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Iron in PDB 3mv6: 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: 3mv6 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) 29.09 / 1.86
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.142, 140.831, 167.830, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.9

Other elements in 3mv6:

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 3mv6). 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: 3mv6:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3mv6

Go back to Iron Binding Sites List in 3mv6
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:30.1
occ:0.75
O4 M:DHB539 2.0 23.9 0.8
O3 M:DHB539 2.1 32.2 0.8
OH M:TYR408 2.1 21.3 1.0
OH M:TYR462 2.1 28.7 1.0
NE2 M:HIS460 2.2 20.5 1.0
C4 M:DHB539 2.8 27.9 0.8
C3 M:DHB539 2.8 27.5 0.8
CE1 M:HIS460 3.0 17.9 1.0
CZ M:TYR462 3.0 21.2 1.0
CE2 M:TYR462 3.1 21.8 1.0
CZ M:TYR408 3.1 21.3 1.0
CD2 M:HIS460 3.4 20.0 1.0
CE2 M:TYR408 3.7 20.9 1.0
O A:HOH374 3.7 6.1 0.2
O M:HOH540 3.9 34.7 1.0
NH1 M:ARG457 3.9 17.8 1.0
CE1 M:TYR408 4.1 21.1 1.0
C5 M:DHB539 4.1 30.1 0.8
C2 M:DHB539 4.1 31.0 0.8
ND1 M:HIS460 4.2 18.9 1.0
CE1 M:TYR462 4.3 21.4 1.0
O M:HOH551 4.4 18.9 1.0
CG M:HIS460 4.4 17.8 1.0
CD2 M:TYR462 4.5 20.4 1.0
CG M:ARG457 4.7 16.9 1.0
O A:HOH374 4.9 18.9 0.8
OE1 M:GLN477 5.0 21.8 1.0

Iron binding site 2 out of 3 in 3mv6

Go back to Iron Binding Sites List in 3mv6
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:32.5
occ:0.80
O4 N:DHB540 1.9 27.4 0.8
OH N:TYR408 2.0 20.4 1.0
O3 N:DHB540 2.2 31.8 0.8
NE2 N:HIS460 2.3 18.4 1.0
OH N:TYR462 2.4 27.4 1.0
C4 N:DHB540 2.8 30.6 0.8
C3 N:DHB540 2.9 31.2 0.8
CE1 N:HIS460 3.0 19.4 1.0
CZ N:TYR408 3.0 19.7 1.0
CE2 N:TYR462 3.1 21.2 1.0
CZ N:TYR462 3.1 22.4 1.0
CD2 N:HIS460 3.4 19.9 1.0
CE2 N:TYR408 3.7 18.6 1.0
O B:HOH249 3.9 6.3 0.2
O N:HOH2 3.9 31.3 1.0
CE1 N:TYR408 4.0 20.4 1.0
NH2 N:ARG457 4.0 18.1 1.0
C5 N:DHB540 4.2 32.0 0.8
ND1 N:HIS460 4.2 19.5 1.0
C2 N:DHB540 4.3 33.0 0.8
CD2 N:TYR462 4.4 19.7 1.0
CE1 N:TYR462 4.4 21.7 1.0
CG N:HIS460 4.5 17.6 1.0
O N:HOH177 4.5 19.5 1.0
CG N:ARG457 4.7 17.1 1.0
O B:HOH249 4.9 19.3 0.8

Iron binding site 3 out of 3 in 3mv6

Go back to Iron Binding Sites List in 3mv6
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:31.8
occ:0.75
O4 O:DHB539 2.1 33.4 0.8
OH O:TYR408 2.1 20.5 1.0
O3 O:DHB539 2.2 39.9 0.8
NE2 O:HIS460 2.3 19.1 1.0
OH O:TYR462 2.3 30.1 1.0
C4 O:DHB539 2.9 35.5 0.8
C3 O:DHB539 3.0 35.5 0.8
CE2 O:TYR462 3.0 23.5 1.0
CZ O:TYR462 3.0 24.1 1.0
CE1 O:HIS460 3.0 20.2 1.0
CZ O:TYR408 3.1 20.1 1.0
CD2 O:HIS460 3.4 19.1 1.0
O O:HOH3 3.8 32.5 1.0
CE2 O:TYR408 3.8 20.1 1.0
O C:HOH206 3.9 3.6 0.2
NH1 O:ARG457 4.0 19.1 1.0
CE1 O:TYR408 4.1 19.1 1.0
C5 O:DHB539 4.2 36.7 0.8
ND1 O:HIS460 4.3 19.1 1.0
C2 O:DHB539 4.3 35.5 0.8
CE1 O:TYR462 4.3 22.8 1.0
CD2 O:TYR462 4.3 19.9 1.0
CG O:HIS460 4.4 17.6 1.0
O O:HOH259 4.5 19.5 1.0
CG O:ARG457 4.7 19.2 1.0
O C:HOH206 4.9 21.3 0.8
OE1 O:GLN477 5.0 22.9 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 Dec 13 15:12:56 2020

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