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

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

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

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate, PDB code: 3pci was solved by A.M.Orville, N.Elango, 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 / 2.21
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 197.000, 127.070, 134.080, 90.00, 97.53, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3pci:

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate also contains other interesting chemical elements:

Iodine (I) 12 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate (pdb code 3pci). 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-Iodo-4- Hydroxybenzoate, PDB code: 3pci:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3pci

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Iron binding site 1 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- 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-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:28.7
occ:1.00
O4 M:IHB550 1.6 23.0 1.0
OH M:TYR408 1.8 17.9 1.0
OH M:TYR447 2.2 18.1 1.0
NE2 M:HIS460 2.3 15.6 1.0
NE2 M:HIS462 2.3 15.8 1.0
C4 M:IHB550 2.8 26.6 1.0
CZ M:TYR408 2.9 17.9 1.0
CE1 M:HIS460 3.0 14.2 1.0
CE1 M:HIS462 3.2 14.3 1.0
CD2 M:HIS462 3.4 14.2 1.0
CE2 M:TYR408 3.4 17.8 1.0
CZ M:TYR447 3.4 17.6 1.0
C5 M:IHB550 3.4 26.2 1.0
CD2 M:HIS460 3.5 14.5 1.0
CE2 M:TYR447 3.8 17.0 1.0
C3 M:IHB550 3.9 28.4 1.0
CE1 M:TYR408 4.0 18.0 1.0
O M:HOH625 4.0 13.9 1.0
ND1 M:HIS460 4.2 14.3 1.0
ND1 M:HIS462 4.3 14.0 1.0
I3 M:IHB550 4.4 34.4 1.0
CG M:HIS462 4.4 13.7 1.0
O A:HOH205 4.5 17.0 1.0
CG M:HIS460 4.5 14.2 1.0
CE1 M:TYR447 4.5 17.5 1.0
NH1 M:ARG457 4.6 14.4 1.0
CD2 M:TYR408 4.7 18.6 1.0
C6 M:IHB550 4.8 25.7 1.0
OE1 M:GLN477 5.0 14.8 1.0

Iron binding site 2 out of 6 in 3pci

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Iron binding site 2 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- 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-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:28.8
occ:1.00
O4 N:IHB550 1.6 23.1 1.0
OH N:TYR408 1.8 17.6 1.0
OH N:TYR447 2.1 17.8 1.0
NE2 N:HIS460 2.3 15.3 1.0
NE2 N:HIS462 2.4 15.4 1.0
C4 N:IHB550 2.7 26.6 1.0
CZ N:TYR408 2.9 17.5 1.0
CE1 N:HIS460 3.1 14.1 1.0
CE1 N:HIS462 3.2 14.6 1.0
CZ N:TYR447 3.3 18.0 1.0
C5 N:IHB550 3.3 26.2 1.0
CD2 N:HIS460 3.3 14.3 1.0
CD2 N:HIS462 3.4 13.8 1.0
CE1 N:TYR408 3.6 17.6 1.0
CE2 N:TYR447 3.8 17.2 1.0
C3 N:IHB550 3.8 28.4 1.0
CE2 N:TYR408 3.9 18.1 1.0
O N:HOH631 4.1 13.7 1.0
ND1 N:HIS460 4.2 14.3 1.0
I3 N:IHB550 4.3 34.5 1.0
ND1 N:HIS462 4.4 14.4 1.0
O B:HOH252 4.4 17.1 1.0
CG N:HIS460 4.4 14.9 1.0
CE1 N:TYR447 4.5 17.7 1.0
CG N:HIS462 4.5 14.0 1.0
NH1 N:ARG457 4.6 13.5 1.0
C6 N:IHB550 4.7 25.6 1.0
CD1 N:TYR408 4.9 18.7 1.0

Iron binding site 3 out of 6 in 3pci

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Iron binding site 3 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- 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-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:28.8
occ:1.00
O4 O:IHB550 1.6 23.2 0.8
OH O:TYR408 1.9 18.4 1.0
OH O:TYR447 2.2 17.9 1.0
NE2 O:HIS462 2.2 16.1 1.0
NE2 O:HIS460 2.2 15.6 1.0
C4 O:IHB550 2.9 26.7 0.8
CZ O:TYR408 3.0 18.0 1.0
CE1 O:HIS460 3.1 14.4 1.0
CE1 O:HIS462 3.1 14.8 1.0
CD2 O:HIS462 3.2 14.6 1.0
CD2 O:HIS460 3.2 15.1 1.0
CZ O:TYR447 3.4 17.8 1.0
C5 O:IHB550 3.5 26.2 0.8
CE1 O:TYR408 3.7 18.4 1.0
CE2 O:TYR447 3.8 17.4 1.0
CE2 O:TYR408 3.9 18.1 1.0
C3 O:IHB550 3.9 28.5 0.8
O O:HOH632 4.0 14.4 1.0
ND1 O:HIS460 4.3 14.5 1.0
ND1 O:HIS462 4.3 14.4 1.0
CG O:HIS462 4.3 14.2 1.0
CG O:HIS460 4.3 15.1 1.0
NH1 O:ARG457 4.4 14.2 1.0
I3 O:IHB550 4.4 34.6 0.8
O C:HOH205 4.5 17.0 1.0
CE1 O:TYR447 4.5 17.6 1.0
C6 O:IHB550 4.9 25.7 0.8

