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Iodine in PDB 3pci: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate

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

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

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate, PDB code: 3pci was solved by A.M.Orville, N.Elango, 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 / 2.21
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 197.000, 127.070, 134.080, 90.00, 97.53, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3pci:

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate also contains other interesting chemical elements:

Iron (Fe) 6 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate (pdb code 3pci). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate, PDB code: 3pci:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 3pci

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Iodine binding site 1 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:I550

b:34.4
occ:1.00
 I3 M:IHB550 0.0 34.4 1.0
C3 M:IHB550 2.0 28.4 1.0
C2 M:IHB550 2.9 26.9 1.0
C4 M:IHB550 3.0 26.6 1.0
O4 M:IHB550 3.1 23.0 1.0
NH1 M:ARG457 3.5 14.4 1.0
CD1 M:ILE491 3.7 17.9 1.0
NE2 M:GLN477 3.8 12.4 1.0
CA A:GLY14 3.8 16.9 1.0
CG2 A:THR12 3.9 13.3 1.0
O M:HOH742 4.1 21.4 1.0
CE1 M:HIS462 4.2 14.3 1.0
C1 M:IHB550 4.3 25.3 1.0
CZ M:ARG457 4.3 14.8 1.0
C5 M:IHB550 4.3 26.2 1.0
FE M:FE600 4.4 28.7 1.0
N A:GLY14 4.5 15.8 1.0
CD M:ARG457 4.5 15.3 1.0
OH M:TYR447 4.6 18.1 1.0
OE1 M:GLN477 4.6 14.8 1.0
CD A:PRO15 4.6 19.1 1.0
CD M:GLN477 4.6 14.2 1.0
NE M:ARG457 4.6 15.4 1.0
C6 M:IHB550 4.8 25.7 1.0
NE2 M:HIS462 4.8 15.8 1.0
O A:THR12 5.0 14.3 1.0

Iodine binding site 2 out of 12 in 3pci

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Iodine binding site 2 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:I551

b:20.9
occ:1.00
 I3 M:IHB551 0.0 20.9 1.0
C3 M:IHB551 2.0 18.9 1.0
C4 M:IHB551 3.0 17.7 1.0
C2 M:IHB551 3.0 18.2 1.0
O4 M:IHB551 3.1 17.5 1.0
O M:HOH745 3.9 18.5 1.0
CD M:ARG333 4.0 15.0 1.0
O O:HOH603 4.0 18.4 1.0
NH2 O:ARG333 4.2 14.3 1.0
NE O:ARG333 4.3 15.3 1.0
C5 M:IHB551 4.3 17.2 1.0
C1 M:IHB551 4.3 18.1 1.0
CD2 O:LEU320 4.3 14.7 1.0
I3 N:IHB551 4.4 20.8 1.0
I3 O:IHB551 4.4 20.8 1.0
NE M:ARG333 4.5 15.4 1.0
CZ O:ARG333 4.5 14.6 1.0
C6 M:IHB551 4.8 17.5 1.0
O M:HOH748 4.9 18.5 1.0
CD2 M:LEU320 5.0 14.6 1.0

Iodine binding site 3 out of 12 in 3pci

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Iodine binding site 3 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:I550

b:34.5
occ:1.00
 I3 N:IHB550 0.0 34.5 1.0
C3 N:IHB550 2.0 28.4 1.0
C4 N:IHB550 2.9 26.6 1.0
C2 N:IHB550 3.0 26.9 1.0
O4 N:IHB550 3.1 23.1 1.0
NH1 N:ARG457 3.5 13.5 1.0
CD1 N:ILE491 3.6 17.5 1.0
NE2 N:GLN477 3.8 13.2 1.0
CA B:GLY14 3.9 16.9 1.0
CG2 B:THR12 4.0 11.7 1.0
O N:HOH758 4.0 21.5 1.0
CE1 N:HIS462 4.0 14.6 1.0
C5 N:IHB550 4.3 26.2 1.0
C1 N:IHB550 4.3 25.4 1.0
FE N:FE600 4.3 28.8 1.0
CZ N:ARG457 4.5 14.2 1.0
OH N:TYR447 4.5 17.8 1.0
N B:GLY14 4.6 15.9 1.0
CD N:ARG457 4.6 15.0 1.0
CD B:PRO15 4.6 19.2 1.0
CD N:GLN477 4.6 13.3 1.0
OE1 N:GLN477 4.7 13.1 1.0
NE2 N:HIS462 4.7 15.4 1.0
C6 N:IHB550 4.8 25.6 1.0
O B:THR12 4.8 13.8 1.0
NE N:ARG457 4.9 14.6 1.0
CG N:ARG457 5.0 14.6 1.0

