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Iron in PDB 3pcb: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3- Hydroxybenzoate

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

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

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3- Hydroxybenzoate, PDB code: 3pcb was solved by N.Elango, 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 / 2.19
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.950, 127.560, 134.310, 90.00, 97.60, 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- Hydroxybenzoate (pdb code 3pcb). 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- Hydroxybenzoate, PDB code: 3pcb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3pcb

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Iron binding site 1 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3- Hydroxybenzoate


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

b:26.9
occ:1.00
OH M:TYR408 2.0 17.5 1.0
OH M:TYR447 2.0 22.0 1.0
NE2 M:HIS460 2.4 15.3 1.0
NE2 M:HIS462 2.4 14.0 1.0
CZ M:TYR408 3.0 18.2 1.0
CE1 M:HIS462 3.1 13.4 1.0
CE1 M:HIS460 3.1 14.4 1.0
C4 M:3HB550 3.3 26.3 1.0
CZ M:TYR447 3.3 20.9 1.0
O3 M:3HB550 3.4 23.7 1.0
CE2 M:TYR408 3.4 18.9 1.0
CD2 M:HIS460 3.5 14.6 1.0
CD2 M:HIS462 3.7 13.3 1.0
C3 M:3HB550 3.7 26.0 1.0
CE2 M:TYR447 3.8 20.6 1.0
CE1 M:TYR408 4.1 18.8 1.0
O M:HOH624 4.3 14.7 1.0
ND1 M:HIS462 4.3 13.5 1.0
NH1 M:ARG457 4.3 15.5 1.0
ND1 M:HIS460 4.3 14.6 1.0
O A:HOH203 4.3 16.9 1.0
CE1 M:TYR447 4.4 20.3 1.0
C5 M:3HB550 4.4 26.5 1.0
CG M:HIS460 4.5 14.4 1.0
CG M:HIS462 4.6 13.5 1.0
CD2 M:TYR408 4.7 19.7 1.0
CD2 A:TYR16 4.9 22.2 1.0

Iron binding site 2 out of 6 in 3pcb

Go back to Iron Binding Sites List in 3pcb
Iron binding site 2 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3- Hydroxybenzoate


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

b:27.4
occ:1.00
OH N:TYR408 1.8 17.0 1.0
OH N:TYR447 2.1 21.2 1.0
NE2 N:HIS462 2.3 13.2 1.0
NE2 N:HIS460 2.3 15.5 1.0
CZ N:TYR408 2.8 18.2 1.0
CE1 N:HIS462 3.1 12.7 1.0
CE1 N:HIS460 3.2 14.8 1.0
O3 N:3HB550 3.3 23.6 1.0
CZ N:TYR447 3.3 21.2 1.0
C4 N:3HB550 3.4 26.2 1.0
CD2 N:HIS462 3.4 12.6 1.0
CD2 N:HIS460 3.4 15.7 1.0
CE1 N:TYR408 3.5 19.0 1.0
C3 N:3HB550 3.7 26.1 1.0
CE2 N:TYR447 3.8 21.0 1.0
CE2 N:TYR408 3.8 18.5 1.0
O B:HOH242 4.2 16.6 1.0
O N:HOH630 4.3 14.2 1.0
ND1 N:HIS462 4.3 13.3 1.0
ND1 N:HIS460 4.4 14.9 1.0
CE1 N:TYR447 4.5 20.4 1.0
CG N:HIS462 4.5 13.0 1.0
NH1 N:ARG457 4.5 14.7 1.0
CG N:HIS460 4.5 15.0 1.0
C5 N:3HB550 4.5 26.4 1.0
CD1 N:TYR408 4.8 19.4 1.0
CD2 B:TYR16 4.8 22.5 1.0
OE1 N:GLN477 5.0 14.0 1.0

Iron binding site 3 out of 6 in 3pcb

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


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

b:27.1
occ:1.00
OH O:TYR408 1.9 18.7 1.0
OH O:TYR447 2.0 20.7 1.0
NE2 O:HIS462 2.2 13.9 1.0
NE2 O:HIS460 2.3 15.2 1.0
CE1 O:HIS462 2.9 13.5 1.0
CZ O:TYR408 3.0 18.3 1.0
CE1 O:HIS460 3.0 14.9 1.0
C4 O:3HB550 3.3 26.1 1.0
CZ O:TYR447 3.4 20.9 1.0
CD2 O:HIS462 3.4 13.6 1.0
O3 O:3HB550 3.4 23.7 1.0
CD2 O:HIS460 3.4 14.9 1.0
CE1 O:TYR408 3.6 19.2 1.0
C3 O:3HB550 3.8 25.9 1.0
CE2 O:TYR447 4.0 20.8 1.0
CE2 O:TYR408 4.0 18.9 1.0
ND1 O:HIS462 4.1 13.6 1.0
O O:HOH631 4.2 14.6 1.0
ND1 O:HIS460 4.3 15.4 1.0
O C:HOH207 4.3 16.9 1.0
CG O:HIS462 4.4 13.6 1.0
NH1 O:ARG457 4.4 15.2 1.0
CE1 O:TYR447 4.4 20.5 1.0
CG O:HIS460 4.4 15.3 1.0
C5 O:3HB550 4.5 26.5 1.0
CD1 O:TYR408 5.0 19.3 1.0

