.0 O K:HOH5606 3.9 18.1 1.0 C5 L:DHB5550 4.0 88.2 1.0 NH1 L:ARG457 4.1 16.8 1.0 CE2 L:TYR447 4.2 27.2 1.0 O L:HOH5643 4.3 20.4 1.0 ND1 L:HIS460 4.4 14.4 1.0 CG L:HIS460 4.6 15.5 1.0 CE1 L:HIS408 4.6 29.5 1.0 ND1 L:HIS462 4.6 16.9 1.0 CG L:HIS462 4.7 17.3 1.0 OE1 L:GLN477 4.7 17.8 1.0 CE1 L:TYR447 4.8 27.6 1.0 CD2 L:HIS408 4.8 28.2 1.0 CD2 K:TYR16 4.8 32.1 1.0 C2 L:DHB5550 5.0 87.9 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