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Iron in PDB 3mi5: 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: 3mi5 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) 30.62 / 1.78
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 190.543, 167.995, 128.342, 90.00, 132.40, 90.00
R / Rfree (%) 15.1 / 18.5

Other elements in 3mi5:

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) 5 atoms

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 3mi5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 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: 3mi5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3mi5

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Iron binding site 1 out of 6 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:20.9
occ:0.65
OH M:TYR462 1.9 20.6 1.0
O3 M:CAQ539 2.0 22.0 0.7
OH M:TYR408 2.1 19.2 1.0
O4 M:CAQ539 2.1 20.3 0.7
NE2 M:HIS460 2.2 16.5 1.0
CZ M:TYR462 2.8 17.1 1.0
C3 M:CAQ539 2.8 22.0 0.7
C4 M:CAQ539 2.9 20.1 0.7
CE1 M:HIS460 3.0 16.1 1.0
CE1 M:HIS447 3.0 21.1 0.5
CE2 M:TYR462 3.0 17.5 1.0
CZ M:TYR408 3.1 14.9 1.0
CD2 M:HIS460 3.4 16.5 1.0
NE2 M:HIS447 3.6 22.8 0.5
CE2 M:TYR408 3.8 16.1 1.0
NH1 M:ARG457 3.8 13.2 1.0
O M:HOH861 3.9 19.2 1.0
O M:HOH2030 3.9 29.9 1.0
CE1 M:TYR408 4.0 13.6 1.0
ND1 M:HIS447 4.1 21.4 0.5
CE1 M:TYR462 4.1 16.1 1.0
C2 M:CAQ539 4.2 21.8 0.7
ND1 M:HIS460 4.2 14.9 1.0
C5 M:CAQ539 4.2 22.7 0.7
CD2 M:TYR462 4.4 15.4 1.0
CG M:HIS460 4.4 13.2 1.0
O M:HOH161 4.5 17.6 1.0
OE1 M:GLN477 4.9 16.8 1.0
CG M:ARG457 4.9 13.6 1.0
CD2 M:HIS447 4.9 20.6 0.5
O A:HOH220 4.9 20.4 1.0

Iron binding site 2 out of 6 in 3mi5

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Iron binding site 2 out of 6 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:21.5
occ:0.65
OH N:TYR462 2.0 24.3 1.0
O4 N:CAQ3 2.1 28.3 0.7
OH N:TYR408 2.1 17.5 1.0
O3 N:CAQ3 2.2 25.1 0.7
NE2 N:HIS460 2.2 14.5 1.0
CZ N:TYR462 2.9 18.9 1.0
C4 N:CAQ3 2.9 25.5 0.7
C3 N:CAQ3 2.9 24.4 0.7
CE1 N:HIS460 3.0 15.4 1.0
CE1 N:HIS447 3.0 21.0 0.5
CE2 N:TYR462 3.1 17.9 1.0
CZ N:TYR408 3.1 17.2 1.0
CD2 N:HIS460 3.4 15.6 1.0
NE2 N:HIS447 3.7 22.6 0.5
CE2 N:TYR408 3.8 17.6 1.0
O N:HOH563 3.9 18.7 1.0
NH1 N:ARG457 3.9 15.6 1.0
O B:HOH2031 4.0 26.6 1.0
CE1 N:TYR408 4.0 16.5 1.0
ND1 N:HIS447 4.0 21.2 0.5
ND1 N:HIS460 4.2 15.1 1.0
CE1 N:TYR462 4.2 14.9 1.0
C5 N:CAQ3 4.3 26.4 0.7
C2 N:CAQ3 4.3 24.1 0.7
CD2 N:TYR462 4.4 15.7 1.0
CG N:HIS460 4.4 13.3 1.0
O N:HOH279 4.5 15.9 1.0
CG N:ARG457 4.8 14.1 1.0
CD2 N:HIS447 4.9 20.9 0.5
OE1 N:GLN477 4.9 16.9 1.0
O B:HOH461 5.0 22.9 1.0

