Atomistry » Iron » PDB 3p4r-3pcn » 3pca
Atomistry »
  Iron »
    PDB 3p4r-3pcn »
      3pca »

Iron in PDB 3pca: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate

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

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

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate, PDB code: 3pca 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 / 2.20
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.300, 127.200, 133.800, 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 3,4- Dihydroxybenzoate (pdb code 3pca). 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- Dihydroxybenzoate, PDB code: 3pca:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3pca

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


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

b:24.5
occ:1.00
OH M:TYR408 1.9 16.5 1.0
O4 M:DHB550 2.0 19.1 1.0
NE2 M:HIS462 2.2 13.0 1.0
NE2 M:HIS460 2.2 13.7 1.0
O3 M:DHB550 2.5 17.0 1.0
C4 M:DHB550 2.9 17.9 1.0
CE1 M:HIS460 3.0 12.4 1.0
CE1 M:HIS462 3.0 12.1 1.0
C3 M:DHB550 3.1 16.9 1.0
CZ M:TYR408 3.1 17.4 1.0
CD2 M:HIS462 3.3 12.0 1.0
CD2 M:HIS460 3.4 13.2 1.0
CE2 M:TYR408 3.7 17.9 1.0
NH1 M:ARG457 4.1 13.2 1.0
CE1 M:TYR408 4.1 17.8 1.0
ND1 M:HIS460 4.2 12.9 1.0
ND1 M:HIS462 4.2 12.1 1.0
C5 M:DHB550 4.2 17.3 1.0
O A:HOH206 4.3 16.2 1.0
O M:HOH621 4.3 12.9 1.0
CG M:HIS462 4.3 12.2 1.0
CG M:HIS460 4.4 12.6 1.0
C2 M:DHB550 4.4 16.6 1.0
OE1 M:GLN477 4.7 13.1 1.0
CD2 M:TYR408 5.0 18.8 1.0

Iron binding site 2 out of 6 in 3pca

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


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

b:23.9
occ:1.00
OH N:TYR408 2.0 17.0 1.0
NE2 N:HIS462 2.2 12.2 1.0
O4 N:DHB550 2.2 18.9 1.0
NE2 N:HIS460 2.3 13.3 1.0
O3 N:DHB550 2.5 16.9 1.0
CE1 N:HIS462 3.0 11.6 1.0
C4 N:DHB550 3.0 17.8 1.0
C3 N:DHB550 3.1 17.0 1.0
CZ N:TYR408 3.1 17.7 1.0
CE1 N:HIS460 3.3 12.6 1.0
CD2 N:HIS462 3.3 11.3 1.0
CD2 N:HIS460 3.3 12.9 1.0
CE2 N:TYR408 3.7 18.0 1.0
CE1 N:TYR408 4.1 17.8 1.0
ND1 N:HIS462 4.2 11.4 1.0
O B:HOH238 4.2 15.8 1.0
NH1 N:ARG457 4.3 12.9 1.0
O N:HOH631 4.3 12.8 1.0
C5 N:DHB550 4.3 17.3 1.0
CG N:HIS462 4.3 11.4 1.0
ND1 N:HIS460 4.4 13.1 1.0
C2 N:DHB550 4.4 16.6 1.0
CG N:HIS460 4.5 12.8 1.0
OE1 N:GLN477 4.7 12.3 1.0
CD2 N:TYR408 5.0 18.7 1.0

Iron binding site 3 out of 6 in 3pca

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


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

b:23.6
occ:1.00
OH O:TYR408 2.0 17.3 1.0
O4 O:DHB550 2.1 18.8 1.0
NE2 O:HIS460 2.2 13.2 1.0
NE2 O:HIS462 2.2 12.9 1.0
O3 O:DHB550 2.5 17.1 1.0
C4 O:DHB550 3.0 17.6 1.0
CE1 O:HIS460 3.0 12.7 1.0
C3 O:DHB550 3.1 16.8 1.0
CE1 O:HIS462 3.1 12.2 1.0
CZ O:TYR408 3.2 17.4 1.0
CD2 O:HIS462 3.2 12.2 1.0
CD2 O:HIS460 3.2 13.0 1.0
CE1 O:TYR408 3.9 18.2 1.0
CE2 O:TYR408 4.1 17.6 1.0
NH1 O:ARG457 4.1 13.5 1.0
ND1 O:HIS460 4.2 13.4 1.0
O O:HOH629 4.2 13.1 1.0
C5 O:DHB550 4.3 17.2 1.0
ND1 O:HIS462 4.3 12.0 1.0
O C:HOH206 4.3 16.0 1.0
CG O:HIS462 4.3 11.9 1.0
CG O:HIS460 4.3 13.1 1.0
C2 O:DHB550 4.5 16.7 1.0
OE1 O:GLN477 4.7 13.1 1.0

