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Iron in PDB 3pcn: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate

Enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate

All present enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate:
1.13.11.3;

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate, PDB code: 3pcn was solved by A.M.Orville, J.D.Lipscomb, D.H.Ohlendorf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.40
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.600, 127.500, 134.300, 90.00, 97.70, 90.00
R / Rfree (%) n/a / n/a

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate (pdb code 3pcn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate, PDB code: 3pcn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3pcn

Go back to Iron Binding Sites List in 3pcn
Iron binding site 1 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:23.5
occ:1.00
 O3 M:DHY550 1.6 16.8 0.5
OH M:TYR408 1.8 16.6 1.0
O4 M:DHY550 1.9 17.3 0.5
O3 M:DHY550 1.9 16.9 0.5
O4 M:DHY550 2.1 17.1 0.5
NE2 M:HIS460 2.2 13.4 1.0
NE2 M:HIS462 2.3 12.9 1.0
C3 M:DHY550 2.5 16.1 0.5
C3 M:DHY550 2.6 16.2 0.5
C4 M:DHY550 2.6 16.3 0.5
C4 M:DHY550 2.7 16.1 0.5
CZ M:TYR408 3.0 16.9 1.0
CE1 M:HIS460 3.0 12.7 1.0
CE1 M:HIS462 3.1 12.0 1.0
CD2 M:HIS460 3.4 12.8 1.0
CD2 M:HIS462 3.4 11.8 1.0
CE2 M:TYR408 3.6 17.3 1.0
C2 M:DHY550 3.8 16.1 0.5
C2 M:DHY550 4.0 16.3 0.5
C5 M:DHY550 4.0 16.4 0.5
CE1 M:TYR408 4.0 17.5 1.0
C5 M:DHY550 4.1 16.1 0.5
NH1 M:ARG457 4.2 12.3 1.0
ND1 M:HIS460 4.2 12.7 1.0
O M:HOH623 4.3 13.4 1.0
ND1 M:HIS462 4.3 12.2 1.0
O A:HOH204 4.3 16.8 1.0
CG M:HIS460 4.4 12.6 1.0
CG M:HIS462 4.5 12.0 1.0
OE1 M:GLN477 4.8 12.1 1.0
C1 M:DHY550 4.9 15.9 0.5
CD2 M:TYR408 4.9 18.1 1.0
C1 M:DHY550 5.0 16.1 0.5
C6 M:DHY550 5.0 16.0 0.5
C6 M:DHY550 5.0 16.2 0.5

Iron binding site 2 out of 6 in 3pcn

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Iron binding site 2 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:23.4
occ:1.00
 O3 N:DHY550 1.6 16.9 0.5
O3 N:DHY550 1.8 16.8 0.5
OH N:TYR408 1.8 16.8 1.0
O4 N:DHY550 1.9 17.6 0.5
O4 N:DHY550 2.0 16.9 0.5
NE2 N:HIS462 2.2 12.7 1.0
NE2 N:HIS460 2.3 13.4 1.0
C3 N:DHY550 2.5 16.1 0.5
C3 N:DHY550 2.6 16.4 0.5
C4 N:DHY550 2.6 16.1 0.5
C4 N:DHY550 2.7 16.4 0.5
CZ N:TYR408 2.9 16.9 1.0
CE1 N:HIS462 3.0 11.9 1.0
CD2 N:HIS460 3.3 12.9 1.0
CE1 N:HIS460 3.3 12.5 1.0
CD2 N:HIS462 3.3 11.9 1.0
CE2 N:TYR408 3.6 17.5 1.0
C2 N:DHY550 3.8 16.1 0.5
CE1 N:TYR408 3.9 17.2 1.0
C2 N:DHY550 3.9 16.4 0.5
C5 N:DHY550 4.0 16.0 0.5
C5 N:DHY550 4.0 16.4 0.5
ND1 N:HIS462 4.2 12.0 1.0
O N:HOH629 4.2 13.2 1.0
NH1 N:ARG457 4.2 11.5 1.0
O B:HOH235 4.3 16.6 1.0
CG N:HIS462 4.4 11.8 1.0
ND1 N:HIS460 4.4 12.5 1.0
CG N:HIS460 4.4 12.7 1.0
OE1 N:GLN477 4.8 11.7 1.0
C1 N:DHY550 4.9 16.0 0.5
CD2 N:TYR408 4.9 18.5 1.0
C6 N:DHY550 4.9 16.2 0.5
C1 N:DHY550 4.9 16.2 0.5
C6 N:DHY550 5.0 16.1 0.5

