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Iron in PDB 3pck: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide

Enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide

All present enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide:
1.13.11.3;

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide, PDB code: 3pck 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 (°) 196.900, 127.800, 134.400, 90.00, 97.80, 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 6- Hydroxynicotinic Acid N-Oxide (pdb code 3pck). 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 6- Hydroxynicotinic Acid N-Oxide, PDB code: 3pck:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3pck

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

b:22.4
occ:1.00
OH M:TYR408 1.9 14.2 1.0
NE2 M:HIS462 2.1 11.7 1.0
O4 M:NNO550 2.2 18.6 0.9
O M:HOH744 2.3 16.6 1.0
NE2 M:HIS460 2.4 11.8 1.0
O3 M:NNO550 2.4 16.2 0.9
C6 M:NNO550 2.9 19.4 0.9
CZ M:TYR408 3.0 14.0 1.0
N1 M:NNO550 3.0 18.1 0.9
CE1 M:HIS462 3.0 10.8 1.0
CE1 M:HIS460 3.2 10.9 1.0
CD2 M:HIS462 3.2 10.3 1.0
CD2 M:HIS460 3.5 11.5 1.0
CE2 M:TYR408 3.5 14.4 1.0
CE1 M:TYR408 4.0 14.3 1.0
C5 M:NNO550 4.1 19.4 0.9
ND1 M:HIS462 4.2 11.2 1.0
C2 M:NNO550 4.2 19.5 0.9
O M:HOH628 4.2 10.7 1.0
CG M:HIS462 4.3 10.4 1.0
O A:HOH606 4.3 13.8 1.0
ND1 M:HIS460 4.3 11.4 1.0
NH1 M:ARG457 4.4 11.4 1.0
CG M:HIS460 4.5 11.0 1.0
CD2 M:TYR408 4.9 15.6 1.0

Iron binding site 2 out of 6 in 3pck

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

b:21.6
occ:1.00
OH N:TYR408 2.1 13.5 1.0
NE2 N:HIS462 2.2 11.2 1.0
O N:HOH853 2.2 16.6 1.0
O4 N:NNO550 2.2 18.6 0.9
O3 N:NNO550 2.3 16.5 0.9
NE2 N:HIS460 2.4 11.8 1.0
C6 N:NNO550 2.8 19.3 0.9
N1 N:NNO550 2.9 18.2 0.9
CE1 N:HIS462 2.9 10.5 1.0
CZ N:TYR408 3.1 13.8 1.0
CE1 N:HIS460 3.2 10.6 1.0
CD2 N:HIS462 3.3 10.1 1.0
CD2 N:HIS460 3.4 11.7 1.0
CE2 N:TYR408 3.8 14.6 1.0
C2 N:NNO550 4.1 19.5 0.9
CE1 N:TYR408 4.1 14.0 1.0
C5 N:NNO550 4.1 19.6 0.9
ND1 N:HIS462 4.1 10.9 1.0
O B:HOH606 4.2 13.8 1.0
NH1 N:ARG457 4.3 11.0 1.0
CG N:HIS462 4.4 10.3 1.0
O N:HOH729 4.4 10.9 1.0
ND1 N:HIS460 4.4 11.2 1.0
CG N:HIS460 4.5 11.7 1.0
OE1 N:GLN477 4.8 10.3 1.0

Iron binding site 3 out of 6 in 3pck

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

b:22.5
occ:1.00
OH O:TYR408 2.0 14.6 1.0
O4 O:NNO550 2.0 19.0 0.9
NE2 O:HIS462 2.3 11.3 1.0
O O:HOH891 2.3 16.6 1.0
NE2 O:HIS460 2.3 11.8 1.0
O3 O:NNO550 2.4 16.4 0.9
C6 O:NNO550 2.8 19.5 0.9
N1 O:NNO550 3.0 18.1 0.9
CE1 O:HIS460 3.0 10.9 1.0
CZ O:TYR408 3.0 14.6 1.0
CE1 O:HIS462 3.2 10.6 1.0
CD2 O:HIS462 3.3 10.4 1.0
CD2 O:HIS460 3.6 11.7 1.0
CE1 O:TYR408 3.7 15.2 1.0
CE2 O:TYR408 3.9 14.6 1.0
C5 O:NNO550 4.0 19.4 0.9
O O:HOH765 4.1 11.1 1.0
C2 O:NNO550 4.2 19.5 0.9
NH1 O:ARG457 4.2 11.8 1.0
ND1 O:HIS460 4.3 11.4 1.0
O C:HOH606 4.3 13.6 1.0
ND1 O:HIS462 4.4 11.1 1.0
CG O:HIS462 4.4 10.5 1.0
CG O:HIS460 4.5 11.7 1.0
CD1 O:TYR408 5.0 15.7 1.0