Iron binding site 3 out of 6 in 3mi5

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Iron binding site 3 out of 6 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:21.8
occ:0.65
OH O:TYR462 2.0 20.4 1.0
OH O:TYR408 2.0 15.1 1.0
O4 O:CAQ4 2.1 23.2 0.7
O3 O:CAQ4 2.1 21.1 0.7
NE2 O:HIS460 2.3 14.5 1.0
C4 O:CAQ4 2.9 22.3 0.7
C3 O:CAQ4 2.9 22.2 0.7
CZ O:TYR462 2.9 16.3 1.0
CE1 O:HIS460 3.0 17.2 1.0
CE1 O:HIS447 3.0 21.9 0.5
CZ O:TYR408 3.1 14.1 1.0
CE2 O:TYR462 3.1 14.9 1.0
CD2 O:HIS460 3.5 16.3 1.0
NE2 O:HIS447 3.6 24.0 0.5
CE2 O:TYR408 3.8 14.3 1.0
O O:HOH2032 3.8 27.0 1.0
O O:HOH698 3.9 19.4 1.0
CE1 O:TYR408 3.9 16.6 1.0
NH1 O:ARG457 4.0 14.5 1.0
ND1 O:HIS447 4.1 22.1 0.5
ND1 O:HIS460 4.2 14.3 1.0
C5 O:CAQ4 4.2 22.1 0.7
C2 O:CAQ4 4.2 21.1 0.7
CE1 O:TYR462 4.2 15.2 1.0
CD2 O:TYR462 4.5 13.3 1.0
CG O:HIS460 4.5 14.1 1.0
O O:HOH120 4.5 15.2 1.0
CG O:ARG457 4.8 14.4 1.0
CD2 O:HIS447 4.8 20.5 0.5
O C:HOH599 4.9 20.6 1.0
OE1 O:GLN477 5.0 17.6 1.0

Iron binding site 4 out of 6 in 3mi5

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Iron binding site 4 out of 6 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 4 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
P:Fe600

b:21.1
occ:0.65
OH P:TYR462 1.9 21.3 1.0
OH P:TYR408 2.0 17.2 1.0
O3 P:CAQ542 2.1 19.9 0.7
O4 P:CAQ542 2.1 23.7 0.7
NE2 P:HIS460 2.2 15.9 1.0
CZ P:TYR462 2.9 16.0 1.0
C3 P:CAQ542 2.9 21.6 0.7
C4 P:CAQ542 2.9 23.1 0.7
CE1 P:HIS460 3.0 15.5 1.0
CE1 P:HIS447 3.0 21.8 0.5
CE2 P:TYR462 3.1 16.6 1.0
CZ P:TYR408 3.1 16.0 1.0
CD2 P:HIS460 3.4 15.3 1.0
NE2 P:HIS447 3.6 23.5 0.5
CE2 P:TYR408 3.7 15.2 1.0
O P:HOH815 3.8 17.8 1.0
O P:HOH2033 3.9 28.3 1.0
NH1 P:ARG457 3.9 13.9 1.0
CE1 P:TYR408 4.0 13.6 1.0
ND1 P:HIS447 4.1 21.2 0.5
CE1 P:TYR462 4.1 16.2 1.0
ND1 P:HIS460 4.2 15.4 1.0
C2 P:CAQ542 4.2 23.4 0.7
C5 P:CAQ542 4.2 22.2 0.7
CG P:HIS460 4.4 13.5 1.0
CD2 P:TYR462 4.4 13.9 1.0
O P:HOH146 4.5 17.1 1.0
CD2 P:HIS447 4.8 20.3 0.5
O D:HOH305 4.9 18.8 1.0
CG P:ARG457 4.9 13.6 1.0
OE1 P:GLN477 5.0 16.8 1.0

