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Iron in PDB 3pcg: Structure of Protocatechuate 3,4-Dioxygenase Complexed with the Inhibitor 4-Hydroxyphenylacetate

Enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with the Inhibitor 4-Hydroxyphenylacetate

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

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with the Inhibitor 4-Hydroxyphenylacetate, PDB code: 3pcg 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 / 1.96
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.320, 127.120, 134.130, 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 the Inhibitor 4-Hydroxyphenylacetate (pdb code 3pcg). 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 the Inhibitor 4-Hydroxyphenylacetate, PDB code: 3pcg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3pcg

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


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 the Inhibitor 4-Hydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:14.0
occ:0.80
O4 M:4HP550 1.7 17.4 1.0
OH M:TYR408 1.8 14.9 1.0
OH M:TYR447 1.8 16.7 1.0
NE2 M:HIS460 2.2 11.5 1.0
NE2 M:HIS462 2.3 12.6 1.0
C4 M:4HP550 2.7 18.6 1.0
CZ M:TYR408 2.9 14.1 1.0
CE1 M:HIS460 2.9 11.2 1.0
CZ M:TYR447 3.0 17.0 1.0
CE1 M:HIS462 3.2 12.1 1.0
CE2 M:TYR408 3.3 14.9 1.0
CD2 M:HIS460 3.3 11.2 1.0
CD2 M:HIS462 3.4 11.7 1.0
C5 M:4HP550 3.4 19.0 1.0
CE2 M:TYR447 3.5 17.2 1.0
C3 M:4HP550 3.5 18.2 1.0
CE1 M:TYR408 4.0 14.6 1.0
O M:HOH627 4.0 10.8 1.0
ND1 M:HIS460 4.1 10.9 1.0
CE1 M:TYR447 4.2 16.9 1.0
O A:HOH203 4.3 13.9 1.0
ND1 M:HIS462 4.4 11.4 1.0
CG M:HIS460 4.4 11.0 1.0
CG M:HIS462 4.4 11.6 1.0
NH1 M:ARG457 4.5 10.1 1.0
C6 M:4HP550 4.7 19.6 1.0
CD2 M:TYR408 4.7 15.5 1.0
C2 M:4HP550 4.7 19.1 1.0
CD2 M:TYR447 4.9 17.2 1.0
OE1 M:GLN477 5.0 9.9 1.0
CD2 A:TYR16 5.0 20.1 1.0

Iron binding site 2 out of 6 in 3pcg

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


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 the Inhibitor 4-Hydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:13.3
occ:0.80
OH N:TYR408 1.7 12.5 1.0
O4 N:4HP550 1.8 17.3 1.0
OH N:TYR447 2.1 16.0 1.0
NE2 N:HIS460 2.2 11.1 1.0
NE2 N:HIS462 2.2 11.5 1.0
C4 N:4HP550 2.7 18.4 1.0
CZ N:TYR408 2.8 13.7 1.0
CE1 N:HIS460 3.0 10.6 1.0
CE1 N:HIS462 3.1 12.0 1.0
CD2 N:HIS462 3.2 10.5 1.0
CZ N:TYR447 3.3 17.4 1.0
CD2 N:HIS460 3.3 11.4 1.0
CE2 N:TYR408 3.4 14.9 1.0
C5 N:4HP550 3.5 19.2 1.0
C3 N:4HP550 3.5 18.3 1.0
CE2 N:TYR447 3.7 18.1 1.0
CE1 N:TYR408 3.9 14.7 1.0
O N:HOH628 4.2 11.0 1.0
ND1 N:HIS460 4.2 10.8 1.0
O B:HOH245 4.2 13.7 1.0
ND1 N:HIS462 4.3 11.2 1.0
CG N:HIS460 4.4 11.1 1.0
NH1 N:ARG457 4.4 11.0 1.0
CG N:HIS462 4.4 11.0 1.0
CE1 N:TYR447 4.4 16.7 1.0
C6 N:4HP550 4.7 19.6 1.0
CD2 N:TYR408 4.7 15.7 1.0
C2 N:4HP550 4.8 19.1 1.0
OE1 N:GLN477 4.9 10.0 1.0

Iron binding site 3 out of 6 in 3pcg

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


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 the Inhibitor 4-Hydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:13.7
occ:0.80
O4 O:4HP550 1.7 17.3 1.0
OH O:TYR408 1.8 13.8 1.0
OH O:TYR447 2.0 15.7 1.0
NE2 O:HIS460 2.1 11.5 1.0
NE2 O:HIS462 2.2 11.7 1.0
C4 O:4HP550 2.7 18.5 1.0
CE1 O:HIS460 2.9 11.1 1.0
CZ O:TYR408 2.9 14.0 1.0
CE1 O:HIS462 3.1 11.6 1.0
CZ O:TYR447 3.2 16.9 1.0
CD2 O:HIS460 3.3 11.8 1.0
CD2 O:HIS462 3.3 11.5 1.0
C5 O:4HP550 3.5 19.0 1.0
C3 O:4HP550 3.6 18.3 1.0
CE1 O:TYR408 3.6 14.7 1.0
CE2 O:TYR447 3.7 17.6 1.0
CE2 O:TYR408 3.9 14.5 1.0
O O:HOH631 4.0 11.3 1.0
ND1 O:HIS460 4.1 11.5 1.0
O C:HOH204 4.3 13.9 1.0
ND1 O:HIS462 4.3 11.1 1.0
CG O:HIS460 4.3 11.4 1.0
CG O:HIS462 4.4 11.6 1.0
NH1 O:ARG457 4.4 9.9 1.0
CE1 O:TYR447 4.4 17.2 1.0
C6 O:4HP550 4.7 19.7 1.0
C2 O:4HP550 4.8 19.1 1.0
OE1 O:GLN477 4.9 10.7 1.0
CD1 O:TYR408 4.9 15.7 1.0

