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Iron in PDB 3t67: Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

Enzymatic activity of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

All present enzymatic activity of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase:
1.13.11.3;

Protein crystallography data

The structure of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase, PDB code: 3t67 was solved by V.M.Purpero, J.D.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.68 / 1.67
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.009, 140.782, 168.189, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.9

Iron Binding Sites:

The binding sites of Iron atom in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase (pdb code 3t67). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase, PDB code: 3t67:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3t67

Go back to Iron Binding Sites List in 3t67
Iron binding site 1 out of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:18.0
occ:0.70
OH M:TYR408 1.9 21.1 1.0
NE2 M:HIS460 2.1 15.9 1.0
O4 M:CAQ1 2.1 24.6 1.0
OH M:TYR447 2.2 19.0 0.5
NE2 M:HIS462 2.2 15.3 1.0
O3 M:CAQ1 2.5 30.3 1.0
C4 M:CAQ1 2.9 28.2 1.0
CE1 M:HIS460 2.9 16.5 1.0
CZ M:TYR408 3.0 17.7 1.0
CE1 M:HIS462 3.1 15.8 1.0
C3 M:CAQ1 3.1 28.1 1.0
CD2 M:HIS460 3.2 15.8 1.0
CD2 M:HIS462 3.2 16.0 1.0
CZ M:TYR447 3.4 17.6 0.5
CE2 M:TYR408 3.7 17.7 1.0
CE2 M:TYR447 3.8 18.0 0.5
CE1 M:TYR408 3.9 18.0 1.0
O M:HOH794 4.1 18.2 1.0
ND1 M:HIS460 4.1 15.1 1.0
O M:HOH233 4.1 16.4 1.0
NH1 M:ARG457 4.2 16.0 1.0
C5 M:CAQ1 4.2 29.0 1.0
ND1 M:HIS462 4.2 14.5 1.0
CG M:HIS460 4.3 14.8 1.0
O A:HOH238 4.3 18.6 1.0
CG M:HIS462 4.3 14.8 1.0
C2 M:CAQ1 4.4 29.1 1.0
CE1 M:TYR447 4.5 18.7 0.5
OE1 M:GLN477 4.8 17.0 1.0

Iron binding site 2 out of 3 in 3t67

Go back to Iron Binding Sites List in 3t67
Iron binding site 2 out of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:17.2
occ:0.70
OH N:TYR408 1.9 20.8 1.0
O4 N:CAQ1 2.1 23.7 1.0
NE2 N:HIS462 2.1 16.3 1.0
NE2 N:HIS460 2.1 15.7 1.0
OH N:TYR447 2.2 19.4 0.5
O3 N:CAQ1 2.3 30.6 1.0
C4 N:CAQ1 2.8 28.0 1.0
CE1 N:HIS460 3.0 17.3 1.0
C3 N:CAQ1 3.0 28.5 1.0
CZ N:TYR408 3.0 18.8 1.0
CE1 N:HIS462 3.0 15.9 1.0
CD2 N:HIS462 3.2 15.3 1.0
CD2 N:HIS460 3.3 16.8 1.0
CZ N:TYR447 3.4 19.1 0.5
CE2 N:TYR408 3.8 17.7 1.0
CE1 N:TYR408 3.8 18.9 1.0
CE1 N:TYR447 3.9 20.0 0.5
O N:HOH785 4.0 17.0 1.0
O N:HOH38 4.1 15.0 1.0
C5 N:CAQ1 4.1 28.3 1.0
ND1 N:HIS460 4.1 16.2 1.0
ND1 N:HIS462 4.2 16.0 1.0
NH1 N:ARG457 4.2 17.0 1.0
O B:HOH209 4.2 19.1 1.0
CG N:HIS462 4.3 15.4 1.0
C2 N:CAQ1 4.3 29.5 1.0
CG N:HIS460 4.3 14.3 1.0
CE2 N:TYR447 4.5 20.6 0.5
OE1 N:GLN477 4.8 17.6 1.0

Iron binding site 3 out of 3 in 3t67

Go back to Iron Binding Sites List in 3t67
Iron binding site 3 out of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:18.9
occ:0.70
OH O:TYR408 1.9 23.3 1.0
NE2 O:HIS460 2.1 15.3 1.0
OH O:TYR447 2.1 17.6 0.5
NE2 O:HIS462 2.1 17.1 1.0
O3 O:CAQ1 2.2 24.4 1.0
O4 O:CAQ1 2.4 31.1 1.0
CE1 O:HIS460 2.9 16.2 1.0
C3 O:CAQ1 3.0 28.9 1.0
CE1 O:HIS462 3.0 17.1 1.0
CZ O:TYR408 3.0 22.0 1.0
C4 O:CAQ1 3.1 28.0 1.0
CD2 O:HIS462 3.2 17.0 1.0
CD2 O:HIS460 3.2 17.7 1.0
CZ O:TYR447 3.3 17.8 0.5
CE2 O:TYR408 3.8 20.3 1.0
CE1 O:TYR447 3.8 17.6 0.5
CE1 O:TYR408 3.9 22.4 1.0
O O:HOH787 4.0 16.9 1.0
ND1 O:HIS460 4.1 16.0 1.0
ND1 O:HIS462 4.2 16.6 1.0
O O:HOH121 4.2 15.8 1.0
NH1 O:ARG457 4.2 16.1 1.0
CG O:HIS460 4.3 15.3 1.0
C2 O:CAQ1 4.3 28.3 1.0
CG O:HIS462 4.3 15.6 1.0
O C:HOH207 4.3 20.5 1.0
C5 O:CAQ1 4.4 30.2 1.0
CE2 O:TYR447 4.4 18.6 0.5
OE1 O:GLN477 4.8 18.1 1.0

Reference:

V.M.Purpero, J.D.Lipscomb. Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase To Be Published.
Page generated: Sun Aug 4 20:17:43 2024

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