Iron binding site 4 out of 6 in 3pcb

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


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

b:27.1
occ:1.00
OH P:TYR408 1.8 17.7 1.0
OH P:TYR447 2.1 21.5 1.0
NE2 P:HIS460 2.3 15.6 1.0
NE2 P:HIS462 2.3 13.4 1.0
CZ P:TYR408 2.9 17.9 1.0
CE1 P:HIS460 3.0 15.1 1.0
CE1 P:HIS462 3.1 12.8 1.0
CZ P:TYR447 3.3 21.0 1.0
CD2 P:HIS462 3.4 12.4 1.0
CD2 P:HIS460 3.4 14.8 1.0
O3 P:3HB550 3.4 23.7 1.0
CE1 P:TYR408 3.5 18.8 1.0
C4 P:3HB550 3.5 26.2 1.0
CE2 P:TYR447 3.8 21.1 1.0
CE2 P:TYR408 3.9 18.5 1.0
C3 P:3HB550 3.9 25.9 1.0
O P:HOH633 4.1 14.7 1.0
O D:HOH714 4.1 17.3 1.0
ND1 P:HIS460 4.2 14.9 1.0
ND1 P:HIS462 4.2 12.8 1.0
CG P:HIS462 4.4 13.0 1.0
CG P:HIS460 4.4 14.9 1.0
CE1 P:TYR447 4.4 20.2 1.0
NH1 P:ARG457 4.4 15.9 1.0
C5 P:3HB550 4.6 26.4 1.0
CD1 P:TYR408 4.8 19.3 1.0
CD2 D:TYR16 4.9 22.4 1.0

Iron binding site 5 out of 6 in 3pcb

Go back to Iron Binding Sites List in 3pcb
Iron binding site 5 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3- Hydroxybenzoate


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

b:27.9
occ:1.00
OH Q:TYR408 1.9 18.5 1.0
OH Q:TYR447 2.0 21.5 1.0
NE2 Q:HIS462 2.2 13.8 1.0
NE2 Q:HIS460 2.2 15.6 1.0
CE1 Q:HIS462 3.0 12.8 1.0
CZ Q:TYR408 3.0 18.3 1.0
CE1 Q:HIS460 3.2 14.7 1.0
CD2 Q:HIS460 3.2 14.6 1.0
CZ Q:TYR447 3.3 21.2 1.0
CD2 Q:HIS462 3.3 13.2 1.0
C4 Q:3HB550 3.5 26.2 1.0
O3 Q:3HB550 3.6 23.5 1.0
CE1 Q:TYR408 3.7 18.8 1.0
CE2 Q:TYR447 3.8 21.1 1.0
C3 Q:3HB550 3.9 25.9 1.0
CE2 Q:TYR408 3.9 18.7 1.0
ND1 Q:HIS462 4.2 13.1 1.0
O Q:HOH987 4.2 14.9 1.0
NH1 Q:ARG457 4.3 16.1 1.0
O E:HOH207 4.3 17.2 1.0
ND1 Q:HIS460 4.3 15.1 1.0
CG Q:HIS462 4.3 13.4 1.0
CG Q:HIS460 4.3 15.1 1.0
CE1 Q:TYR447 4.4 20.1 1.0
C5 Q:3HB550 4.6 26.4 1.0
OE1 Q:GLN477 4.8 14.9 1.0

Iron binding site 6 out of 6 in 3pcb

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


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

b:26.7
occ:1.00
OH R:TYR408 1.8 17.7 1.0
OH R:TYR447 2.1 21.3 1.0
NE2 R:HIS460 2.3 15.2 1.0
NE2 R:HIS462 2.4 13.8 1.0
CZ R:TYR408 2.9 18.6 1.0
CE1 R:HIS460 3.2 14.9 1.0
CE1 R:HIS462 3.2 13.7 1.0
O3 R:3HB550 3.2 23.9 1.0
CZ R:TYR447 3.2 20.8 1.0
CD2 R:HIS460 3.4 15.1 1.0
C4 R:3HB550 3.4 26.2 1.0
CE2 R:TYR408 3.5 19.1 1.0
CD2 R:HIS462 3.5 13.2 1.0
CE2 R:TYR447 3.6 20.8 1.0
C3 R:3HB550 3.7 25.9 1.0
CE1 R:TYR408 3.9 18.6 1.0
O F:HOH1186 4.2 17.0 1.0
O R:HOH1223 4.2 14.8 1.0
NH1 R:ARG457 4.3 16.0 1.0
ND1 R:HIS460 4.3 15.1 1.0
ND1 R:HIS462 4.4 14.1 1.0
CE1 R:TYR447 4.4 20.4 1.0
CG R:HIS460 4.4 15.1 1.0
CG R:HIS462 4.6 13.4 1.0
C5 R:3HB550 4.6 26.4 1.0
CD2 R:TYR408 4.8 19.8 1.0
OE1 R:GLN477 4.9 14.4 1.0

Reference:

A.M.Orville, N.Elango, J.D.Lipscomb, D.H.Ohlendorf. Structures of Competitive Inhibitor Complexes of Protocatechuate 3,4-Dioxygenase: Multiple Exogenous Ligand Binding Orientations Within the Active Site. Biochemistry V. 36 10039 1997.
ISSN: ISSN 0006-2960
PubMed: 9254599
DOI: 10.1021/BI970468N
Page generated: Tue Aug 5 05:36:01 2025

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