Iron binding site 4 out of 6 in 3pci

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Iron binding site 4 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- 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-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe600

b:28.1
occ:1.00
O4 P:IHB550 1.6 23.0 1.0
OH P:TYR408 1.8 18.4 1.0
OH P:TYR447 2.1 18.1 1.0
NE2 P:HIS460 2.2 15.5 1.0
NE2 P:HIS462 2.3 15.4 1.0
C4 P:IHB550 2.8 26.7 1.0
CZ P:TYR408 2.9 17.8 1.0
CE1 P:HIS460 2.9 14.6 1.0
CE1 P:HIS462 3.1 14.1 1.0
CZ P:TYR447 3.3 18.1 1.0
CD2 P:HIS462 3.3 14.4 1.0
CD2 P:HIS460 3.4 15.0 1.0
C5 P:IHB550 3.4 26.1 1.0
CE2 P:TYR408 3.5 17.3 1.0
CE2 P:TYR447 3.7 17.6 1.0
C3 P:IHB550 3.9 28.4 1.0
CE1 P:TYR408 4.0 17.7 1.0
O P:HOH631 4.0 14.4 1.0
ND1 P:HIS460 4.2 14.4 1.0
O D:HOH744 4.2 17.2 1.0
ND1 P:HIS462 4.2 14.1 1.0
I3 P:IHB550 4.3 34.7 1.0
NH1 P:ARG457 4.4 14.3 1.0
CG P:HIS460 4.4 14.8 1.0
CG P:HIS462 4.4 14.2 1.0
CE1 P:TYR447 4.4 17.4 1.0
CD2 P:TYR408 4.8 18.1 1.0
C6 P:IHB550 4.8 25.7 1.0

Iron binding site 5 out of 6 in 3pci

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Iron binding site 5 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- 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-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe600

b:28.4
occ:1.00
O4 Q:IHB550 1.5 23.4 1.0
OH Q:TYR408 1.8 18.4 1.0
OH Q:TYR447 2.0 18.2 1.0
NE2 Q:HIS460 2.1 15.8 1.0
NE2 Q:HIS462 2.3 16.0 1.0
C4 Q:IHB550 2.8 26.8 1.0
CZ Q:TYR408 2.9 18.4 1.0
CE1 Q:HIS460 3.1 15.1 1.0
CD2 Q:HIS460 3.2 14.8 1.0
CE1 Q:HIS462 3.2 15.0 1.0
CD2 Q:HIS462 3.3 15.1 1.0
CZ Q:TYR447 3.3 18.1 1.0
C5 Q:IHB550 3.5 26.2 1.0
CE1 Q:TYR408 3.5 18.1 1.0
CE2 Q:TYR408 3.9 18.3 1.0
CE2 Q:TYR447 3.9 17.4 1.0
C3 Q:IHB550 3.9 28.6 1.0
O Q:HOH1027 4.0 14.5 1.0
ND1 Q:HIS460 4.2 14.7 1.0
O E:HOH205 4.2 17.3 1.0
CG Q:HIS460 4.3 15.0 1.0
ND1 Q:HIS462 4.3 14.7 1.0
I3 Q:IHB550 4.4 34.8 1.0
CG Q:HIS462 4.4 15.1 1.0
CE1 Q:TYR447 4.4 17.5 1.0
NH1 Q:ARG457 4.5 14.4 1.0
CD1 Q:TYR408 4.8 19.0 1.0
C6 Q:IHB550 4.9 25.7 1.0
OE1 Q:GLN477 4.9 13.8 1.0

Iron binding site 6 out of 6 in 3pci

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Iron binding site 6 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- 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-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe600

b:28.6
occ:1.00
O4 R:IHB550 1.5 23.1 1.0
OH R:TYR408 2.0 18.7 1.0
OH R:TYR447 2.2 18.0 1.0
NE2 R:HIS460 2.2 15.7 1.0
NE2 R:HIS462 2.3 15.9 1.0
C4 R:IHB550 2.8 26.7 1.0
CZ R:TYR408 3.0 18.1 1.0
CE1 R:HIS460 3.1 14.4 1.0
CE1 R:HIS462 3.3 15.2 1.0
CD2 R:HIS462 3.3 14.7 1.0
CD2 R:HIS460 3.3 15.1 1.0
CZ R:TYR447 3.4 17.8 1.0
C5 R:IHB550 3.6 26.2 1.0
CE2 R:TYR408 3.6 18.1 1.0
C3 R:IHB550 3.9 28.6 1.0
CE2 R:TYR447 4.0 17.5 1.0
CE1 R:TYR408 4.0 18.4 1.0
O R:HOH1273 4.1 13.9 1.0
I3 R:IHB550 4.2 34.6 1.0
O F:HOH1236 4.3 17.3 1.0
ND1 R:HIS460 4.3 14.4 1.0
CG R:HIS460 4.4 14.9 1.0
ND1 R:HIS462 4.4 14.4 1.0
CG R:HIS462 4.4 14.4 1.0
NH1 R:ARG457 4.4 14.9 1.0
CE1 R:TYR447 4.5 17.6 1.0
CD2 R:TYR408 4.9 18.8 1.0
C6 R:IHB550 5.0 25.7 1.0
OE1 R:GLN477 5.0 14.8 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: Sun Aug 4 17:51:25 2024

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