Iron binding site 4 out of 6 in 3pck

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

b:21.0
occ:1.00
O4 P:NNO550 2.0 19.0 0.9
O P:HOH784 2.1 16.7 1.0
OH P:TYR408 2.1 13.6 1.0
NE2 P:HIS462 2.3 11.3 1.0
O3 P:NNO550 2.3 16.4 0.9
NE2 P:HIS460 2.4 11.9 1.0
C6 P:NNO550 2.7 19.7 0.9
N1 P:NNO550 2.8 18.3 0.9
CE1 P:HIS460 3.0 10.7 1.0
CZ P:TYR408 3.1 14.3 1.0
CE1 P:HIS462 3.1 10.5 1.0
CD2 P:HIS462 3.4 10.3 1.0
CE2 P:TYR408 3.6 14.5 1.0
CD2 P:HIS460 3.6 11.6 1.0
C5 P:NNO550 4.0 19.5 0.9
CE1 P:TYR408 4.1 14.1 1.0
C2 P:NNO550 4.1 19.5 0.9
O D:HOH606 4.1 13.8 1.0
NH1 P:ARG457 4.1 11.5 1.0
O P:HOH665 4.3 10.9 1.0
ND1 P:HIS462 4.3 10.8 1.0
ND1 P:HIS460 4.3 11.9 1.0
CG P:HIS462 4.4 10.4 1.0
CG P:HIS460 4.6 11.5 1.0
CD2 P:TYR408 4.9 15.4 1.0
C4 P:NNO550 5.0 19.6 0.9

Iron binding site 5 out of 6 in 3pck

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

b:23.2
occ:1.00
OH Q:TYR408 1.9 14.0 1.0
O4 Q:NNO550 2.2 19.1 0.9
O Q:HOH776 2.2 16.6 1.0
NE2 Q:HIS462 2.3 12.0 1.0
NE2 Q:HIS460 2.5 12.7 1.0
O3 Q:NNO550 2.7 16.9 0.9
CZ Q:TYR408 2.9 14.1 1.0
C6 Q:NNO550 2.9 19.6 0.9
N1 Q:NNO550 3.1 18.4 0.9
CE1 Q:HIS462 3.2 11.1 1.0
CD2 Q:HIS462 3.2 11.1 1.0
CE1 Q:HIS460 3.4 11.0 1.0
CE2 Q:TYR408 3.5 14.3 1.0
CD2 Q:HIS460 3.5 12.2 1.0
CE1 Q:TYR408 3.8 14.4 1.0
O E:HOH606 4.1 14.1 1.0
C5 Q:NNO550 4.1 19.4 0.9
O Q:HOH650 4.2 10.9 1.0
ND1 Q:HIS462 4.3 11.3 1.0
C2 Q:NNO550 4.4 19.5 0.9
CG Q:HIS462 4.4 11.1 1.0
NH1 Q:ARG457 4.5 11.7 1.0
ND1 Q:HIS460 4.5 11.7 1.0
CG Q:HIS460 4.6 11.6 1.0
CD2 Q:TYR408 4.8 15.7 1.0
CD2 E:TYR16 4.9 18.8 1.0
CD1 Q:TYR408 5.0 15.1 1.0

Iron binding site 6 out of 6 in 3pck

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

b:22.7
occ:1.00
OH R:TYR408 2.0 14.5 1.0
NE2 R:HIS462 2.1 11.8 1.0
O R:HOH891 2.1 16.6 1.0
O4 R:NNO550 2.2 18.7 0.9
O3 R:NNO550 2.4 16.6 0.9
NE2 R:HIS460 2.5 11.8 1.0
C6 R:NNO550 2.8 19.3 0.9
N1 R:NNO550 2.9 18.4 0.9
CE1 R:HIS462 3.0 11.0 1.0
CZ R:TYR408 3.1 14.4 1.0
CD2 R:HIS462 3.1 10.8 1.0
CE1 R:HIS460 3.3 10.6 1.0
CD2 R:HIS460 3.6 11.5 1.0
CE1 R:TYR408 3.8 14.8 1.0
O F:HOH606 4.0 14.0 1.0
CE2 R:TYR408 4.0 14.8 1.0
C5 R:NNO550 4.1 19.5 0.9
ND1 R:HIS462 4.1 11.2 1.0
C2 R:NNO550 4.2 19.5 0.9
CG R:HIS462 4.2 10.8 1.0
NH1 R:ARG457 4.4 12.1 1.0
O R:HOH765 4.4 10.8 1.0
ND1 R:HIS460 4.5 10.9 1.0
CG R:HIS460 4.6 11.4 1.0
OE1 R:GLN477 4.9 11.4 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 17:52:40 2024

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