Iodine binding site 4 out of 12 in 3pci

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Iodine binding site 4 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:I551

b:20.8
occ:1.00
 I3 N:IHB551 0.0 20.8 1.0
C3 N:IHB551 2.0 18.8 1.0
C2 N:IHB551 3.0 18.1 1.0
C4 N:IHB551 3.0 17.8 1.0
O4 N:IHB551 3.2 17.7 1.0
O M:HOH750 3.9 18.4 1.0
O M:HOH748 4.0 18.5 1.0
CD N:ARG333 4.0 14.7 1.0
NE M:ARG333 4.2 15.4 1.0
NH2 M:ARG333 4.3 14.7 1.0
O N:HOH763 4.3 18.6 0.8
C1 N:IHB551 4.3 18.2 1.0
C5 N:IHB551 4.3 17.3 1.0
NE N:ARG333 4.3 15.0 1.0
I3 M:IHB551 4.4 20.9 1.0
I3 O:IHB551 4.4 20.8 1.0
CD2 M:LEU320 4.4 14.6 1.0
CZ M:ARG333 4.5 15.1 1.0
C6 N:IHB551 4.8 17.3 1.0

Iodine binding site 5 out of 12 in 3pci

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Iodine binding site 5 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
O:I550

b:34.6
occ:0.80
 I3 O:IHB550 0.0 34.6 0.8
C3 O:IHB550 2.0 28.5 0.8
C2 O:IHB550 3.0 26.9 0.8
C4 O:IHB550 3.0 26.7 0.8
O4 O:IHB550 3.1 23.2 0.8
NH1 O:ARG457 3.4 14.2 1.0
CD1 O:ILE491 3.6 17.9 1.0
CA C:GLY14 3.8 17.1 1.0
CG2 C:THR12 3.8 12.8 1.0
NE2 O:GLN477 3.9 12.9 1.0
CE1 O:HIS462 4.0 14.8 1.0
O O:HOH760 4.1 21.4 1.0
C1 O:IHB550 4.3 25.3 0.8
C5 O:IHB550 4.3 26.2 0.8
CD C:PRO15 4.4 19.1 1.0
CZ O:ARG457 4.4 14.7 1.0
FE O:FE600 4.4 28.8 1.0
N C:GLY14 4.5 15.8 1.0
OH O:TYR447 4.6 17.9 1.0
OE1 O:GLN477 4.6 14.5 1.0
CD O:ARG457 4.7 15.2 1.0
CD O:GLN477 4.7 13.8 1.0
NE2 O:HIS462 4.7 16.1 1.0
O C:THR12 4.7 14.0 1.0
C6 O:IHB550 4.8 25.7 0.8
NE O:ARG457 4.9 15.2 1.0
OH O:TYR324 5.0 15.0 1.0

Iodine binding site 6 out of 12 in 3pci

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Iodine binding site 6 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
O:I551

b:20.8
occ:1.00
 I3 O:IHB551 0.0 20.8 1.0
C3 O:IHB551 2.0 18.6 1.0
C4 O:IHB551 2.9 17.5 1.0
C2 O:IHB551 3.0 17.8 1.0
O4 O:IHB551 3.1 17.3 1.0
O N:HOH763 3.7 18.6 0.8
O N:HOH765 4.0 18.6 0.8
CD O:ARG333 4.0 14.5 1.0
NH2 N:ARG333 4.1 14.6 1.0
C5 O:IHB551 4.2 17.0 1.0
NE N:ARG333 4.3 15.0 1.0
CD2 N:LEU320 4.3 14.7 1.0
C1 O:IHB551 4.3 17.9 1.0
NE O:ARG333 4.4 15.3 1.0
I3 N:IHB551 4.4 20.8 1.0
I3 M:IHB551 4.4 20.9 1.0
CZ N:ARG333 4.4 14.6 1.0
C6 O:IHB551 4.8 17.2 1.0
O O:HOH603 4.9 18.4 1.0

Iodine binding site 7 out of 12 in 3pci

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Iodine binding site 7 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
P:I550

b:34.7
occ:1.00
 I3 P:IHB550 0.0 34.7 1.0
C3 P:IHB550 2.0 28.4 1.0
C2 P:IHB550 3.0 26.9 1.0
C4 P:IHB550 3.0 26.7 1.0
O4 P:IHB550 3.1 23.0 1.0
NH1 P:ARG457 3.3 14.3 1.0
CD1 P:ILE491 3.7 18.4 1.0
CA D:GLY14 3.9 16.9 1.0
NE2 P:GLN477 3.9 13.0 1.0
CE1 P:HIS462 4.0 14.1 1.0
CG2 D:THR12 4.1 11.9 1.0
O P:HOH749 4.2 21.6 1.0
CZ P:ARG457 4.2 14.3 1.0
C5 P:IHB550 4.3 26.1 1.0
C1 P:IHB550 4.3 25.3 1.0
FE P:FE600 4.3 28.1 1.0
OH P:TYR447 4.5 18.1 1.0
CD D:PRO15 4.5 19.3 1.0
N D:GLY14 4.6 16.0 1.0
OE1 P:GLN477 4.6 14.4 1.0
CD P:ARG457 4.6 14.9 1.0
CD P:GLN477 4.6 14.1 1.0
NE P:ARG457 4.7 15.1 1.0
NE2 P:HIS462 4.7 15.4 1.0
C6 P:IHB550 4.8 25.7 1.0
O D:THR12 5.0 14.2 1.0