Iron binding site 4 out of 6 in 3pcg

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


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 the Inhibitor 4-Hydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe600

b:14.0
occ:0.80
OH P:TYR408 1.7 14.3 1.0
O4 P:4HP550 1.7 17.1 1.0
OH P:TYR447 1.8 16.5 1.0
NE2 P:HIS460 2.1 12.0 1.0
NE2 P:HIS462 2.2 12.5 1.0
C4 P:4HP550 2.8 18.7 1.0
CZ P:TYR408 2.8 14.0 1.0
CE1 P:HIS460 2.9 11.6 1.0
CZ P:TYR447 3.0 17.2 1.0
CE1 P:HIS462 3.1 11.9 1.0
CD2 P:HIS460 3.2 11.9 1.0
CD2 P:HIS462 3.3 11.7 1.0
CE2 P:TYR408 3.3 14.4 1.0
CE2 P:TYR447 3.5 17.5 1.0
C5 P:4HP550 3.5 19.1 1.0
C3 P:4HP550 3.7 18.2 1.0
CE1 P:TYR408 3.9 14.5 1.0
O P:HOH634 4.0 11.2 1.0
ND1 P:HIS460 4.1 11.0 1.0
CE1 P:TYR447 4.2 17.0 1.0
CG P:HIS460 4.3 11.6 1.0
ND1 P:HIS462 4.3 11.8 1.0
O D:HOH723 4.3 14.2 1.0
CG P:HIS462 4.4 11.6 1.0
NH1 P:ARG457 4.5 10.1 1.0
CD2 P:TYR408 4.7 15.4 1.0
C6 P:4HP550 4.8 19.6 1.0
CD2 P:TYR447 4.9 17.0 1.0
C2 P:4HP550 4.9 19.0 1.0

Iron binding site 5 out of 6 in 3pcg

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


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 the Inhibitor 4-Hydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe600

b:14.6
occ:0.80
OH Q:TYR408 1.8 14.3 1.0
O4 Q:4HP550 1.9 17.8 1.0
OH Q:TYR447 1.9 16.6 1.0
NE2 Q:HIS460 2.0 12.3 1.0
NE2 Q:HIS462 2.2 12.4 1.0
C4 Q:4HP550 2.8 18.5 1.0
CZ Q:TYR408 3.0 14.7 1.0
CD2 Q:HIS460 3.0 12.0 1.0
CE1 Q:HIS460 3.0 11.3 1.0
CZ Q:TYR447 3.1 17.4 1.0
CD2 Q:HIS462 3.2 10.9 1.0
CE1 Q:HIS462 3.2 11.4 1.0
C5 Q:4HP550 3.5 19.1 1.0
CE1 Q:TYR408 3.6 14.9 1.0
CE2 Q:TYR447 3.6 17.6 1.0
C3 Q:4HP550 3.6 18.2 1.0
CE2 Q:TYR408 4.0 15.1 1.0
O Q:HOH999 4.1 11.7 1.0
ND1 Q:HIS460 4.1 11.9 1.0
CG Q:HIS460 4.1 11.4 1.0
O Q:HOH962 4.2 14.0 1.0
NH1 Q:ARG457 4.2 10.6 1.0
ND1 Q:HIS462 4.3 11.9 1.0
CE1 Q:TYR447 4.3 17.1 1.0
CG Q:HIS462 4.3 11.3 1.0
C6 Q:4HP550 4.8 19.7 1.0
C2 Q:4HP550 4.8 19.1 1.0
OE1 Q:GLN477 4.9 10.2 1.0
CD1 Q:TYR408 4.9 15.5 1.0
CD2 Q:TYR447 5.0 17.3 1.0

Iron binding site 6 out of 6 in 3pcg

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


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 the Inhibitor 4-Hydroxyphenylacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe600

b:13.7
occ:0.80
O4 R:4HP550 1.8 17.2 1.0
OH R:TYR408 1.8 14.0 1.0
OH R:TYR447 2.0 16.4 1.0
NE2 R:HIS460 2.3 12.4 1.0
NE2 R:HIS462 2.3 12.0 1.0
C4 R:4HP550 2.6 18.6 1.0
CZ R:TYR408 2.9 14.2 1.0
CE1 R:HIS460 3.1 11.6 1.0
CZ R:TYR447 3.2 17.6 1.0
CE1 R:HIS462 3.2 11.8 1.0
C5 R:4HP550 3.3 19.0 1.0
CD2 R:HIS460 3.3 11.9 1.0
CD2 R:HIS462 3.4 11.9 1.0
CE2 R:TYR408 3.5 14.9 1.0
C3 R:4HP550 3.6 18.2 1.0
CE2 R:TYR447 3.6 17.4 1.0
CE1 R:TYR408 3.9 14.8 1.0
O R:HOH1238 4.0 11.2 1.0
O F:HOH1201 4.2 14.3 1.0
ND1 R:HIS460 4.3 10.9 1.0
CE1 R:TYR447 4.3 17.0 1.0
CG R:HIS460 4.4 11.7 1.0
ND1 R:HIS462 4.4 11.2 1.0
NH1 R:ARG457 4.5 10.3 1.0
CG R:HIS462 4.5 11.6 1.0
C6 R:4HP550 4.6 19.7 1.0
C2 R:4HP550 4.7 19.2 1.0
CD2 R:TYR408 4.8 16.0 1.0
CD2 R:TYR447 5.0 17.7 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 17:50:32 2024

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