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Iron in PDB 3pcj: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 2- Hydroxyisonicotinic Acid N-Oxide

Enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 2- Hydroxyisonicotinic Acid N-Oxide

All present enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 2- Hydroxyisonicotinic Acid N-Oxide:
1.13.11.3;

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 2- Hydroxyisonicotinic Acid N-Oxide, PDB code: 3pcj 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 / 2.13
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.200, 127.100, 133.700, 90.00, 97.70, 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 2- Hydroxyisonicotinic Acid N-Oxide (pdb code 3pcj). 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 2- Hydroxyisonicotinic Acid N-Oxide, PDB code: 3pcj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3pcj

Go back to Iron Binding Sites List in 3pcj
Iron binding site 1 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 2- Hydroxyisonicotinic Acid N-Oxide


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 2- Hydroxyisonicotinic Acid N-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:33.8
occ:1.00
O4 M:INO550 1.9 24.2 1.0
O M:HOH744 2.0 22.1 0.8
OH M:TYR408 2.1 22.4 1.0
NE2 M:HIS462 2.3 18.9 1.0
NE2 M:HIS460 2.4 19.5 1.0
O3 M:INO550 2.5 22.8 1.0
N1 M:INO550 2.7 24.6 1.0
C2 M:INO550 2.9 23.7 1.0
CZ M:TYR408 3.1 22.4 1.0
CE1 M:HIS462 3.1 17.8 1.0
CE1 M:HIS460 3.2 18.0 1.0
CD2 M:HIS462 3.5 17.4 1.0
CD2 M:HIS460 3.6 19.0 1.0
CE2 M:TYR408 3.6 22.6 1.0
C6 M:INO550 3.9 24.3 1.0
CE1 M:TYR408 4.1 22.9 1.0
O A:HOH606 4.2 21.4 1.0
NH1 M:ARG457 4.2 18.4 1.0
C3 M:INO550 4.3 24.0 1.0
ND1 M:HIS462 4.3 17.7 1.0
ND1 M:HIS460 4.4 18.5 1.0
O M:HOH625 4.4 17.5 1.0
CG M:HIS462 4.5 17.7 1.0
CG M:HIS460 4.6 18.3 1.0
OE1 M:GLN477 4.9 18.9 1.0
CD2 M:TYR408 4.9 22.9 1.0
CD2 A:TYR16 5.0 26.8 1.0

Iron binding site 2 out of 6 in 3pcj

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Iron binding site 2 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 2- Hydroxyisonicotinic Acid N-Oxide


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 2- Hydroxyisonicotinic Acid N-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:33.2
occ:1.00
OH N:TYR408 1.9 21.0 1.0
O N:HOH850 2.0 22.1 0.8
O4 N:INO550 2.1 24.3 1.0
NE2 N:HIS462 2.3 18.9 1.0
O3 N:INO550 2.4 23.0 1.0
NE2 N:HIS460 2.6 19.1 1.0
N1 N:INO550 2.8 24.4 1.0
C2 N:INO550 2.9 23.9 1.0
CZ N:TYR408 2.9 21.9 1.0
CE1 N:HIS462 3.2 18.3 1.0
CD2 N:HIS462 3.3 17.7 1.0
CE1 N:HIS460 3.4 17.8 1.0
CE2 N:TYR408 3.5 22.5 1.0
CD2 N:HIS460 3.6 18.2 1.0
CE1 N:TYR408 3.9 22.5 1.0
C6 N:INO550 4.0 24.1 1.0
O B:HOH606 4.0 21.4 1.0
C3 N:INO550 4.3 24.0 1.0
NH1 N:ARG457 4.3 17.0 1.0
ND1 N:HIS462 4.3 17.8 1.0
CG N:HIS462 4.4 17.4 1.0
O N:HOH724 4.4 17.5 1.0
ND1 N:HIS460 4.6 18.1 1.0
CG N:HIS460 4.7 17.9 1.0
CD2 N:TYR408 4.8 23.3 1.0
CD2 B:TYR16 4.8 27.0 1.0
OE1 N:GLN477 5.0 17.9 1.0

Iron binding site 3 out of 6 in 3pcj

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Iron binding site 3 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 2- Hydroxyisonicotinic Acid N-Oxide


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 2- Hydroxyisonicotinic Acid N-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:33.2
occ:1.00
O4 O:INO550 2.0 24.5 1.0
O O:HOH851 2.0 22.1 0.8
OH O:TYR408 2.1 22.6 1.0
NE2 O:HIS462 2.2 18.9 1.0
NE2 O:HIS460 2.3 19.1 1.0
O3 O:INO550 2.4 22.9 1.0
N1 O:INO550 2.8 24.5 1.0
C2 O:INO550 3.0 23.8 1.0
CE1 O:HIS460 3.0 17.9 1.0
CE1 O:HIS462 3.1 18.1 1.0
CZ O:TYR408 3.2 22.3 1.0
CD2 O:HIS462 3.3 18.5 1.0
CD2 O:HIS460 3.4 18.6 1.0
CE1 O:TYR408 3.9 23.0 1.0
C6 O:INO550 4.0 24.1 1.0
CE2 O:TYR408 4.0 22.7 1.0
NH1 O:ARG457 4.2 18.4 1.0
ND1 O:HIS460 4.2 18.4 1.0
O O:HOH643 4.2 17.9 1.0
O C:HOH606 4.3 21.3 1.0
ND1 O:HIS462 4.3 17.9 1.0
C3 O:INO550 4.3 24.0 1.0
CG O:HIS462 4.4 18.3 1.0
CG O:HIS460 4.4 18.4 1.0
OE1 O:GLN477 4.9 19.1 1.0

