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

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

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

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide, PDB code: 3pcm 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 / 2.25
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.100, 127.300, 134.500, 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 6- Hydroxynicotinic Acid N-Oxide and Cyanide (pdb code 3pcm). 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 and Cyanide, PDB code: 3pcm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3pcm

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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 and Cyanide


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 and Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:21.0
occ:0.80
OH M:TYR408 2.0 15.8 1.0
O4 M:NNO550 2.1 18.7 0.9
NE2 M:HIS462 2.2 12.9 1.0
O3 M:NNO550 2.3 16.3 0.9
NE2 M:HIS460 2.3 12.9 1.0
C M:CYN575 2.4 17.5 1.0
C6 M:NNO550 2.8 19.0 0.9
N1 M:NNO550 2.8 18.1 0.9
CZ M:TYR408 3.0 16.7 1.0
CE1 M:HIS462 3.1 11.9 1.0
CE1 M:HIS460 3.1 12.1 1.0
CD2 M:HIS462 3.3 12.2 1.0
N M:CYN575 3.3 18.1 1.0
CD2 M:HIS460 3.5 12.3 1.0
CE2 M:TYR408 3.6 17.0 1.0
C5 M:NNO550 4.0 19.4 0.9
CE1 M:TYR408 4.0 17.3 1.0
C2 M:NNO550 4.1 19.0 0.9
NH1 M:ARG457 4.2 12.6 1.0
ND1 M:HIS462 4.3 12.0 1.0
ND1 M:HIS460 4.3 12.0 1.0
O M:HOH624 4.3 11.8 1.0
CG M:HIS462 4.4 12.0 1.0
CG M:HIS460 4.5 11.7 1.0
O M:HOH602 4.6 16.4 1.0
OE1 M:GLN477 4.9 11.9 1.0
CD2 M:TYR408 4.9 17.7 1.0

Iron binding site 2 out of 6 in 3pcm

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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 and Cyanide


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 and Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:20.5
occ:0.80
OH N:TYR408 2.0 15.6 1.0
NE2 N:HIS462 2.1 12.5 1.0
C N:CYN575 2.2 17.3 1.0
O4 N:NNO550 2.2 18.6 0.9
O3 N:NNO550 2.4 16.3 0.9
NE2 N:HIS460 2.4 12.3 1.0
C6 N:NNO550 2.9 19.1 0.9
N1 N:NNO550 3.0 18.1 0.9
CE1 N:HIS462 3.0 12.1 1.0
CZ N:TYR408 3.0 16.2 1.0
CD2 N:HIS462 3.2 12.1 1.0
N N:CYN575 3.3 17.9 1.0
CE1 N:HIS460 3.3 12.0 1.0
CD2 N:HIS460 3.5 12.2 1.0
CE2 N:TYR408 3.7 16.8 1.0
CE1 N:TYR408 4.0 16.7 1.0
C5 N:NNO550 4.2 19.4 0.9
ND1 N:HIS462 4.2 11.9 1.0
C2 N:NNO550 4.2 19.1 0.9
CG N:HIS462 4.3 12.0 1.0
O N:HOH629 4.4 11.6 1.0
NH1 N:ARG457 4.4 11.6 1.0
ND1 N:HIS460 4.5 11.7 1.0
O B:HOH242 4.5 16.6 1.0
CG N:HIS460 4.6 11.9 1.0
OE1 N:GLN477 4.7 10.9 1.0
CD2 N:TYR408 5.0 17.9 1.0

Iron binding site 3 out of 6 in 3pcm

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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 and Cyanide


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 and Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:21.2
occ:0.80
C O:CYN575 2.0 17.3 1.0
OH O:TYR408 2.0 15.8 1.0
O4 O:NNO550 2.1 18.7 0.9
NE2 O:HIS462 2.2 12.6 1.0
NE2 O:HIS460 2.2 12.6 1.0
O3 O:NNO550 2.3 16.6 0.9
C6 O:NNO550 2.8 19.1 0.9
N1 O:NNO550 2.8 18.1 0.9
CE1 O:HIS460 3.1 12.1 1.0
CZ O:TYR408 3.1 16.8 1.0
N O:CYN575 3.1 17.9 1.0
CE1 O:HIS462 3.2 12.1 1.0
CD2 O:HIS462 3.2 12.4 1.0
CD2 O:HIS460 3.3 12.0 1.0
CE1 O:TYR408 3.7 17.4 1.0
CE2 O:TYR408 4.0 17.4 1.0
C5 O:NNO550 4.1 19.3 0.9
C2 O:NNO550 4.1 19.0 0.9
O O:HOH632 4.2 11.8 1.0
NH1 O:ARG457 4.2 12.1 1.0
ND1 O:HIS460 4.3 12.2 1.0
ND1 O:HIS462 4.3 12.0 1.0
CG O:HIS462 4.4 12.2 1.0
CG O:HIS460 4.4 11.9 1.0
O O:HOH608 4.4 16.4 1.0
OE1 O:GLN477 4.9 11.2 1.0

