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

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

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

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Chloro- 4-Hydroxybenzoate, PDB code: 3pch 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 / 2.05
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 195.390, 126.520, 133.330, 90.00, 97.77, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3pch:

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

Chlorine (Cl) 12 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 3pch

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

b:19.0
occ:1.00
OH M:TYR408 1.9 17.3 1.0
O4 M:CHB550 2.0 18.7 1.0
O M:HOH742 2.0 18.3 1.0
OH M:TYR447 2.2 22.1 1.0
NE2 M:HIS460 2.2 13.9 1.0
NE2 M:HIS462 2.3 14.4 1.0
CZ M:TYR408 2.9 17.5 1.0
CE1 M:HIS460 3.1 12.5 1.0
CE1 M:HIS462 3.2 13.2 1.0
C4 M:CHB550 3.2 20.2 1.0
CD2 M:HIS462 3.3 13.7 1.0
CD2 M:HIS460 3.4 13.1 1.0
CZ M:TYR447 3.4 22.4 1.0
CE2 M:TYR408 3.5 17.4 1.0
CE1 M:TYR447 3.8 22.4 1.0
CE1 M:TYR408 3.9 17.8 1.0
C5 M:CHB550 4.0 20.9 1.0
C3 M:CHB550 4.2 19.8 1.0
O M:HOH625 4.2 11.7 1.0
NH1 M:ARG457 4.3 12.3 1.0
ND1 M:HIS460 4.3 11.9 1.0
O A:HOH606 4.3 15.2 1.0
CL3 M:CHB550 4.3 20.2 1.0
ND1 M:HIS462 4.3 13.1 1.0
CG M:HIS462 4.4 13.3 1.0
CG M:HIS460 4.4 12.3 1.0
CE2 M:TYR447 4.6 21.9 1.0
CD2 M:TYR408 4.9 17.9 1.0
CD2 A:TYR16 5.0 20.8 1.0

Iron binding site 2 out of 6 in 3pch

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

b:20.0
occ:1.00
OH N:TYR408 1.8 16.2 1.0
O4 N:CHB550 2.0 18.5 1.0
O N:HOH846 2.0 17.8 1.0
NE2 N:HIS460 2.2 14.4 1.0
OH N:TYR447 2.3 21.5 1.0
NE2 N:HIS462 2.3 14.0 1.0
CZ N:TYR408 2.9 16.7 1.0
CE1 N:HIS460 2.9 12.7 1.0
C4 N:CHB550 3.2 19.8 1.0
CE1 N:HIS462 3.2 13.6 1.0
CD2 N:HIS462 3.2 12.9 1.0
CD2 N:HIS460 3.3 13.9 1.0
CZ N:TYR447 3.5 22.5 1.0
CE2 N:TYR408 3.6 17.2 1.0
CE1 N:TYR408 3.8 16.9 1.0
C5 N:CHB550 4.0 20.8 1.0
CE1 N:TYR447 4.0 22.3 1.0
C3 N:CHB550 4.0 19.9 1.0
ND1 N:HIS460 4.1 13.0 1.0
CL3 N:CHB550 4.1 19.5 1.0
NH1 N:ARG457 4.2 11.6 1.0
O N:HOH721 4.2 11.8 1.0
O B:HOH606 4.2 14.9 1.0
ND1 N:HIS462 4.3 13.6 1.0
CG N:HIS460 4.4 12.9 1.0
CG N:HIS462 4.4 13.3 1.0
CE2 N:TYR447 4.6 22.4 1.0
OE1 N:GLN477 4.9 10.3 1.0
CD2 N:TYR408 4.9 18.1 1.0

Iron binding site 3 out of 6 in 3pch

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

b:20.4
occ:1.00
OH O:TYR408 1.9 16.8 1.0
O O:HOH861 2.0 18.4 1.0
O4 O:CHB550 2.0 18.9 1.0
NE2 O:HIS462 2.0 14.9 1.0
OH O:TYR447 2.1 21.6 1.0
NE2 O:HIS460 2.1 14.1 1.0
CE1 O:HIS460 2.9 13.4 1.0
CZ O:TYR408 3.0 17.3 1.0
CE1 O:HIS462 3.0 14.5 1.0
CD2 O:HIS462 3.0 14.2 1.0
C4 O:CHB550 3.3 20.1 1.0
CD2 O:HIS460 3.3 13.3 1.0
CZ O:TYR447 3.4 22.4 1.0
CE1 O:TYR408 3.8 17.1 1.0
CE2 O:TYR408 3.8 17.4 1.0
CE1 O:TYR447 4.0 22.6 1.0
O O:HOH643 4.0 12.1 1.0
C5 O:CHB550 4.0 20.6 1.0
ND1 O:HIS460 4.1 13.0 1.0
C3 O:CHB550 4.1 20.0 1.0
ND1 O:HIS462 4.2 13.2 1.0
CG O:HIS462 4.2 13.5 1.0
CL3 O:CHB550 4.2 19.8 1.0
NH1 O:ARG457 4.3 11.2 1.0
CG O:HIS460 4.3 12.8 1.0
O C:HOH606 4.3 15.2 1.0
CE2 O:TYR447 4.4 22.6 1.0
OE1 O:GLN477 4.8 9.9 1.0

