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Chlorine 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:

Iron (Fe) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase, PDB code: 3mi5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 3mi5

Go back to Chlorine Binding Sites List in 3mi5
Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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:Cl2

b:59.4
occ:1.00
 N M:SER433 3.2 22.0 1.0
CB M:ASP432 3.6 20.9 1.0
OG M:SER433 3.6 26.7 1.0
CB M:SER433 3.7 23.5 1.0
CA M:ASP432 3.9 20.9 1.0
C M:ASP432 4.0 21.4 1.0
CA M:SER433 4.0 22.8 1.0
O M:HOH2218 4.4 38.4 1.0
CG M:ASP432 4.7 23.4 1.0
ND2 M:ASN394 5.0 20.9 0.5

Chlorine binding site 2 out of 5 in 3mi5

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Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl 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:Cl539

b:45.8
occ:1.00
 N N:ARG450 3.0 17.1 1.0
CB N:ARG450 3.7 20.5 1.0
CA N:TRP449 3.7 16.4 1.0
O B:HOH2302 3.7 30.0 1.0
CG N:ARG450 3.7 21.9 1.0
CB N:TRP449 3.8 16.8 1.0
C N:TRP449 3.8 16.7 1.0
CA N:ARG450 3.9 19.2 1.0
O N:HOH2182 4.1 50.9 1.0
C1 N:CAQ3 4.4 23.8 0.7
CD N:ARG450 4.5 29.1 1.0
C N:ARG450 4.7 19.5 1.0
C6 N:CAQ3 4.8 25.3 0.7
NE N:ARG450 4.8 35.0 1.0
O N:ARG450 4.9 21.9 1.0
O N:HOH2087 5.0 22.1 0.5
O N:PRO448 5.0 15.4 1.0

Chlorine binding site 3 out of 5 in 3mi5

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Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl 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:Cl541

b:47.8
occ:1.00
 N O:ARG450 3.0 18.7 1.0
O1 O:SO412 3.1 58.9 0.8
CA O:TRP449 3.7 16.9 1.0
CB O:TRP449 3.7 16.7 1.0
CB O:ARG450 3.8 21.5 1.0
C O:TRP449 3.8 17.3 1.0
CA O:ARG450 3.9 20.4 1.0
CG O:ARG450 3.9 24.5 1.0
O C:HOH2173 4.1 34.8 1.0
S O:SO412 4.1 60.0 0.8
O3 O:SO412 4.1 59.4 0.8
C1 O:CAQ4 4.3 21.6 0.7
C6 O:CAQ4 4.5 22.2 0.7
CD O:ARG450 4.6 29.3 1.0
O4 O:SO412 4.6 59.0 0.8
C O:ARG450 4.7 20.6 1.0
O C:HOH2174 4.7 45.5 1.0
CG O:TRP449 5.0 16.3 1.0
O O:ARG450 5.0 23.1 1.0

Chlorine binding site 4 out of 5 in 3mi5

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Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl 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
Q:Cl541

b:46.5
occ:1.00
 N Q:ARG450 3.1 17.4 1.0
O E:HOH2288 3.7 26.9 0.5
CA Q:TRP449 3.8 16.3 1.0
CB Q:ARG450 3.8 19.4 0.5
CB Q:ARG450 3.8 19.4 0.5
CB Q:TRP449 3.8 16.9 1.0
CG Q:ARG450 3.8 21.4 0.5
NH1 Q:ARG414 3.9 39.5 0.5
CG Q:ARG450 3.9 21.4 0.5
O E:HOH2288 3.9 30.2 0.5
C Q:TRP449 4.0 16.7 1.0
CA Q:ARG450 4.0 18.9 0.5
CA Q:ARG450 4.0 18.9 0.5
O Q:HOH2247 4.2 51.5 1.0
C6 Q:CAQ6 4.3 23.2 0.7
CD Q:ARG450 4.6 29.9 0.5
C1 Q:CAQ6 4.6 23.3 0.7
CD Q:ARG450 4.7 29.9 0.5
C Q:ARG450 4.8 19.2 1.0
NE Q:ARG450 4.8 35.8 0.5
CZ Q:ARG414 4.8 38.7 0.5
NH1 Q:ARG450 4.9 40.7 0.5

Chlorine binding site 5 out of 5 in 3mi5

Go back to Chlorine Binding Sites List in 3mi5
Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl 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
R:Cl539

b:54.5
occ:1.00
 O R:HOH2255 3.5 41.5 1.0
NE R:ARG450 3.8 34.1 1.0
O F:HOH2162 3.9 42.8 1.0
O R:HOH2179 4.0 32.8 1.0
CD R:ARG450 4.0 28.6 1.0
CG R:ARG450 4.8 22.9 1.0
CD R:ARG414 5.0 29.3 0.5

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: Fri Jul 11 07:53:45 2025

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