Iron binding site 4 out of 6 in 3pcm

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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 and Cyanide


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 and Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe600

b:21.8
occ:0.80
OH P:TYR408 1.9 15.2 1.0
C P:CYN575 2.1 17.4 1.0
O4 P:NNO550 2.2 18.7 0.9
NE2 P:HIS460 2.2 12.6 1.0
NE2 P:HIS462 2.2 12.7 1.0
O3 P:NNO550 2.3 16.3 0.9
C6 P:NNO550 2.8 19.2 0.9
N1 P:NNO550 2.8 18.1 0.9
CE1 P:HIS460 2.9 11.7 1.0
CZ P:TYR408 2.9 16.6 1.0
CE1 P:HIS462 3.1 12.4 1.0
N P:CYN575 3.2 18.2 1.0
CD2 P:HIS462 3.3 12.1 1.0
CD2 P:HIS460 3.4 12.2 1.0
CE2 P:TYR408 3.5 17.1 1.0
CE1 P:TYR408 4.0 16.6 1.0
C5 P:NNO550 4.1 19.4 0.9
C2 P:NNO550 4.1 19.1 0.9
ND1 P:HIS460 4.2 12.2 1.0
O P:HOH630 4.2 11.4 0.8
ND1 P:HIS462 4.3 12.6 1.0
CG P:HIS462 4.4 11.9 1.0
CG P:HIS460 4.4 12.0 1.0
NH1 P:ARG457 4.5 11.4 1.0
O P:HOH610 4.5 16.6 0.8
CD2 P:TYR408 4.8 17.5 1.0
OE1 P:GLN477 5.0 11.4 1.0

Iron binding site 5 out of 6 in 3pcm

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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 and Cyanide


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 and Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe600

b:21.5
occ:0.80
OH Q:TYR408 1.9 16.1 1.0
C Q:CYN575 2.1 17.5 1.0
O4 Q:NNO550 2.2 18.7 0.9
NE2 Q:HIS462 2.2 13.0 1.0
NE2 Q:HIS460 2.3 13.1 1.0
O3 Q:NNO550 2.6 16.6 0.9
C6 Q:NNO550 3.0 19.1 0.9
CZ Q:TYR408 3.0 16.7 1.0
N1 Q:NNO550 3.1 18.2 0.9
CE1 Q:HIS462 3.1 12.1 1.0
CE1 Q:HIS460 3.2 12.0 1.0
CD2 Q:HIS462 3.2 12.7 1.0
N Q:CYN575 3.3 18.1 1.0
CD2 Q:HIS460 3.4 12.3 1.0
CE1 Q:TYR408 3.7 17.1 1.0
CE2 Q:TYR408 3.8 16.9 1.0
O Q:HOH987 4.2 11.9 1.0
C5 Q:NNO550 4.2 19.4 0.9
ND1 Q:HIS462 4.3 11.8 1.0
NH1 Q:ARG457 4.3 12.5 1.0
ND1 Q:HIS460 4.3 12.1 1.0
CG Q:HIS462 4.3 12.1 1.0
C2 Q:NNO550 4.4 19.2 0.9
CG Q:HIS460 4.5 12.0 1.0
O E:HOH206 4.6 16.8 0.8
OE1 Q:GLN477 4.8 11.8 1.0

Iron binding site 6 out of 6 in 3pcm

Go back to Iron Binding Sites List in 3pcm
Iron binding site 6 out of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide


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 and Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe600

b:22.6
occ:1.00
OH R:TYR408 2.0 16.5 1.0
C R:CYN575 2.1 17.3 1.0
O4 R:NNO550 2.2 18.7 0.9
NE2 R:HIS462 2.2 13.0 1.0
NE2 R:HIS460 2.3 12.8 1.0
O3 R:NNO550 2.4 16.5 0.9
C6 R:NNO550 2.9 19.0 0.9
N1 R:NNO550 2.9 18.1 0.9
CE1 R:HIS462 3.0 12.1 1.0
CZ R:TYR408 3.1 16.9 1.0
CE1 R:HIS460 3.2 11.8 1.0
N R:CYN575 3.2 17.9 1.0
CD2 R:HIS462 3.4 12.5 1.0
CD2 R:HIS460 3.4 12.3 1.0
CE2 R:TYR408 3.7 17.2 1.0
C5 R:NNO550 4.1 19.3 0.9
CE1 R:TYR408 4.1 17.5 1.0
C2 R:NNO550 4.2 19.0 0.9
ND1 R:HIS462 4.2 11.7 1.0
NH1 R:ARG457 4.3 11.9 1.0
ND1 R:HIS460 4.4 11.8 1.0
O R:HOH1223 4.4 11.5 1.0
CG R:HIS462 4.4 11.9 1.0
CG R:HIS460 4.5 12.0 1.0
O R:HOH1186 4.6 16.7 1.0
OE1 R:GLN477 4.9 10.7 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: Tue Aug 5 05:39:52 2025

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