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Iron in PDB 2boy: Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP

Enzymatic activity of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP

All present enzymatic activity of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP:
1.13.11.1;

Protein crystallography data

The structure of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP, PDB code: 2boy was solved by M.Ferraroni, I.P.Solyanikova, M.P.Kolomytseva, A.Scozzafava, L.A.Golovleva, F.Briganti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.51 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 83.179, 86.610, 93.447, 85.37, 66.53, 76.94
R / Rfree (%) 17.6 / 21.9

Other elements in 2boy:

The structure of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP also contains other interesting chemical elements:

Magnesium (Mg) 16 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP (pdb code 2boy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP, PDB code: 2boy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2boy

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Iron binding site 1 out of 8 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1255

b:19.8
occ:1.00
 N A:BHO1256 1.7 32.1 1.0
OH A:TYR133 1.9 17.9 1.0
NE2 A:HIS191 2.0 14.1 1.0
OH A:TYR167 2.1 18.7 0.5
NE2 A:HIS193 2.2 15.3 1.0
C A:BHO1256 2.5 29.9 1.0
O2 A:BHO1256 2.6 37.5 1.0
O1 A:BHO1256 2.7 37.1 1.0
CE1 A:HIS191 3.0 15.7 1.0
CZ A:TYR133 3.0 17.7 1.0
CD2 A:HIS191 3.1 15.3 1.0
CD2 A:HIS193 3.1 12.8 1.0
CZ A:TYR167 3.1 18.1 0.5
CE1 A:HIS193 3.2 17.7 1.0
CE2 A:TYR167 3.5 18.9 0.5
CE1 A:TYR133 3.6 19.7 1.0
C1 A:BHO1256 3.9 27.1 1.0
CE2 A:TYR133 4.0 19.3 1.0
NH1 A:ARG188 4.0 18.2 1.0
O A:HOH2211 4.0 18.6 1.0
ND1 A:HIS191 4.1 17.6 1.0
CG A:HIS191 4.2 16.9 1.0
CG A:HIS193 4.3 16.5 1.0
ND1 A:HIS193 4.3 16.7 1.0
CE1 A:TYR167 4.3 19.4 0.5
O A:HOH2266 4.3 15.5 1.0
C6 A:BHO1256 4.4 29.0 1.0
CD2 A:TYR167 4.9 18.3 0.5
CD1 A:TYR133 5.0 18.3 1.0

Iron binding site 2 out of 8 in 2boy

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Iron binding site 2 out of 8 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1255

b:21.6
occ:1.00
 O1 B:BHO1256 1.8 30.2 0.5
OH B:TYR133 2.0 22.5 1.0
NE2 B:HIS191 2.0 19.1 1.0
N B:BHO1256 2.1 24.1 0.5
NE2 B:HIS193 2.1 16.6 1.0
OH B:TYR167 2.2 21.2 0.5
O1 B:BHO1256 2.4 18.1 0.5
C B:BHO1256 2.5 19.8 0.5
O2 B:BHO1256 2.8 25.1 0.5
C B:BHO1256 2.9 28.1 0.5
CZ B:TYR133 3.0 21.7 1.0
CE1 B:HIS191 3.0 19.8 1.0
CD2 B:HIS191 3.0 18.3 1.0
CE1 B:HIS193 3.1 17.4 1.0
CD2 B:HIS193 3.1 15.6 1.0
CZ B:TYR167 3.2 24.7 0.5
N B:BHO1256 3.5 30.3 0.5
CE2 B:TYR167 3.6 24.6 0.5
CE1 B:TYR133 3.7 23.4 1.0
O B:HOH2142 4.0 19.2 1.0
NH2 B:ARG188 4.0 19.4 1.0
CE2 B:TYR133 4.0 23.2 1.0
C1 B:BHO1256 4.0 20.3 0.5
C1 B:BHO1256 4.1 28.1 0.5
ND1 B:HIS191 4.1 19.7 1.0
CG B:HIS191 4.2 18.1 1.0
ND1 B:HIS193 4.2 17.9 1.0
CG B:HIS193 4.2 16.2 1.0
O B:HOH2240 4.3 20.3 1.0
C2 B:BHO1256 4.4 27.5 0.5
CE1 B:TYR167 4.4 25.3 0.5
O2 B:BHO1256 4.7 30.3 0.5
C6 B:BHO1256 4.7 20.9 0.5
CD2 B:TYR167 4.9 24.1 0.5
OE1 B:GLN207 4.9 20.1 1.0
CD1 B:TYR133 5.0 24.0 1.0