Iron binding site 5 out of 6 in 3mi5

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Iron binding site 5 out of 6 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 5 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
Q:Fe600

b:21.6
occ:0.65
OH Q:TYR462 2.0 25.3 1.0
O3 Q:CAQ6 2.1 25.4 0.7
O4 Q:CAQ6 2.2 23.0 0.7
OH Q:TYR408 2.2 20.5 1.0
NE2 Q:HIS460 2.2 13.2 1.0
CZ Q:TYR462 2.9 19.4 1.0
C3 Q:CAQ6 2.9 23.5 0.7
C4 Q:CAQ6 2.9 22.5 0.7
CE1 Q:HIS460 3.0 15.7 1.0
CE1 Q:HIS447 3.0 22.5 0.5
CE2 Q:TYR462 3.1 16.3 1.0
CZ Q:TYR408 3.2 19.0 1.0
CD2 Q:HIS460 3.4 14.6 1.0
NE2 Q:HIS447 3.6 24.4 0.5
NH1 Q:ARG457 3.8 16.1 1.0
O Q:HOH618 3.8 20.2 1.0
CE2 Q:TYR408 3.9 17.6 1.0
O Q:HOH2045 3.9 26.1 1.0
CE1 Q:TYR408 4.0 16.2 1.0
ND1 Q:HIS447 4.1 22.4 0.5
CE1 Q:TYR462 4.2 15.6 1.0
ND1 Q:HIS460 4.2 14.7 1.0
C2 Q:CAQ6 4.3 24.2 0.7
C5 Q:CAQ6 4.3 23.1 0.7
CD2 Q:TYR462 4.4 15.6 1.0
CG Q:HIS460 4.4 13.8 1.0
O Q:HOH180 4.5 15.1 1.0
CG Q:ARG457 4.8 15.8 1.0
OE1 Q:GLN477 4.8 17.7 1.0
CD2 Q:HIS447 4.9 21.3 0.5
O E:HOH246 5.0 23.7 1.0

Iron binding site 6 out of 6 in 3mi5

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Iron binding site 6 out of 6 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 6 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
R:Fe600

b:22.0
occ:0.65
OH R:TYR462 1.9 22.8 1.0
OH R:TYR408 2.1 16.1 1.0
O4 R:CAQ1 2.1 23.1 0.7
O3 R:CAQ1 2.1 21.3 0.7
NE2 R:HIS460 2.3 14.1 1.0
CZ R:TYR462 2.9 17.1 1.0
C4 R:CAQ1 2.9 22.7 0.7
C3 R:CAQ1 2.9 22.1 0.7
CE1 R:HIS460 3.0 16.6 1.0
CE1 R:HIS447 3.0 20.3 0.5
CE2 R:TYR462 3.1 15.9 1.0
CZ R:TYR408 3.1 14.7 1.0
CD2 R:HIS460 3.4 16.0 1.0
NE2 R:HIS447 3.6 23.2 0.5
O R:HOH2037 3.8 28.0 1.0
CE2 R:TYR408 3.8 15.0 1.0
O R:HOH750 3.8 21.0 1.0
NH1 R:ARG457 3.9 16.1 1.0
CE1 R:TYR408 4.0 16.4 1.0
ND1 R:HIS447 4.1 21.9 0.5
CE1 R:TYR462 4.1 15.8 1.0
ND1 R:HIS460 4.2 13.8 1.0
C5 R:CAQ1 4.3 22.8 0.7
C2 R:CAQ1 4.3 21.3 0.7
CD2 R:TYR462 4.4 14.3 1.0
CG R:HIS460 4.5 12.7 1.0
O R:HOH170 4.5 16.5 1.0
O F:HOH211 4.9 21.1 1.0
CG R:ARG457 4.9 14.0 1.0
CD2 R:HIS447 4.9 19.5 0.5
OE1 R: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 14:48:23 2024

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