Iron binding site 3 out of 6 in 3pcn

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Iron binding site 3 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:23.8
occ:1.00
 O3 O:DHY550 1.5 16.9 0.5
O3 O:DHY550 1.8 16.7 0.5
O4 O:DHY550 1.9 17.5 0.5
OH O:TYR408 1.9 16.4 1.0
O4 O:DHY550 2.1 16.9 0.5
NE2 O:HIS460 2.2 13.2 1.0
NE2 O:HIS462 2.2 12.8 1.0
C3 O:DHY550 2.5 16.1 0.5
C3 O:DHY550 2.6 16.2 0.5
C4 O:DHY550 2.6 16.4 0.5
C4 O:DHY550 2.7 16.1 0.5
CE1 O:HIS460 2.9 12.8 1.0
CE1 O:HIS462 3.0 12.3 1.0
CZ O:TYR408 3.1 16.7 1.0
CD2 O:HIS460 3.3 13.1 1.0
CD2 O:HIS462 3.4 12.2 1.0
CE1 O:TYR408 3.7 17.6 1.0
C2 O:DHY550 3.8 16.1 0.5
C2 O:DHY550 3.9 16.3 0.5
C5 O:DHY550 3.9 16.4 0.5
C5 O:DHY550 4.0 16.0 0.5
CE2 O:TYR408 4.0 17.5 1.0
ND1 O:HIS460 4.1 12.9 1.0
NH1 O:ARG457 4.1 11.9 1.0
O O:HOH628 4.1 13.3 0.8
ND1 O:HIS462 4.2 12.1 1.0
CG O:HIS460 4.3 12.9 1.0
O C:HOH207 4.4 16.9 1.0
CG O:HIS462 4.4 12.2 1.0
C1 O:DHY550 4.8 16.0 0.5
OE1 O:GLN477 4.9 12.2 1.0
C1 O:DHY550 4.9 16.2 0.5
C6 O:DHY550 4.9 16.0 0.5
C6 O:DHY550 5.0 16.2 0.5

Iron binding site 4 out of 6 in 3pcn

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Iron binding site 4 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe600

b:23.6
occ:1.00
 O3 P:DHY550 1.7 16.9 0.5
O4 P:DHY550 1.8 17.3 0.5
O3 P:DHY550 1.9 16.7 0.5
OH P:TYR408 1.9 16.6 1.0
O4 P:DHY550 2.0 17.0 0.5
NE2 P:HIS462 2.2 12.6 1.0
NE2 P:HIS460 2.2 13.3 1.0
C4 P:DHY550 2.6 16.5 0.5
C3 P:DHY550 2.6 16.2 0.5
C3 P:DHY550 2.6 16.2 0.5
C4 P:DHY550 2.7 16.1 0.5
CE1 P:HIS462 3.0 11.7 1.0
CZ P:TYR408 3.0 16.9 1.0
CE1 P:HIS460 3.0 12.9 1.0
CD2 P:HIS460 3.3 12.9 1.0
CD2 P:HIS462 3.3 11.7 1.0
CE2 P:TYR408 3.7 17.2 1.0
C5 P:DHY550 3.9 16.4 0.5
C2 P:DHY550 3.9 16.1 0.5
C2 P:DHY550 4.0 16.2 0.5
CE1 P:TYR408 4.0 17.4 1.0
C5 P:DHY550 4.0 16.0 0.5
ND1 P:HIS462 4.2 12.2 1.0
O P:HOH627 4.2 13.3 0.8
NH1 P:ARG457 4.2 12.1 1.0
ND1 P:HIS460 4.2 13.1 1.0
O D:HOH693 4.2 16.8 0.8
CG P:HIS462 4.3 12.0 1.0
CG P:HIS460 4.4 13.1 1.0
OE1 P:GLN477 4.9 12.4 1.0
C6 P:DHY550 4.9 16.1 0.5
C1 P:DHY550 4.9 16.2 0.5
C1 P:DHY550 4.9 16.0 0.5
CD2 P:TYR408 5.0 18.1 1.0