Iron binding site 3 out of 8 in 2boy

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Iron binding site 3 out of 8 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1255

b:21.5
occ:1.00
 O1 C:BHO1256 1.6 26.9 0.5
OH C:TYR167 1.8 33.4 0.4
N C:BHO1256 1.9 25.3 0.5
OH C:TYR133 1.9 21.8 1.0
NE2 C:HIS191 2.1 21.0 1.0
NE2 C:HIS193 2.2 16.5 1.0
O2 C:BHO1256 2.2 17.6 0.5
C C:BHO1256 2.3 25.1 0.5
N C:BHO1256 2.4 26.7 0.5
C C:BHO1256 2.7 21.9 0.5
O1 C:BHO1256 2.7 21.0 0.5
O2 C:BHO1256 2.7 22.7 0.5
CZ C:TYR167 2.8 31.1 0.4
CZ C:TYR133 3.0 21.9 1.0
CE1 C:HIS191 3.0 22.0 1.0
CD2 C:HIS193 3.1 13.8 1.0
CD2 C:HIS191 3.1 19.5 1.0
CE1 C:TYR167 3.1 31.5 0.4
CE1 C:HIS193 3.2 20.6 1.0
CE1 C:TYR133 3.7 21.9 1.0
C1 C:BHO1256 3.7 27.4 0.5
CE2 C:TYR133 3.9 21.9 1.0
CE2 C:TYR167 3.9 32.4 0.4
O C:HOH2119 4.0 20.9 1.0
NH1 C:ARG188 4.1 17.2 0.7
C1 C:BHO1256 4.1 24.0 0.5
ND1 C:HIS191 4.2 21.3 1.0
CG C:HIS191 4.2 20.2 1.0
O C:HOH2203 4.3 16.2 1.0
CG C:HIS193 4.3 17.4 1.0
ND1 C:HIS193 4.3 15.7 1.0
C6 C:BHO1256 4.4 27.9 0.5
CD1 C:TYR167 4.4 29.9 0.4
NH2 C:ARG188 4.7 24.4 0.3
C2 C:BHO1256 4.8 26.9 0.5
C6 C:BHO1256 4.8 23.7 0.5
OE1 C:GLN207 4.9 23.4 1.0
CD1 C:TYR133 5.0 19.7 1.0

Iron binding site 4 out of 8 in 2boy

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Iron binding site 4 out of 8 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1255

b:23.6
occ:1.00
 N D:BHO1256 1.6 32.5 0.5
OH D:TYR133 1.9 24.7 1.0
O1 D:BHO1256 2.0 27.1 0.5
NE2 D:HIS191 2.1 20.7 1.0
NE2 D:HIS193 2.2 20.3 1.0
OH D:TYR167 2.2 23.8 0.5
O2 D:BHO1256 2.2 39.1 0.5
O2 D:BHO1256 2.2 25.8 0.5
N D:BHO1256 2.5 27.9 0.5
C D:BHO1256 2.5 25.9 0.5
C D:BHO1256 2.6 29.7 0.5
CE1 D:HIS191 3.0 20.4 1.0
CZ D:TYR133 3.0 22.9 1.0
O1 D:BHO1256 3.0 32.4 0.5
CD2 D:HIS191 3.1 20.5 1.0
CE1 D:HIS193 3.1 18.6 1.0
CD2 D:HIS193 3.2 18.1 1.0
CZ D:TYR167 3.2 24.7 0.5
CE1 D:TYR167 3.6 26.5 0.5
CE1 D:TYR133 3.6 25.8 1.0
NH2 D:ARG188 3.9 30.5 0.4
C1 D:BHO1256 4.0 27.5 1.0
CE2 D:TYR133 4.0 21.1 1.0
O D:HOH2140 4.0 20.1 1.0
NH1 D:ARG188 4.0 16.0 0.6
ND1 D:HIS191 4.1 21.4 1.0
CG D:HIS191 4.2 22.0 1.0
ND1 D:HIS193 4.3 18.2 1.0
CG D:HIS193 4.3 19.8 1.0
O D:HOH2241 4.4 18.2 1.0
CE2 D:TYR167 4.4 26.9 0.5
NE D:ARG188 4.5 30.1 0.4
C6 D:BHO1256 4.5 26.9 1.0
CZ D:ARG188 4.7 31.7 0.4
CD1 D:TYR133 4.9 22.9 1.0
CD1 D:TYR167 5.0 27.1 0.5

