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Iron in PDB 1ykk: Protocatechuate 3,4-Dioxygenase Y408C Mutant

Enzymatic activity of Protocatechuate 3,4-Dioxygenase Y408C Mutant

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

Protein crystallography data

The structure of Protocatechuate 3,4-Dioxygenase Y408C Mutant, PDB code: 1ykk 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) 26.09 / 2.06
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 194.870, 126.961, 132.764, 90.00, 96.39, 90.00
R / Rfree (%) 21 / 21.9

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 1ykk

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

b:41.6
occ:1.00
 OH B:TYR447 1.9 42.4 1.0
NE2 B:HIS462 2.2 29.2 1.0
NE2 B:HIS460 2.4 24.2 1.0
O B:HOH680 2.5 31.5 1.0
CZ B:TYR447 2.8 37.6 1.0
CE1 B:HIS462 3.0 25.3 1.0
CE2 B:TYR447 3.1 38.1 1.0
CE1 B:HIS460 3.3 23.5 1.0
CD2 B:HIS462 3.3 23.9 1.0
O B:HOH686 3.3 42.3 1.0
CD2 B:HIS460 3.4 22.6 1.0
O B:HOH623 4.1 25.7 1.0
CE1 B:TYR447 4.1 37.2 1.0
ND1 B:HIS462 4.2 23.6 1.0
O B:HOH678 4.2 27.8 1.0
O A:HOH204 4.3 19.9 1.0
CG B:HIS462 4.3 24.8 1.0
ND1 B:HIS460 4.4 21.1 1.0
CG B:HIS460 4.5 22.9 1.0
CD2 B:TYR447 4.5 35.5 1.0
NH1 B:ARG457 4.7 29.8 1.0
O B:HOH685 5.0 61.0 1.0
CD2 A:TYR16 5.0 37.0 1.0

Iron binding site 2 out of 6 in 1ykk

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

b:38.2
occ:1.00
 OH D:TYR447 1.9 40.6 1.0
NE2 D:HIS462 2.1 23.1 1.0
NE2 D:HIS460 2.4 25.3 1.0
O D:HOH682 2.4 35.2 1.0
CE1 D:HIS462 2.9 23.1 1.0
CZ D:TYR447 3.0 35.5 1.0
CE1 D:HIS460 3.2 24.5 1.0
CD2 D:HIS462 3.2 21.4 1.0
O D:HOH688 3.3 47.1 1.0
CE2 D:TYR447 3.3 35.4 1.0
CD2 D:HIS460 3.4 24.3 1.0
ND1 D:HIS462 4.1 20.4 1.0
O C:HOH205 4.1 17.9 1.0
O D:HOH624 4.2 22.4 1.0
O D:HOH679 4.2 29.1 1.0
CE1 D:TYR447 4.2 34.2 1.0
CG D:HIS462 4.3 22.5 1.0
ND1 D:HIS460 4.4 26.1 1.0
CG D:HIS460 4.5 24.5 1.0
NH1 D:ARG457 4.6 23.5 1.0
CD2 D:TYR447 4.8 33.2 1.0
O D:HOH687 4.8 64.0 1.0
SG D:CYS408 4.9 38.8 0.5
CD2 C:TYR16 4.9 35.7 1.0

Iron binding site 3 out of 6 in 1ykk

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

b:44.9
occ:1.00
 OH F:TYR447 2.1 42.6 1.0
NE2 F:HIS460 2.2 25.6 1.0
NE2 F:HIS462 2.3 28.3 1.0
O F:HOH682 2.5 31.4 1.0
CZ F:TYR447 3.1 37.5 1.0
CE1 F:HIS460 3.1 26.3 1.0
CD2 F:HIS460 3.2 24.5 1.0
CD2 F:HIS462 3.3 25.1 1.0
CE1 F:HIS462 3.3 26.3 1.0
CE2 F:TYR447 3.4 37.2 1.0
O F:HOH689 3.5 46.5 1.0
O F:HOH621 3.9 25.5 1.0
O F:HOH679 4.2 33.8 1.0
ND1 F:HIS460 4.3 26.9 1.0
O E:HOH270 4.3 24.3 1.0
CG F:HIS460 4.4 24.8 1.0
CE1 F:TYR447 4.4 35.1 1.0
ND1 F:HIS462 4.4 25.1 1.0
CG F:HIS462 4.4 25.1 1.0
NH1 F:ARG457 4.4 26.8 1.0
O F:HOH688 4.6 66.0 1.0
CD2 F:TYR447 4.8 33.4 1.0
SG F:CYS408 4.9 41.5 0.5
OE1 F:GLN477 5.0 22.1 1.0

