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Iron in PDB 1ykl: Protocatechuate 3,4-Dioxygenase Y408C Mutant Bound to Dhb

Enzymatic activity of Protocatechuate 3,4-Dioxygenase Y408C Mutant Bound to Dhb

All present enzymatic activity of Protocatechuate 3,4-Dioxygenase Y408C Mutant Bound to Dhb:
1.13.11.3;

Protein crystallography data

The structure of Protocatechuate 3,4-Dioxygenase Y408C Mutant Bound to Dhb, PDB code: 1ykl 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) 25.64 / 2.25
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.700, 127.200, 133.900, 90.00, 97.60, 90.00
R / Rfree (%) 15.8 / 19.9

Iron Binding Sites:

The binding sites of Iron atom in the Protocatechuate 3,4-Dioxygenase Y408C Mutant Bound to Dhb (pdb code 1ykl). 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 Y408C Mutant Bound to Dhb, PDB code: 1ykl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1ykl

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Iron binding site 1 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant Bound to Dhb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe600

b:85.2
occ:1.00
 OH B:TYR447 2.2 40.3 1.0
O4 B:DHB550 2.3 61.6 1.0
NE2 B:HIS462 2.6 23.2 1.0
NE2 B:HIS460 2.7 24.6 1.0
O B:HOH901 3.2 35.5 1.0
C4 B:DHB550 3.3 59.7 1.0
CZ B:TYR447 3.5 37.6 1.0
CD2 B:HIS462 3.5 20.3 1.0
CE1 B:HIS460 3.6 23.0 1.0
CE1 B:HIS462 3.6 19.0 1.0
CD2 B:HIS460 3.8 22.9 1.0
O3 B:DHB550 3.8 59.3 1.0
CE2 B:TYR447 3.9 37.8 1.0
O A:HOH606 4.0 21.9 1.0
C3 B:DHB550 4.0 59.3 1.0
C5 B:DHB550 4.2 59.1 1.0
O B:HOH643 4.4 27.6 1.0
SG B:CYS408 4.6 31.1 0.5
CD2 A:TYR16 4.6 39.4 1.0
ND1 B:HIS462 4.7 19.9 1.0
CE1 B:TYR447 4.7 34.7 1.0
CG B:HIS462 4.7 19.6 1.0
ND1 B:HIS460 4.7 25.4 1.0
NH1 B:ARG457 4.8 20.9 1.0
CG B:HIS460 4.9 23.9 1.0

Iron binding site 2 out of 6 in 1ykl

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Iron binding site 2 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant Bound to Dhb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe600

b:81.8
occ:1.00
 OH D:TYR447 2.3 40.9 1.0
NE2 D:HIS462 2.3 21.3 1.0
NE2 D:HIS460 2.5 22.9 1.0
O4 D:DHB1550 2.6 59.7 1.0
O D:HOH1901 3.1 33.0 1.0
CE1 D:HIS462 3.2 18.2 1.0
CD2 D:HIS462 3.3 19.1 1.0
CE1 D:HIS460 3.4 22.8 1.0
CD2 D:HIS460 3.5 22.0 1.0
CZ D:TYR447 3.6 37.9 1.0
C4 D:DHB1550 3.6 59.5 1.0
O3 D:DHB1550 3.8 60.1 1.0
CE2 D:TYR447 4.0 36.5 1.0
C3 D:DHB1550 4.1 59.2 1.0
O D:HOH1643 4.1 21.6 1.0
O C:HOH1606 4.2 19.3 1.0
ND1 D:HIS462 4.4 20.6 1.0
NH1 D:ARG457 4.4 17.8 1.0
CG D:HIS462 4.4 19.7 1.0
ND1 D:HIS460 4.6 24.9 1.0
C5 D:DHB1550 4.6 59.0 1.0
CG D:HIS460 4.6 22.9 1.0
CE1 D:TYR447 4.7 33.5 1.0

Iron binding site 3 out of 6 in 1ykl

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Iron binding site 3 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant Bound to Dhb within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe600

b:79.2
occ:1.00
 OH F:TYR447 2.1 43.9 1.0
NE2 F:HIS460 2.2 25.2 1.0
NE2 F:HIS462 2.4 23.8 1.0
O4 F:DHB2550 2.7 59.5 1.0
CE1 F:HIS460 3.0 21.3 1.0
O F:HOH2901 3.1 31.2 1.0
CD2 F:HIS462 3.2 18.8 1.0
CD2 F:HIS460 3.4 21.6 1.0
CZ F:TYR447 3.4 39.4 1.0
O3 F:DHB2550 3.4 52.4 1.0
CE1 F:HIS462 3.5 24.1 1.0
C4 F:DHB2550 3.7 56.7 1.0
CE2 F:TYR447 4.0 38.8 1.0
C3 F:DHB2550 4.0 56.3 1.0
NH1 F:ARG457 4.1 23.8 1.0
O F:HOH2643 4.2 31.2 1.0
ND1 F:HIS460 4.2 22.8 1.0
O E:HOH2606 4.3 23.5 1.0
CG F:HIS460 4.4 23.4 1.0
CG F:HIS462 4.4 19.2 1.0
ND1 F:HIS462 4.5 21.6 1.0
CE1 F:TYR447 4.6 37.9 1.0
OE1 F:GLN477 4.7 19.9 1.0
C5 F:DHB2550 4.9 57.8 1.0
CD2 E:TYR16 5.0 41.8 1.0
SG F:CYS408 5.0 28.1 0.5