Iron binding site 4 out of 6 in 3pch

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

b:18.9
occ:1.00
OH P:TYR408 1.8 17.0 1.0
NE2 P:HIS462 2.2 13.2 1.0
OH P:TYR447 2.2 21.2 1.0
O P:HOH778 2.2 18.3 0.8
O4 P:CHB550 2.2 18.9 1.0
NE2 P:HIS460 2.3 14.2 1.0
CZ P:TYR408 2.9 17.0 1.0
CE1 P:HIS460 3.0 13.3 1.0
CE1 P:HIS462 3.0 12.4 1.0
CD2 P:HIS462 3.2 12.1 1.0
CD2 P:HIS460 3.3 13.1 1.0
C4 P:CHB550 3.4 20.0 1.0
CZ P:TYR447 3.5 22.2 1.0
CE2 P:TYR408 3.6 17.8 1.0
CE1 P:TYR408 3.8 17.5 1.0
O D:HOH606 4.0 15.3 1.0
CE2 P:TYR447 4.1 22.3 1.0
O P:HOH666 4.1 11.9 1.0
ND1 P:HIS462 4.2 12.6 1.0
C5 P:CHB550 4.2 20.8 1.0
CL3 P:CHB550 4.2 19.3 1.0
C3 P:CHB550 4.2 19.8 1.0
ND1 P:HIS460 4.2 13.8 1.0
NH1 P:ARG457 4.3 12.7 1.0
CG P:HIS462 4.3 11.6 1.0
CG P:HIS460 4.4 13.3 1.0
CE1 P:TYR447 4.6 21.9 1.0
CD2 P:TYR408 4.9 18.2 1.0
CD2 D:TYR16 5.0 21.4 1.0
OE1 P:GLN477 5.0 10.7 1.0

Iron binding site 5 out of 6 in 3pch

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

b:18.3
occ:0.80
OH Q:TYR408 1.8 16.4 1.0
OH Q:TYR447 2.0 20.9 1.0
O4 Q:CHB550 2.1 19.2 1.0
O Q:HOH774 2.2 18.3 0.8
NE2 Q:HIS462 2.2 13.6 1.0
NE2 Q:HIS460 2.2 13.7 1.0
CZ Q:TYR408 2.9 17.0 1.0
CE1 Q:HIS460 3.1 12.5 1.0
CE1 Q:HIS462 3.1 13.1 1.0
CD2 Q:HIS462 3.2 12.9 1.0
CD2 Q:HIS460 3.2 12.6 1.0
CZ Q:TYR447 3.3 22.3 1.0
C4 Q:CHB550 3.3 20.2 1.0
CE2 Q:TYR408 3.7 17.4 1.0
CE1 Q:TYR408 3.8 17.1 1.0
CE1 Q:TYR447 4.0 22.5 1.0
C5 Q:CHB550 4.1 20.7 1.0
NH1 Q:ARG457 4.1 12.2 1.0
O E:HOH606 4.2 15.4 1.0
CL3 Q:CHB550 4.2 19.4 1.0
O Q:HOH651 4.2 12.2 1.0
C3 Q:CHB550 4.2 20.0 1.0
ND1 Q:HIS460 4.2 12.8 1.0
ND1 Q:HIS462 4.3 12.8 1.0
CG Q:HIS462 4.3 13.0 1.0
CG Q:HIS460 4.3 12.9 1.0
CE2 Q:TYR447 4.4 21.9 1.0
OE1 Q:GLN477 4.7 11.1 1.0
CD2 Q:TYR408 5.0 18.2 1.0

Iron binding site 6 out of 6 in 3pch

Go back to Iron Binding Sites List in 3pch
Iron binding site 6 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Chloro- 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-Chloro- 4-Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe600

b:19.8
occ:1.00
OH R:TYR408 1.8 16.3 1.0
O4 R:CHB550 2.0 18.8 1.0
O R:HOH861 2.1 18.0 1.0
NE2 R:HIS462 2.2 14.1 1.0
OH R:TYR447 2.2 21.8 1.0
NE2 R:HIS460 2.3 14.3 1.0
CZ R:TYR408 2.9 17.1 1.0
CE1 R:HIS462 3.1 13.7 1.0
CD2 R:HIS462 3.2 13.2 1.0
C4 R:CHB550 3.2 20.1 1.0
CE1 R:HIS460 3.2 13.6 1.0
CD2 R:HIS460 3.4 13.7 1.0
CZ R:TYR447 3.5 22.7 1.0
CE1 R:TYR408 3.7 17.2 1.0
CE2 R:TYR408 3.9 17.6 1.0
CE2 R:TYR447 3.9 23.1 1.0
C5 R:CHB550 4.0 21.0 1.0
C3 R:CHB550 4.0 19.9 1.0
CL3 R:CHB550 4.1 20.0 1.0
NH1 R:ARG457 4.1 12.8 1.0
O F:HOH606 4.2 15.4 1.0
O R:HOH643 4.2 11.7 1.0
ND1 R:HIS462 4.3 13.0 1.0
CG R:HIS462 4.3 13.0 1.0
ND1 R:HIS460 4.4 13.1 1.0
CG R:HIS460 4.5 13.6 1.0
CE1 R:TYR447 4.6 22.3 1.0
OE1 R:GLN477 4.8 10.6 1.0
CD1 R:TYR408 5.0 18.2 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 Dec 13 15:17:17 2020

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