Iodine binding site 8 out of 12 in 3pci

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Iodine binding site 8 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
P:I551

b:21.9
occ:1.00
 I3 P:IHB551 0.0 21.9 1.0
C3 P:IHB551 2.0 18.9 1.0
C4 P:IHB551 3.0 17.8 1.0
C2 P:IHB551 3.0 17.9 1.0
O4 P:IHB551 3.2 17.3 1.0
O R:HOH983 3.7 18.7 1.0
O R:HOH967 3.7 18.6 1.0
CD P:ARG333 4.0 14.9 1.0
O R:HOH1213 4.0 18.4 1.0
NH2 R:ARG333 4.2 14.9 1.0
CD2 R:LEU320 4.2 13.9 1.0
C5 P:IHB551 4.3 17.3 1.0
NE P:ARG333 4.3 15.7 1.0
NE R:ARG333 4.3 15.4 1.0
C1 P:IHB551 4.3 18.3 1.0
I3 Q:IHB551 4.4 22.4 1.0
I3 R:IHB551 4.4 20.8 1.0
CZ R:ARG333 4.5 15.2 1.0
C6 P:IHB551 4.8 17.4 1.0
CD1 R:LEU320 5.0 15.0 1.0
CD2 P:LEU320 5.0 14.6 1.0

Iodine binding site 9 out of 12 in 3pci

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Iodine binding site 9 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:I550

b:34.8
occ:1.00
 I3 Q:IHB550 0.0 34.8 1.0
C3 Q:IHB550 2.0 28.6 1.0
C4 Q:IHB550 3.0 26.8 1.0
C2 Q:IHB550 3.0 26.9 1.0
O4 Q:IHB550 3.1 23.4 1.0
NH1 Q:ARG457 3.4 14.4 1.0
CD1 Q:ILE491 3.5 18.0 1.0
CA E:GLY14 3.8 17.0 1.0
NE2 Q:GLN477 3.9 13.4 1.0
CG2 E:THR12 4.0 13.1 1.0
O Q:HOH1225 4.0 21.4 1.0
CE1 Q:HIS462 4.0 15.0 1.0
C5 Q:IHB550 4.3 26.2 1.0
C1 Q:IHB550 4.3 25.4 1.0
CZ Q:ARG457 4.3 15.3 1.0
FE Q:FE600 4.4 28.4 1.0
OE1 Q:GLN477 4.4 13.8 1.0
N E:GLY14 4.5 15.9 1.0
CD Q:GLN477 4.5 14.1 1.0
CD Q:ARG457 4.6 15.5 1.0
CD E:PRO15 4.6 19.1 1.0
NE2 Q:HIS462 4.6 16.0 1.0
OH Q:TYR447 4.7 18.2 1.0
NE Q:ARG457 4.8 15.4 1.0
C6 Q:IHB550 4.8 25.7 1.0
O E:THR12 4.9 14.4 1.0
OH Q:TYR324 4.9 16.2 1.0
CG1 Q:ILE491 5.0 18.5 1.0

Iodine binding site 10 out of 12 in 3pci

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Iodine binding site 10 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Iodo-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:I551

b:22.4
occ:1.00
 I3 Q:IHB551 0.0 22.4 1.0
C3 Q:IHB551 2.0 19.1 1.0
C2 Q:IHB551 3.0 18.1 1.0
C4 Q:IHB551 3.0 17.8 1.0
O4 Q:IHB551 3.2 17.7 1.0
O R:HOH1213 3.5 18.4 1.0
O Q:HOH1229 4.0 18.8 1.0
CD Q:ARG333 4.1 15.4 1.0
NE P:ARG333 4.1 15.7 1.0
NH2 P:ARG333 4.1 15.1 1.0
CD2 P:LEU320 4.2 14.6 1.0
C1 Q:IHB551 4.3 18.1 1.0
C5 Q:IHB551 4.3 17.2 1.0
CZ P:ARG333 4.4 14.8 1.0
I3 P:IHB551 4.4 21.9 1.0
I3 R:IHB551 4.4 20.8 1.0
NE Q:ARG333 4.4 15.9 1.0
C6 Q:IHB551 4.8 17.5 1.0
O Q:HOH1459 4.8 18.6 1.0
CD1 P:LEU320 4.9 14.7 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 Dec 13 19:29:02 2020

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