Iron binding site 4 out of 6 in 1ykl

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Iron binding site 4 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant Bound to Dhb within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe600

b:84.2
occ:1.00
 OH H:TYR447 2.1 44.3 1.0
O4 H:DHB3550 2.3 74.1 1.0
NE2 H:HIS462 2.4 23.7 1.0
NE2 H:HIS460 2.4 20.1 1.0
O H:HOH3901 2.8 31.3 1.0
CD2 H:HIS462 3.2 19.9 1.0
CE1 H:HIS460 3.2 20.4 1.0
CZ H:TYR447 3.3 40.4 1.0
CD2 H:HIS460 3.4 20.3 1.0
CE1 H:HIS462 3.5 21.5 1.0
C4 H:DHB3550 3.6 72.2 1.0
CE2 H:TYR447 3.7 40.4 1.0
O H:HOH3643 4.0 29.3 1.0
O3 H:DHB3550 4.1 71.8 1.0
O G:HOH3606 4.2 25.4 1.0
C3 H:DHB3550 4.3 72.8 1.0
CG H:HIS462 4.4 20.5 1.0
ND1 H:HIS460 4.4 22.4 1.0
C5 H:DHB3550 4.5 71.4 1.0
ND1 H:HIS462 4.5 21.4 1.0
CG H:HIS460 4.5 22.6 1.0
CE1 H:TYR447 4.6 39.2 1.0
NH1 H:ARG457 4.6 29.2 1.0
SG H:CYS408 4.7 26.8 0.5

Iron binding site 5 out of 6 in 1ykl

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Iron binding site 5 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant Bound to Dhb within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe600

b:93.3
occ:1.00
 NE2 J:HIS462 2.3 22.6 1.0
OH J:TYR447 2.3 41.7 1.0
NE2 J:HIS460 2.5 25.8 1.0
O J:HOH4901 3.0 40.3 1.0
CD2 J:HIS462 3.1 20.4 1.0
O4 J:DHB4550 3.1 67.6 1.0
CE1 J:HIS460 3.3 22.9 1.0
CE1 J:HIS462 3.3 22.6 1.0
CD2 J:HIS460 3.5 25.2 1.0
CZ J:TYR447 3.6 38.6 1.0
O3 J:DHB4550 3.8 67.8 1.0
CE2 J:TYR447 4.1 37.0 1.0
O I:HOH4606 4.1 26.5 1.0
C4 J:DHB4550 4.1 68.3 1.0
O J:HOH4643 4.1 26.2 1.0
CG J:HIS462 4.3 21.1 1.0
ND1 J:HIS462 4.4 24.8 1.0
ND1 J:HIS460 4.4 27.1 1.0
C3 J:DHB4550 4.4 68.5 1.0
CG J:HIS460 4.6 25.4 1.0
NH1 J:ARG457 4.8 24.5 1.0
CE1 J:TYR447 4.8 36.3 1.0
OE1 J:GLN477 4.9 24.1 1.0

Iron binding site 6 out of 6 in 1ykl

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Iron binding site 6 out of 6 in the Protocatechuate 3,4-Dioxygenase Y408C 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 Y408C Mutant Bound to Dhb within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe600

b:76.5
occ:1.00
 OH L:TYR447 2.2 42.4 1.0
NE2 L:HIS462 2.3 25.4 1.0
NE2 L:HIS460 2.4 27.9 1.0
O4 L:DHB5550 2.6 68.3 1.0
CD2 L:HIS462 3.1 22.8 1.0
O L:HOH5901 3.3 35.4 1.0
CE1 L:HIS460 3.3 25.6 1.0
CZ L:TYR447 3.4 39.3 1.0
CD2 L:HIS460 3.4 24.0 1.0
CE1 L:HIS462 3.5 23.6 1.0
C4 L:DHB5550 3.7 67.5 1.0
O3 L:DHB5550 3.7 65.2 1.0
CE2 L:TYR447 3.9 37.5 1.0
O K:HOH5606 4.0 23.9 1.0
C3 L:DHB5550 4.1 67.1 1.0
CG L:HIS462 4.4 22.4 1.0
O L:HOH5643 4.4 28.9 1.0
ND1 L:HIS460 4.4 27.3 1.0
NH1 L:ARG457 4.4 22.6 1.0
ND1 L:HIS462 4.5 23.4 1.0
CG L:HIS460 4.5 25.2 1.0
CE1 L:TYR447 4.7 38.5 1.0
OE1 L:GLN477 4.8 24.4 1.0
C5 L:DHB5550 4.8 68.5 1.0
CD2 K:TYR16 4.9 43.2 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 22:46:03 2025

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