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Iron in PDB 1ykm: Protocatechuate 3,4-Dioxygenase Y408E Mutant

Enzymatic activity of Protocatechuate 3,4-Dioxygenase Y408E Mutant

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

Protein crystallography data

The structure of Protocatechuate 3,4-Dioxygenase Y408E Mutant, PDB code: 1ykm 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) 7.81 / 2.22
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.612, 127.728, 134.321, 90.00, 97.66, 90.00
R / Rfree (%) 16.9 / 19.9

Iron Binding Sites:

The binding sites of Iron atom in the Protocatechuate 3,4-Dioxygenase Y408E Mutant (pdb code 1ykm). 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, PDB code: 1ykm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1ykm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:41.8
occ:1.00
 O B:HOH901 2.1 25.1 1.0
OH B:TYR447 2.2 19.1 1.0
NE2 B:HIS462 2.2 13.5 1.0
NE2 B:HIS460 2.3 13.1 1.0
CE1 B:HIS462 3.0 9.8 1.0
CE1 B:HIS460 3.1 13.3 1.0
O B:HOH801 3.2 6.9 1.0
CZ B:TYR447 3.3 15.8 1.0
CD2 B:HIS460 3.3 12.1 1.0
CD2 B:HIS462 3.4 8.8 1.0
OE1 B:GLU408 3.6 34.3 1.0
CE2 B:TYR447 3.6 15.4 1.0
OE2 B:GLU408 4.1 34.5 1.0
CD B:GLU408 4.1 32.8 1.0
O B:HOH643 4.2 9.3 1.0
ND1 B:HIS462 4.2 8.5 1.0
ND1 B:HIS460 4.3 10.7 1.0
CG B:HIS462 4.4 10.6 1.0
O A:HOH606 4.4 18.6 1.0
CG B:HIS460 4.4 10.1 1.0
CE1 B:TYR447 4.5 15.1 1.0
NH1 B:ARG457 4.5 14.1 1.0

Iron binding site 2 out of 6 in 1ykm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe600

b:40.0
occ:1.00
 OH D:TYR447 2.1 21.1 1.0
NE2 D:HIS462 2.1 10.9 1.0
O D:HOH1901 2.3 24.8 1.0
NE2 D:HIS460 2.4 13.3 1.0
CE1 D:HIS462 2.8 9.3 1.0
O D:HOH1801 3.0 6.6 1.0
CD2 D:HIS462 3.3 8.3 1.0
CE1 D:HIS460 3.4 12.4 1.0
CZ D:TYR447 3.4 14.8 1.0
CD2 D:HIS460 3.5 13.2 1.0
OE1 D:GLU408 3.6 32.5 1.0
CE2 D:TYR447 3.9 15.9 1.0
ND1 D:HIS462 4.0 8.7 1.0
OE2 D:GLU408 4.1 30.1 1.0
CD D:GLU408 4.2 30.6 1.0
O C:HOH1606 4.3 11.3 1.0
CG D:HIS462 4.3 8.5 1.0
O D:HOH1643 4.4 12.8 1.0
NH1 D:ARG457 4.5 10.3 1.0
CE1 D:TYR447 4.5 15.1 1.0
ND1 D:HIS460 4.5 12.3 1.0
CG D:HIS460 4.6 11.5 1.0

Iron binding site 3 out of 6 in 1ykm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe600

b:39.5
occ:1.00
 NE2 F:HIS462 2.1 15.5 1.0
OH F:TYR447 2.1 20.1 1.0
O F:HOH2901 2.3 23.7 1.0
NE2 F:HIS460 2.3 13.6 1.0
CE1 F:HIS462 2.9 14.2 1.0
O F:HOH2801 3.0 2.9 1.0
CD2 F:HIS462 3.2 13.2 1.0
CE1 F:HIS460 3.3 15.5 1.0
CD2 F:HIS460 3.3 12.9 1.0
CZ F:TYR447 3.5 14.3 1.0
OE1 F:GLU408 3.5 32.4 1.0
ND1 F:HIS462 4.1 12.3 1.0
CE2 F:TYR447 4.1 13.5 1.0
NH1 F:ARG457 4.2 12.0 1.0
CG F:HIS462 4.2 13.3 1.0
CD F:GLU408 4.4 30.4 1.0
ND1 F:HIS460 4.4 14.5 1.0
CG F:HIS460 4.4 12.9 1.0
O F:HOH2643 4.5 17.4 1.0
O E:HOH2606 4.5 14.3 1.0
CE1 F:TYR447 4.5 15.6 1.0
OE2 F:GLU408 4.6 30.8 1.0
OE1 F:GLN477 4.7 11.3 1.0