Iron binding site 4 out of 6 in 1ykk

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

b:45.0
occ:1.00
 OH H:TYR447 1.9 43.0 1.0
NE2 H:HIS462 2.3 27.6 1.0
NE2 H:HIS460 2.4 24.8 1.0
O H:HOH680 2.9 32.4 1.0
CZ H:TYR447 2.9 38.6 1.0
CE2 H:TYR447 3.1 38.4 1.0
CE1 H:HIS460 3.2 24.8 1.0
CE1 H:HIS462 3.3 26.2 1.0
O H:HOH686 3.3 44.4 1.0
CD2 H:HIS462 3.3 23.9 1.0
CD2 H:HIS460 3.4 23.2 1.0
O H:HOH623 4.1 31.1 1.0
CE1 H:TYR447 4.2 37.1 1.0
O G:HOH402 4.2 22.7 1.0
ND1 H:HIS460 4.3 23.6 1.0
ND1 H:HIS462 4.4 24.8 1.0
CG H:HIS460 4.5 23.3 1.0
CG H:HIS462 4.5 23.9 1.0
CD2 H:TYR447 4.5 35.8 1.0
O H:HOH685 4.7 68.1 1.0
NH1 H:ARG457 4.7 30.6 1.0
O H:HOH678 4.7 29.6 1.0
CD2 G:TYR16 4.9 38.4 1.0
SG H:CYS408 4.9 36.7 0.5

Iron binding site 5 out of 6 in 1ykk

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

b:51.1
occ:1.00
 OH J:TYR447 2.0 41.4 1.0
NE2 J:HIS460 2.2 26.7 1.0
NE2 J:HIS462 2.3 25.4 1.0
O J:HOH680 2.3 32.3 1.0
CZ J:TYR447 3.0 38.3 1.0
CE1 J:HIS462 3.1 25.8 1.0
CE2 J:TYR447 3.1 37.4 1.0
CE1 J:HIS460 3.1 26.7 1.0
CD2 J:HIS460 3.2 26.9 1.0
CD2 J:HIS462 3.3 23.6 1.0
O J:HOH686 3.5 42.2 1.0
O J:HOH623 3.9 26.3 1.0
O J:HOH685 4.3 65.8 1.0
ND1 J:HIS462 4.3 23.2 1.0
CE1 J:TYR447 4.3 36.4 1.0
ND1 J:HIS460 4.3 27.5 1.0
O J:HOH677 4.3 33.8 1.0
CG J:HIS460 4.3 25.6 1.0
CG J:HIS462 4.4 25.0 1.0
O I:HOH534 4.4 25.9 1.0
CD2 J:TYR447 4.5 35.2 1.0
NH1 J:ARG457 4.6 31.7 1.0
CD2 I:TYR16 4.8 38.1 1.0
SG J:CYS408 4.9 41.5 0.5

Iron binding site 6 out of 6 in 1ykk

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

b:46.3
occ:1.00
 OH L:TYR447 2.1 40.5 1.0
NE2 L:HIS462 2.2 28.2 1.0
NE2 L:HIS460 2.2 27.5 1.0
O L:HOH784 2.4 32.1 1.0
CE1 L:HIS462 3.1 26.6 1.0
CE1 L:HIS460 3.1 27.6 1.0
CD2 L:HIS460 3.2 26.7 1.0
CZ L:TYR447 3.2 36.9 1.0
CD2 L:HIS462 3.2 25.4 1.0
O L:HOH792 3.3 47.0 1.0
CE2 L:TYR447 3.5 36.9 1.0
O L:HOH700 4.1 24.1 1.0
O K:HOH666 4.2 26.0 1.0
ND1 L:HIS462 4.2 24.2 1.0
ND1 L:HIS460 4.2 26.8 1.0
CG L:HIS460 4.3 26.2 1.0
O L:HOH780 4.3 32.2 1.0
CG L:HIS462 4.3 26.7 1.0
O L:HOH791 4.4 71.2 1.0
CE1 L:TYR447 4.4 35.9 1.0
NH1 L:ARG457 4.5 27.6 1.0
CD2 L:TYR447 4.8 34.1 1.0
CD2 K:TYR16 4.9 38.0 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 17:50:28 2024

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