Iron binding site 5 out of 8 in 2boy

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Iron binding site 5 out of 8 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1255

b:20.2
occ:1.00
 O1 E:BHO1256 1.8 22.6 0.5
OH E:TYR133 1.9 19.3 1.0
O1 E:BHO1256 2.0 21.4 0.5
NE2 E:HIS191 2.1 19.5 1.0
NE2 E:HIS193 2.2 19.6 1.0
O2 E:BHO1256 2.3 16.2 0.5
C E:BHO1256 2.4 22.2 0.5
N E:BHO1256 2.4 23.4 0.5
C E:BHO1256 2.8 22.4 0.5
CE2 E:TYR167 2.8 21.8 0.2
CZ E:TYR133 3.0 18.8 1.0
CE1 E:HIS191 3.1 21.0 1.0
CE1 E:HIS193 3.1 20.0 1.0
CD2 E:HIS191 3.2 16.5 1.0
OH E:TYR167 3.2 21.7 0.2
CD2 E:HIS193 3.2 17.8 1.0
N E:BHO1256 3.2 25.5 0.5
CZ E:TYR167 3.4 21.3 0.2
CE1 E:TYR133 3.7 19.9 1.0
C1 E:BHO1256 3.7 21.5 0.5
CD2 E:TYR167 3.8 22.4 0.2
CE2 E:TYR133 3.9 17.8 1.0
O E:HOH2142 3.9 19.7 1.0
C1 E:BHO1256 4.1 21.8 0.5
NH1 E:ARG188 4.1 23.1 1.0
ND1 E:HIS193 4.2 19.5 1.0
ND1 E:HIS191 4.2 19.8 1.0
C6 E:BHO1256 4.3 23.1 0.5
CG E:HIS191 4.3 18.1 1.0
O E:HOH2232 4.3 18.3 1.0
CG E:HIS193 4.3 18.2 1.0
C6 E:BHO1256 4.5 23.6 0.5
O2 E:BHO1256 4.5 27.2 0.5
CE1 E:TYR167 4.7 22.5 0.2
C2 E:BHO1256 4.9 19.4 0.5
CD2 E:TYR78 5.0 22.1 1.0

Iron binding site 6 out of 8 in 2boy

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Iron binding site 6 out of 8 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1255

b:19.1
occ:1.00
 OH F:TYR133 1.9 19.2 1.0
OH F:TYR167 2.0 22.3 0.2
N F:BHO1256 2.0 28.9 0.5
O1 F:BHO1256 2.0 26.6 0.5
NE2 F:HIS191 2.1 17.6 1.0
NE2 F:HIS193 2.1 14.6 1.0
O2 F:BHO1256 2.2 20.6 0.5
N F:BHO1256 2.3 25.9 0.5
C F:BHO1256 2.3 25.6 0.5
O F:HOH2169 2.4 40.2 0.8
C F:BHO1256 2.7 27.4 0.5
O1 F:BHO1256 2.7 24.8 0.5
O2 F:BHO1256 2.9 27.6 0.5
CZ F:TYR167 2.9 22.0 0.2
CZ F:TYR133 3.0 18.1 1.0
CE1 F:HIS191 3.0 19.6 1.0
CE1 F:HIS193 3.1 13.3 1.0
CD2 F:HIS193 3.1 15.2 1.0
CD2 F:HIS191 3.1 16.9 1.0
CE2 F:TYR167 3.2 22.8 0.2
CE1 F:TYR133 3.7 19.8 1.0
C1 F:BHO1256 3.7 26.3 0.5
CE2 F:TYR133 3.9 20.7 1.0
NH1 F:ARG188 4.0 19.4 1.0
O F:HOH2149 4.0 14.7 1.0
CE1 F:TYR167 4.1 22.5 0.2
C1 F:BHO1256 4.1 27.4 0.5
ND1 F:HIS191 4.2 19.1 1.0
ND1 F:HIS193 4.2 16.1 1.0
CG F:HIS191 4.3 18.1 1.0
CG F:HIS193 4.3 17.3 1.0
C6 F:BHO1256 4.3 27.4 0.5
O F:HOH2229 4.3 15.8 1.0
CD2 F:TYR167 4.5 23.1 0.2
C6 F:BHO1256 4.8 29.9 0.5
C2 F:BHO1256 4.8 26.7 0.5
CD2 F:TYR78 5.0 24.0 1.0
CD1 F:TYR133 5.0 18.8 1.0