Iron binding site 4 out of 6 in 1ykm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe600

b:40.6
occ:1.00
 O H:HOH3901 2.1 27.8 1.0
OH H:TYR447 2.1 20.0 1.0
NE2 H:HIS462 2.1 12.1 1.0
NE2 H:HIS460 2.3 12.4 1.0
CE1 H:HIS462 3.0 10.4 1.0
O H:HOH3801 3.2 3.4 1.0
CD2 H:HIS462 3.2 9.1 1.0
CE1 H:HIS460 3.2 13.1 1.0
CD2 H:HIS460 3.3 12.6 1.0
CZ H:TYR447 3.3 15.9 1.0
OE1 H:GLU408 3.7 30.1 1.0
CE2 H:TYR447 3.8 16.4 1.0
OE2 H:GLU408 3.9 29.0 1.0
CD H:GLU408 4.1 28.4 1.0
ND1 H:HIS462 4.1 8.6 1.0
O G:HOH3606 4.3 18.9 1.0
CG H:HIS462 4.3 8.1 1.0
O H:HOH3643 4.3 16.3 1.0
ND1 H:HIS460 4.4 12.0 1.0
CG H:HIS460 4.4 11.5 1.0
NH1 H:ARG457 4.5 12.4 1.0
CE1 H:TYR447 4.5 14.4 1.0

Iron binding site 5 out of 6 in 1ykm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe600

b:46.4
occ:1.00
 NE2 J:HIS462 2.1 14.4 1.0
NE2 J:HIS460 2.2 17.9 1.0
OH J:TYR447 2.2 23.8 1.0
O J:HOH4901 2.2 23.3 1.0
CE1 J:HIS462 2.9 11.3 1.0
O J:HOH4801 3.1 5.5 1.0
CE1 J:HIS460 3.1 17.2 1.0
CD2 J:HIS462 3.2 11.3 1.0
CD2 J:HIS460 3.2 15.7 1.0
CZ J:TYR447 3.4 18.6 1.0
OE1 J:GLU408 3.8 35.1 1.0
CE2 J:TYR447 3.9 18.2 1.0
ND1 J:HIS462 4.1 8.2 1.0
OE2 J:GLU408 4.2 34.3 1.0
O J:HOH4643 4.2 15.0 1.0
CG J:HIS462 4.2 10.9 1.0
ND1 J:HIS460 4.3 16.1 1.0
CD J:GLU408 4.3 33.0 1.0
CG J:HIS460 4.3 14.7 1.0
NH1 J:ARG457 4.4 14.3 1.0
O J:HOH4606 4.5 20.3 1.0
CE1 J:TYR447 4.6 17.3 1.0
OE1 J:GLN477 4.8 12.7 1.0

Iron binding site 6 out of 6 in 1ykm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe600

b:38.3
occ:1.00
 OH L:TYR447 2.0 21.6 1.0
O L:HOH5901 2.1 22.6 1.0
NE2 L:HIS462 2.2 14.7 1.0
NE2 L:HIS460 2.2 13.3 1.0
CE1 L:HIS462 3.0 13.2 1.0
O L:HOH5801 3.1 1.6 1.0
CD2 L:HIS460 3.2 13.4 1.0
CE1 L:HIS460 3.2 13.0 1.0
CD2 L:HIS462 3.3 12.3 1.0
CZ L:TYR447 3.3 15.7 1.0
OE1 L:GLU408 3.7 29.6 1.0
CE2 L:TYR447 3.9 16.3 1.0
O L:HOH5643 4.0 11.0 1.0
ND1 L:HIS462 4.2 12.0 1.0
NH1 L:ARG457 4.3 10.9 1.0
ND1 L:HIS460 4.3 13.9 1.0
CD L:GLU408 4.3 29.6 1.0
OE2 L:GLU408 4.3 30.9 1.0
CG L:HIS460 4.3 12.8 1.0
CG L:HIS462 4.3 11.6 1.0
O K:HOH5606 4.4 18.1 1.0
CE1 L:TYR447 4.4 14.0 1.0
OE1 L:GLN477 5.0 15.7 1.0

Reference:

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
Page generated: Wed Jul 16 22:46:53 2025

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