Iron binding site 4 out of 6 in 3pca

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


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

b:24.8
occ:1.00
OH P:TYR408 2.0 16.9 1.0
O4 P:DHB550 2.2 18.9 1.0
NE2 P:HIS462 2.2 12.2 1.0
NE2 P:HIS460 2.2 13.7 1.0
O3 P:DHB550 2.4 16.9 1.0
C4 P:DHB550 2.9 17.9 1.0
CE1 P:HIS462 3.0 11.8 1.0
C3 P:DHB550 3.0 16.9 1.0
CE1 P:HIS460 3.0 13.0 1.0
CZ P:TYR408 3.0 17.5 1.0
CD2 P:HIS462 3.3 11.5 1.0
CD2 P:HIS460 3.4 13.1 1.0
CE2 P:TYR408 3.6 17.7 1.0
CE1 P:TYR408 4.1 17.8 1.0
NH1 P:ARG457 4.1 13.3 1.0
ND1 P:HIS462 4.2 11.6 1.0
C5 P:DHB550 4.2 17.4 1.0
ND1 P:HIS460 4.3 13.3 1.0
O P:HOH630 4.3 13.0 1.0
O D:HOH702 4.4 16.1 0.8
C2 P:DHB550 4.4 16.8 1.0
CG P:HIS462 4.4 11.7 1.0
CG P:HIS460 4.4 13.1 1.0
OE1 P:GLN477 4.7 12.8 1.0
CD2 P:TYR408 4.9 18.6 1.0

Iron binding site 5 out of 6 in 3pca

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


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

b:24.4
occ:0.80
OH Q:TYR408 1.9 17.3 1.0
NE2 Q:HIS462 2.1 12.9 1.0
O4 Q:DHB550 2.1 18.9 1.0
NE2 Q:HIS460 2.3 13.9 1.0
O3 Q:DHB550 2.7 17.1 1.0
CE1 Q:HIS462 3.0 12.2 1.0
C4 Q:DHB550 3.0 17.7 1.0
CZ Q:TYR408 3.1 17.9 1.0
CD2 Q:HIS462 3.1 12.2 1.0
CD2 Q:HIS460 3.2 13.3 1.0
C3 Q:DHB550 3.2 17.0 1.0
CE1 Q:HIS460 3.3 13.0 1.0
CE2 Q:TYR408 3.7 18.2 1.0
CE1 Q:TYR408 4.1 18.0 1.0
NH1 Q:ARG457 4.1 13.7 1.0
ND1 Q:HIS462 4.2 11.6 1.0
CG Q:HIS462 4.3 11.8 1.0
O Q:HOH971 4.3 13.3 1.0
O E:HOH206 4.3 16.2 0.8
C5 Q:DHB550 4.3 17.4 1.0
CG Q:HIS460 4.4 13.0 1.0
ND1 Q:HIS460 4.4 13.3 1.0
OE1 Q:GLN477 4.6 13.1 1.0
C2 Q:DHB550 4.6 16.7 1.0
CD2 Q:TYR408 5.0 19.0 1.0

Iron binding site 6 out of 6 in 3pca

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


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

b:24.2
occ:1.00
O4 R:DHB550 1.9 18.7 1.0
OH R:TYR408 2.1 17.4 1.0
NE2 R:HIS462 2.2 12.9 1.0
NE2 R:HIS460 2.3 13.4 1.0
O3 R:DHB550 2.4 16.9 1.0
C4 R:DHB550 2.8 17.7 1.0
C3 R:DHB550 3.0 16.8 1.0
CE1 R:HIS462 3.1 12.5 1.0
CE1 R:HIS460 3.2 12.4 1.0
CZ R:TYR408 3.2 17.5 1.0
CD2 R:HIS460 3.3 12.7 1.0
CD2 R:HIS462 3.3 11.8 1.0
CE2 R:TYR408 3.8 18.1 1.0
NH1 R:ARG457 4.0 13.8 1.0
C5 R:DHB550 4.1 17.4 1.0
CE1 R:TYR408 4.2 18.0 1.0
ND1 R:HIS462 4.3 12.1 1.0
O F:HOH1166 4.3 16.3 1.0
C2 R:DHB550 4.3 16.6 1.0
ND1 R:HIS460 4.3 12.9 1.0
O R:HOH1203 4.3 13.0 1.0
CG R:HIS462 4.4 11.7 1.0
CG R:HIS460 4.4 12.7 1.0
OE1 R:GLN477 4.6 13.3 1.0

Reference:

A.M.Orville, J.D.Lipscomb, D.H.Ohlendorf. Crystal Structures of Substrate and Substrate Analog Complexes of Protocatechuate 3,4-Dioxygenase: Endogenous FE3+ Ligand Displacement in Response to Substrate Binding. Biochemistry V. 36 10052 1997.
ISSN: ISSN 0006-2960
PubMed: 9254600
DOI: 10.1021/BI970469F
Page generated: Sun Aug 4 17:44:01 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy