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Iron in PDB 1yko: Protocatechuate 3,4-Dioxygenase Y408H Mutant

Enzymatic activity of Protocatechuate 3,4-Dioxygenase Y408H Mutant

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

Protein crystallography data

The structure of Protocatechuate 3,4-Dioxygenase Y408H Mutant, PDB code: 1yko 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) 37.27 / 2.54
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.590, 127.630, 134.450, 90.00, 97.60, 90.00
R / Rfree (%) 18.3 / 21.7

Iron Binding Sites:

The binding sites of Iron atom in the Protocatechuate 3,4-Dioxygenase Y408H Mutant (pdb code 1yko). 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, PDB code: 1yko:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1yko

Go back to Iron Binding Sites List in 1yko
Iron binding site 1 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:41.5
occ:1.00
 O B:HOH901 2.0 25.6 1.0
OH B:TYR447 2.1 24.1 1.0
NE2 B:HIS462 2.3 15.1 1.0
NE2 B:HIS460 2.4 17.4 1.0
CE1 B:HIS462 2.9 14.1 1.0
O B:HOH801 3.1 5.0 1.0
CE1 B:HIS460 3.2 17.1 1.0
CZ B:TYR447 3.3 19.7 1.0
CD2 B:HIS462 3.4 12.2 1.0
CD2 B:HIS460 3.5 15.8 1.0
CE2 B:TYR447 3.7 19.4 1.0
NE2 B:HIS408 3.9 23.8 1.0
O A:HOH606 4.0 14.3 1.0
ND1 B:HIS462 4.2 11.5 1.0
NH1 B:ARG457 4.2 19.2 1.0
ND1 B:HIS460 4.4 15.4 1.0
CG B:HIS462 4.4 12.1 1.0
CE1 B:TYR447 4.4 19.6 1.0
CE1 B:HIS408 4.5 24.8 1.0
CG B:HIS460 4.5 13.9 1.0
O B:HOH643 4.7 17.4 1.0
OE1 B:GLN477 4.9 15.3 1.0
CD2 B:HIS408 5.0 25.6 1.0

Iron binding site 2 out of 6 in 1yko

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Iron binding site 2 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe600

b:40.8
occ:1.00
 O D:HOH1901 1.9 24.0 1.0
OH D:TYR447 2.0 23.8 1.0
NE2 D:HIS462 2.3 15.4 1.0
NE2 D:HIS460 2.6 16.1 1.0
CE1 D:HIS462 2.9 14.3 1.0
O D:HOH1801 2.9 11.4 1.0
CZ D:TYR447 3.3 19.6 1.0
CE1 D:HIS460 3.4 17.5 1.0
CD2 D:HIS462 3.5 12.2 1.0
CD2 D:HIS460 3.7 14.7 1.0
NE2 D:HIS408 3.9 25.1 1.0
CE2 D:TYR447 3.9 20.4 1.0
O C:HOH1606 3.9 9.2 1.0
ND1 D:HIS462 4.2 11.7 1.0
NH1 D:ARG457 4.2 17.4 1.0
CE1 D:TYR447 4.4 18.6 1.0
CE1 D:HIS408 4.4 25.9 1.0
CG D:HIS462 4.5 12.7 1.0
ND1 D:HIS460 4.6 15.6 1.0
O D:HOH1643 4.6 20.6 1.0
CG D:HIS460 4.8 14.8 1.0
CD2 C:TYR16 4.8 26.9 1.0
CD2 D:HIS408 4.9 26.8 1.0

Iron binding site 3 out of 6 in 1yko

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Iron binding site 3 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe600

b:42.3
occ:1.00
 O F:HOH2901 2.1 24.2 1.0
OH F:TYR447 2.1 26.7 1.0
NE2 F:HIS462 2.2 16.7 1.0
NE2 F:HIS460 2.4 15.9 1.0
O F:HOH2801 3.0 6.5 1.0
CE1 F:HIS462 3.1 15.1 1.0
CE1 F:HIS460 3.3 16.6 1.0
CD2 F:HIS462 3.3 13.5 1.0
CZ F:TYR447 3.4 21.9 1.0
CD2 F:HIS460 3.5 15.2 1.0
CE2 F:TYR447 3.9 20.7 1.0
NE2 F:HIS408 4.0 25.0 1.0
NH1 F:ARG457 4.0 17.5 1.0
O E:HOH2606 4.1 14.1 1.0
ND1 F:HIS462 4.2 11.4 1.0
CG F:HIS462 4.4 13.8 1.0
ND1 F:HIS460 4.5 15.9 1.0
CE1 F:TYR447 4.5 21.8 1.0
O F:HOH2643 4.5 23.8 1.0
CE1 F:HIS408 4.5 25.1 1.0
CG F:HIS460 4.6 14.4 1.0
OE1 F:GLN477 4.9 11.2 1.0

Iron binding site 4 out of 6 in 1yko

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Iron binding site 4 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe600

b:40.8
occ:1.00
 O H:HOH3901 1.9 28.4 1.0
OH H:TYR447 2.1 25.7 1.0
NE2 H:HIS462 2.3 15.8 1.0
NE2 H:HIS460 2.5 16.9 1.0
O H:HOH3801 3.0 9.2 1.0
CE1 H:HIS462 3.1 11.4 1.0
CZ H:TYR447 3.3 20.1 1.0
CE1 H:HIS460 3.4 18.1 1.0
CD2 H:HIS462 3.4 11.6 1.0
CD2 H:HIS460 3.5 16.5 1.0
CE2 H:TYR447 3.8 20.2 1.0
NE2 H:HIS408 3.8 22.1 1.0
O G:HOH3606 4.1 14.2 1.0
ND1 H:HIS462 4.3 9.8 1.0
NH1 H:ARG457 4.4 18.7 1.0
CE1 H:HIS408 4.4 23.1 1.0
CE1 H:TYR447 4.4 20.2 1.0
O H:HOH3643 4.5 25.1 1.0
CG H:HIS462 4.5 11.2 1.0
ND1 H:HIS460 4.6 17.3 1.0
CG H:HIS460 4.7 15.9 1.0
CD2 H:HIS408 4.9 23.7 1.0
CD2 G:TYR16 5.0 28.4 1.0

Iron binding site 5 out of 6 in 1yko

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Iron binding site 5 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe600

b:51.1
occ:1.00
 O J:HOH4901 2.0 25.2 1.0
NE2 J:HIS462 2.1 17.3 1.0
OH J:TYR447 2.2 26.0 1.0
NE2 J:HIS460 2.5 20.2 1.0
CE1 J:HIS462 3.0 16.4 1.0
O J:HOH4801 3.2 10.9 1.0
CD2 J:HIS462 3.2 14.2 1.0
CZ J:TYR447 3.4 22.4 1.0
CE1 J:HIS460 3.4 19.8 1.0
CD2 J:HIS460 3.4 18.1 1.0
NE2 J:HIS408 3.7 27.8 1.0
CE2 J:TYR447 3.7 21.0 1.0
O I:HOH4606 3.8 18.4 1.0
ND1 J:HIS462 4.2 13.9 1.0
NH1 J:ARG457 4.3 21.4 1.0
CG J:HIS462 4.3 13.7 1.0
O J:HOH4643 4.3 24.0 1.0
CE1 J:HIS408 4.5 27.6 1.0
ND1 J:HIS460 4.5 18.5 1.0
CE1 J:TYR447 4.6 21.0 1.0
CG J:HIS460 4.6 17.6 1.0
CD2 J:HIS408 4.7 28.6 1.0

Iron binding site 6 out of 6 in 1yko

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Iron binding site 6 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408H 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 Y408H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe600

b:37.0
occ:1.00
 OH L:TYR447 2.2 28.0 1.0
O L:HOH5901 2.2 22.7 1.0
NE2 L:HIS462 2.2 17.1 1.0
NE2 L:HIS460 2.4 18.2 1.0
O L:HOH5801 2.9 5.7 1.0
CE1 L:HIS462 3.1 15.9 1.0
CE1 L:HIS460 3.3 18.6 1.0
CZ L:TYR447 3.3 22.9 1.0
CD2 L:HIS462 3.4 13.8 1.0
CD2 L:HIS460 3.5 17.2 1.0
CE2 L:TYR447 3.7 21.5 1.0
NE2 L:HIS408 3.8 28.1 1.0
O K:HOH5606 4.0 16.7 1.0
ND1 L:HIS462 4.2 13.4 1.0
NH1 L:ARG457 4.3 18.9 1.0
CG L:HIS462 4.4 14.1 1.0
CE1 L:TYR447 4.5 21.3 1.0
ND1 L:HIS460 4.5 17.5 1.0
CE1 L:HIS408 4.5 26.9 1.0
O L:HOH5643 4.5 22.1 1.0
CG L:HIS460 4.6 16.8 1.0
CD2 L:HIS408 4.9 27.2 1.0
CD2 K:TYR16 4.9 27.6 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: Sat Aug 3 17:52:40 2024

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