Iron binding site 7 out of 8 in 2boy

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Iron binding site 7 out of 8 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1255

b:23.1
occ:1.00
 OH G:TYR133 1.9 22.1 1.0
OH G:TYR167 2.0 26.6 0.2
NE2 G:HIS191 2.0 18.4 1.0
NE2 G:HIS193 2.0 17.0 1.0
O2 G:BHO1256 2.3 41.2 1.0
O1 G:BHO1256 2.3 38.4 1.0
N G:BHO1256 2.4 42.0 1.0
C G:BHO1256 2.6 35.4 1.0
CE1 G:HIS191 3.0 22.6 1.0
CZ G:TYR133 3.0 22.3 1.0
CZ G:TYR167 3.0 26.2 0.2
CE1 G:HIS193 3.0 16.2 1.0
CD2 G:HIS193 3.0 18.5 1.0
CD2 G:HIS191 3.0 19.9 1.0
CE1 G:TYR167 3.2 27.5 0.2
CE1 G:TYR133 3.6 23.6 1.0
O G:HOH2116 3.9 24.8 1.0
CE2 G:TYR133 3.9 20.8 1.0
C1 G:BHO1256 3.9 31.6 1.0
ND1 G:HIS191 4.1 21.6 1.0
ND1 G:HIS193 4.1 20.6 1.0
CG G:HIS191 4.2 23.0 1.0
CG G:HIS193 4.2 17.6 1.0
NH1 G:ARG188 4.2 23.9 1.0
CE2 G:TYR167 4.2 27.6 0.2
O G:HOH2180 4.3 20.6 1.0
C6 G:BHO1256 4.4 31.4 1.0
CD1 G:TYR167 4.5 27.9 0.2
CD1 G:TYR133 4.9 23.6 1.0
CD2 G:TYR78 5.0 24.8 1.0

Iron binding site 8 out of 8 in 2boy

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Iron binding site 8 out of 8 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe1255

b:22.6
occ:1.00
 N H:BHO1256 1.9 30.3 0.5
OH H:TYR133 2.0 19.4 1.0
NE2 H:HIS193 2.0 21.4 1.0
O1 H:BHO1256 2.1 28.2 0.5
NE2 H:HIS191 2.2 20.8 1.0
O2 H:BHO1256 2.3 31.2 0.5
O2 H:BHO1256 2.4 22.6 0.5
C H:BHO1256 2.6 29.6 0.5
C H:BHO1256 2.6 28.4 0.5
O1 H:BHO1256 2.7 29.7 0.5
N H:BHO1256 2.7 28.4 0.5
CE1 H:HIS193 2.9 20.5 1.0
CZ H:TYR133 3.0 18.1 1.0
CE1 H:TYR167 3.1 27.6 0.2
CD2 H:HIS193 3.1 19.9 1.0
CE1 H:HIS191 3.1 22.3 1.0
CD2 H:HIS191 3.2 20.4 1.0
OH H:TYR167 3.5 27.4 0.2
CE1 H:TYR133 3.7 17.7 1.0
CZ H:TYR167 3.7 27.6 0.2
CE2 H:TYR133 3.9 20.8 1.0
C1 H:BHO1256 4.0 27.9 0.5
O H:HOH2135 4.0 20.1 1.0
CD1 H:TYR167 4.0 27.5 0.2
C1 H:BHO1256 4.0 28.8 0.5
ND1 H:HIS193 4.1 19.3 1.0
NH1 H:ARG188 4.1 26.0 1.0
CG H:HIS193 4.2 20.0 1.0
O H:HOH2205 4.3 19.2 1.0
ND1 H:HIS191 4.3 21.0 1.0
CG H:HIS191 4.3 21.5 1.0
C6 H:BHO1256 4.5 29.3 0.5
C6 H:BHO1256 4.7 30.2 0.5
CD2 H:TYR78 4.9 24.9 1.0
CE2 H:TYR167 5.0 27.8 0.2
CD1 H:TYR133 5.0 20.7 1.0

Reference:

M.Ferraroni, M.P.Kolomytseva, I.P.Solyanikova, A.Scozzafava, L.A.Golovleva, F.Briganti. Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase Key Enzyme of A New Modified Ortho-Pathway From the Gram-Positive Rhodococcus Opacus 1CP Grown on 2-Chlorophenol. J. Mol. Biol. V. 360 788 2006.
ISSN: ISSN 0022-2836
PubMed: 16793061
DOI: 10.1016/J.JMB.2006.05.046
Page generated: Sat Aug 3 19:45:00 2024

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