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Iron in PDB 3mfl: 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: 3mfl 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) 23.87 / 1.78
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.319, 140.769, 168.183, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.5

Other elements in 3mfl:

The structure of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

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 3mfl). 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: 3mfl:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3mfl

Go back to Iron Binding Sites List in 3mfl
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:25.1
occ:0.70
O4 M:DHY539 2.0 18.2 0.1
OH M:TYR462 2.0 22.7 1.0
O3 M:DHY539 2.1 22.2 0.6
OH M:TYR408 2.1 17.8 1.0
O4 M:DHY539 2.1 22.4 0.6
O3 M:DHY539 2.2 18.5 0.1
NE2 M:HIS460 2.2 14.2 1.0
C4 M:DHY539 2.7 18.4 0.1
C3 M:DHY539 2.8 18.2 0.1
C3 M:DHY539 2.8 22.4 0.6
C4 M:DHY539 2.8 23.4 0.6
CZ M:TYR462 2.9 17.5 1.0
CE1 M:HIS460 3.0 14.6 1.0
NE2 M:HIS447 3.0 21.4 0.5
CE2 M:TYR462 3.0 16.7 1.0
CZ M:TYR408 3.2 16.0 1.0
CD2 M:HIS460 3.4 14.2 1.0
CE1 M:HIS447 3.7 22.1 0.5
CE2 M:TYR408 3.8 16.7 1.0
O A:HOH232 3.9 21.1 0.5
NH1 M:ARG457 3.9 14.6 1.0
O M:HOH808 3.9 17.9 1.0
CE1 M:TYR408 4.1 14.9 1.0
C5 M:DHY539 4.1 18.2 0.1
CD2 M:HIS447 4.1 20.0 0.5
CE1 M:TYR462 4.2 17.0 1.0
C2 M:DHY539 4.2 23.8 0.6
C2 M:DHY539 4.2 18.3 0.1
C5 M:DHY539 4.2 23.3 0.6
ND1 M:HIS460 4.2 13.5 1.0
CD2 M:TYR462 4.4 16.0 1.0
CG M:HIS460 4.4 11.8 1.0
O M:HOH227 4.5 16.9 1.0
CG M:ARG457 4.8 13.4 1.0
OE1 M:GLN477 4.9 15.9 1.0
O A:HOH232 4.9 9.0 0.5
ND1 M:HIS447 4.9 21.6 0.5

Iron binding site 2 out of 3 in 3mfl

Go back to Iron Binding Sites List in 3mfl
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:24.4
occ:0.70
O4 N:DHY539 2.0 21.4 0.3
OH N:TYR408 2.1 16.8 1.0
OH N:TYR462 2.1 22.3 1.0
O3 N:DHY539 2.2 23.1 0.3
O3 N:DHY539 2.2 22.3 0.3
O4 N:DHY539 2.2 22.5 0.3
NE2 N:HIS460 2.3 13.4 1.0
C4 N:DHY539 2.9 23.0 0.3
C3 N:DHY539 2.9 22.2 0.3
CZ N:TYR462 3.0 16.0 1.0
C3 N:DHY539 3.0 23.5 0.3
CE1 N:HIS460 3.0 16.2 1.0
NE2 N:HIS447 3.0 21.3 0.5
C4 N:DHY539 3.0 24.4 0.3
CZ N:TYR408 3.1 14.6 1.0
CE2 N:TYR462 3.1 15.9 1.0
CD2 N:HIS460 3.4 15.5 1.0
CE2 N:TYR408 3.8 14.5 1.0
CE1 N:HIS447 3.8 21.6 0.5
O N:HOH756 3.8 16.4 1.0
O B:HOH894 3.9 18.1 0.5
NH2 N:ARG457 3.9 13.4 1.0
CD2 N:HIS447 4.0 20.6 0.5
CE1 N:TYR408 4.0 14.7 1.0
C5 N:DHY539 4.2 22.9 0.3
ND1 N:HIS460 4.2 14.3 1.0
CE1 N:TYR462 4.3 14.8 1.0
C2 N:DHY539 4.3 22.7 0.3
C2 N:DHY539 4.3 24.2 0.3
C5 N:DHY539 4.3 24.4 0.3
CD2 N:TYR462 4.4 13.3 1.0
CG N:HIS460 4.5 11.8 1.0
O N:HOH37 4.5 14.6 1.0
CG N:ARG457 4.8 13.4 1.0
O B:HOH894 4.9 8.9 0.5
OE1 N:GLN477 4.9 15.7 1.0
ND1 N:HIS447 5.0 20.5 0.5

Iron binding site 3 out of 3 in 3mfl

Go back to Iron Binding Sites List in 3mfl
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:24.0
occ:0.65
O4 O:DHY540 1.8 15.8 0.1
O3 O:DHY540 2.1 20.6 0.6
OH O:TYR462 2.1 25.5 1.0
OH O:TYR408 2.1 21.1 1.0
O4 O:DHY540 2.2 21.9 0.6
NE2 O:HIS460 2.2 13.5 1.0
O3 O:DHY540 2.4 17.4 0.1
C4 O:DHY540 2.7 16.8 0.1
C3 O:DHY540 2.8 21.6 0.6
C4 O:DHY540 2.9 22.0 0.6
CE1 O:HIS460 2.9 15.4 1.0
C3 O:DHY540 2.9 16.9 0.1
NE2 O:HIS447 3.0 21.9 0.5
CZ O:TYR462 3.0 20.2 1.0
CZ O:TYR408 3.2 18.8 1.0
CE2 O:TYR462 3.2 19.7 1.0
CD2 O:HIS460 3.4 16.3 1.0
CE1 O:HIS447 3.7 22.7 0.5
NH1 O:ARG457 3.8 15.3 1.0
CE2 O:TYR408 3.8 19.4 1.0
O O:HOH770 3.8 19.6 1.0
O O:HOH768 3.9 28.8 1.0
C5 O:DHY540 4.0 16.9 0.1
CD2 O:HIS447 4.0 20.6 0.5
CE1 O:TYR408 4.1 18.1 1.0
C2 O:DHY540 4.1 21.8 0.6
ND1 O:HIS460 4.2 14.9 1.0
C5 O:DHY540 4.2 22.4 0.6
CE1 O:TYR462 4.3 17.0 1.0
C2 O:DHY540 4.3 17.0 0.1
CG O:HIS460 4.4 13.2 1.0
CD2 O:TYR462 4.5 16.7 1.0
O O:HOH827 4.6 15.8 1.0
CG O:ARG457 4.7 13.5 1.0
ND1 O:HIS447 4.9 21.5 0.5
OE1 O:GLN477 4.9 17.9 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 14:46:54 2024

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