Iron binding site 4 out of 6 in 3pcj

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Iron binding site 4 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 2- Hydroxyisonicotinic Acid N-Oxide


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 2- Hydroxyisonicotinic Acid N-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe600

b:33.9
occ:1.00
OH P:TYR408 2.0 22.0 1.0
O P:HOH778 2.1 22.2 0.6
O4 P:INO550 2.2 24.4 1.0
NE2 P:HIS462 2.2 18.3 1.0
NE2 P:HIS460 2.4 18.7 1.0
O3 P:INO550 2.4 22.8 1.0
N1 P:INO550 2.9 24.6 1.0
C2 P:INO550 3.0 23.8 1.0
CE1 P:HIS462 3.1 17.7 1.0
CZ P:TYR408 3.1 22.0 1.0
CE1 P:HIS460 3.2 18.1 1.0
CD2 P:HIS462 3.3 17.5 1.0
CD2 P:HIS460 3.4 18.3 1.0
CE1 P:TYR408 3.7 22.8 1.0
CE2 P:TYR408 4.0 22.7 1.0
C6 P:INO550 4.1 24.2 1.0
O D:HOH606 4.2 21.4 0.8
ND1 P:HIS462 4.2 17.4 1.0
O P:HOH665 4.2 18.1 1.0
NH1 P:ARG457 4.3 17.8 1.0
C3 P:INO550 4.3 23.9 1.0
CG P:HIS462 4.3 17.2 1.0
ND1 P:HIS460 4.4 18.0 1.0
CG P:HIS460 4.5 18.1 1.0
OE1 P:GLN477 4.9 18.7 1.0

Iron binding site 5 out of 6 in 3pcj

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Iron binding site 5 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 2- Hydroxyisonicotinic Acid N-Oxide


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 2- Hydroxyisonicotinic Acid N-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe600

b:33.6
occ:0.80
OH Q:TYR408 2.1 23.0 1.0
O4 Q:INO550 2.1 24.8 1.0
NE2 Q:HIS462 2.1 19.4 1.0
O Q:HOH776 2.3 22.1 0.6
NE2 Q:HIS460 2.3 19.7 1.0
O3 Q:INO550 2.4 23.4 1.0
N1 Q:INO550 2.9 24.6 1.0
C2 Q:INO550 3.0 23.9 1.0
CE1 Q:HIS462 3.0 18.4 1.0
CE1 Q:HIS460 3.2 18.4 1.0
CZ Q:TYR408 3.2 22.6 1.0
CD2 Q:HIS462 3.3 18.0 1.0
CD2 Q:HIS460 3.3 19.2 1.0
CE2 Q:TYR408 3.8 22.5 1.0
O E:HOH606 4.0 21.8 0.8
C6 Q:INO550 4.1 24.2 1.0
CE1 Q:TYR408 4.1 23.2 1.0
NH1 Q:ARG457 4.1 17.3 1.0
ND1 Q:HIS462 4.2 17.5 1.0
C3 Q:INO550 4.3 24.2 1.0
CG Q:HIS462 4.3 17.7 1.0
ND1 Q:HIS460 4.3 18.9 1.0
O Q:HOH651 4.4 18.4 1.0
CG Q:HIS460 4.4 18.7 1.0
OE1 Q:GLN477 4.8 18.6 1.0

Iron binding site 6 out of 6 in 3pcj

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Iron binding site 6 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 2- Hydroxyisonicotinic Acid N-Oxide


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 2- Hydroxyisonicotinic Acid N-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe600

b:33.9
occ:1.00
O4 R:INO550 1.9 24.5 1.0
O R:HOH898 2.0 22.4 0.8
OH R:TYR408 2.0 22.2 1.0
NE2 R:HIS460 2.3 18.9 1.0
NE2 R:HIS462 2.4 19.1 1.0
O3 R:INO550 2.5 22.8 1.0
N1 R:INO550 2.7 24.6 1.0
C2 R:INO550 3.0 23.7 1.0
CZ R:TYR408 3.1 22.6 1.0
CE1 R:HIS462 3.2 18.5 1.0
CE1 R:HIS460 3.2 18.0 1.0
CD2 R:HIS460 3.3 18.6 1.0
CD2 R:HIS462 3.5 18.4 1.0
CE1 R:TYR408 3.8 23.0 1.0
C6 R:INO550 3.9 24.3 1.0
CE2 R:TYR408 4.1 22.8 1.0
NH1 R:ARG457 4.2 18.3 1.0
O R:HOH768 4.3 17.5 1.0
O F:HOH606 4.3 21.8 1.0
C3 R:INO550 4.3 23.9 1.0
ND1 R:HIS462 4.4 18.3 1.0
ND1 R:HIS460 4.4 17.8 1.0
CG R:HIS460 4.5 18.4 1.0
CG R:HIS462 4.5 18.0 1.0
OE1 R:GLN477 4.7 19.1 1.0
CD2 F:TYR16 5.0 27.2 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 Dec 13 15:17:19 2020

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