Iron binding site 5 out of 6 in 3pcn

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Iron binding site 5 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe600

b:24.6
occ:1.00
 O3 Q:DHY550 1.6 16.7 0.5
O4 Q:DHY550 1.8 17.2 0.5
OH Q:TYR408 1.9 16.7 1.0
NE2 Q:HIS462 2.1 13.1 1.0
NE2 Q:HIS460 2.2 13.7 1.0
O3 Q:DHY550 2.5 16.7 0.5
O4 Q:DHY550 2.5 16.7 0.5
C3 Q:DHY550 2.6 16.1 0.5
C4 Q:DHY550 2.7 16.4 0.5
C3 Q:DHY550 2.9 16.3 0.5
C4 Q:DHY550 2.9 16.1 0.5
CZ Q:TYR408 3.0 17.3 1.0
CE1 Q:HIS462 3.0 12.3 1.0
CD2 Q:HIS460 3.2 13.0 1.0
CD2 Q:HIS462 3.2 12.2 1.0
CE1 Q:HIS460 3.2 13.1 1.0
CE2 Q:TYR408 3.6 17.6 1.0
C2 Q:DHY550 3.9 16.1 0.5
CE1 Q:TYR408 3.9 17.8 1.0
C5 Q:DHY550 4.0 16.4 0.5
NH1 Q:ARG457 4.1 12.3 1.0
O Q:HOH959 4.2 13.4 1.0
ND1 Q:HIS462 4.2 12.2 1.0
C2 Q:DHY550 4.3 16.2 0.5
CG Q:HIS462 4.3 12.2 1.0
C5 Q:DHY550 4.3 16.0 0.5
CG Q:HIS460 4.3 12.9 1.0
ND1 Q:HIS460 4.3 12.9 1.0
O E:HOH205 4.4 16.7 0.6
OE1 Q:GLN477 4.8 12.2 1.0
CD2 Q:TYR408 4.9 18.7 1.0
C1 Q:DHY550 5.0 16.1 0.5

Iron binding site 6 out of 6 in 3pcn

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Iron binding site 6 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe600

b:23.8
occ:1.00
 O3 R:DHY550 1.5 16.8 0.5
O4 R:DHY550 1.8 17.3 0.5
O3 R:DHY550 1.9 16.8 0.5
OH R:TYR408 2.0 16.6 1.0
O4 R:DHY550 2.2 17.0 0.5
NE2 R:HIS460 2.2 13.6 1.0
NE2 R:HIS462 2.3 13.0 1.0
C3 R:DHY550 2.5 16.0 0.5
C3 R:DHY550 2.6 16.1 0.5
C4 R:DHY550 2.6 16.4 0.5
C4 R:DHY550 2.7 16.0 0.5
CE1 R:HIS460 3.0 12.9 1.0
CE1 R:HIS462 3.1 12.4 1.0
CZ R:TYR408 3.1 17.1 1.0
CD2 R:HIS460 3.4 13.1 1.0
CD2 R:HIS462 3.5 12.1 1.0
C2 R:DHY550 3.8 16.2 0.5
CE2 R:TYR408 3.8 17.6 1.0
C2 R:DHY550 3.9 16.2 0.5
C5 R:DHY550 3.9 16.5 0.5
CE1 R:TYR408 4.0 17.8 1.0
C5 R:DHY550 4.1 16.0 0.5
NH1 R:ARG457 4.1 12.4 1.0
ND1 R:HIS460 4.2 12.8 1.0
O F:HOH1151 4.3 16.7 0.6
O R:HOH1188 4.3 13.3 1.0
ND1 R:HIS462 4.3 12.5 1.0
CG R:HIS460 4.4 13.1 1.0
CG R:HIS462 4.5 12.0 1.0
OE1 R:GLN477 4.7 12.4 1.0
C1 R:DHY550 4.8 16.1 0.5
C1 R:DHY550 4.9 16.2 0.5
C6 R:DHY550 4.9 16.1 0.5
C6 R:DHY550 5.0 16.1 0.5

Reference:

T.E.Elgren, A.M.Orville, K.A.Kelly, J.D.Lipscomb, D.H.Ohlendorf, L.Que Jr.. Crystal Structure and Resonance Raman Studies of Protocatechuate 3,4-Dioxygenase Complexed with 3,4-Dihydroxyphenylacetate. Biochemistry V. 36 11504 1997.
ISSN: ISSN 0006-2960
PubMed: 9298971
DOI: 10.1021/BI970691K
Page generated: Tue Aug 5 05:40:33 2025

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