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Chlorine in PDB 4kn3: Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol

Protein crystallography data

The structure of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol, PDB code: 4kn3 was solved by C.Wang, L.Lovelace, L.Lebioda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.52 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.982, 67.657, 67.870, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 21.4

Other elements in 4kn3:

The structure of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol (pdb code 4kn3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol, PDB code: 4kn3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4kn3

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Chlorine binding site 1 out of 9 in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:30.9
occ:0.50
 CL2 A:T6C202 0.0 30.9 0.5
C2 A:T6C202 1.7 21.2 0.5
CAD A:HEM201 2.6 64.1 1.0
C1 A:T6C202 2.6 22.5 0.5
C3 A:T6C202 2.7 19.2 0.5
O1 A:T6C202 2.8 20.5 0.5
CBD A:HEM201 2.8 67.6 1.0
O1D A:HEM201 3.0 88.9 1.0
C3D A:HEM201 3.2 50.3 1.0
CGD A:HEM201 3.3 75.1 1.0
ND1 A:HIS55 3.4 28.4 0.5
O A:HOH382 3.5 34.8 1.0
C4D A:HEM201 3.9 43.1 1.0
C6 A:T6C202 3.9 20.4 0.5
C2D A:HEM201 4.0 49.9 1.0
C4 A:T6C202 4.0 17.9 0.5
CHA A:HEM201 4.0 41.6 1.0
CE1 A:HIS55 4.0 28.5 0.5
CE1 A:PHE35 4.3 26.3 1.0
CG A:HIS55 4.4 25.3 0.5
CMD A:HEM201 4.4 42.5 1.0
CD1 A:PHE35 4.5 29.3 1.0
C5 A:T6C202 4.5 18.1 0.5
O2D A:HEM201 4.5 67.5 1.0
CB A:HIS55 4.7 21.2 1.0
ND A:HEM201 4.8 32.4 1.0
C1D A:HEM201 4.9 39.5 1.0

Chlorine binding site 2 out of 9 in 4kn3

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Chlorine binding site 2 out of 9 in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:21.6
occ:0.50
 CL6 A:T6C202 0.0 21.6 0.5
C6 A:T6C202 1.7 20.4 0.5
C5 A:T6C202 2.6 18.1 0.5
C1 A:T6C202 2.7 22.5 0.5
OH A:TYR38 3.1 26.5 1.0
O1 A:T6C202 3.1 20.5 0.5
CE2 A:TYR38 3.2 21.5 1.0
CE2 A:PHE21 3.3 26.0 1.0
CZ A:TYR38 3.5 25.3 1.0
CB A:HIS55 3.5 21.2 1.0
CG2 A:THR56 3.7 18.9 1.0
C4 A:T6C202 3.9 17.9 0.5
CD2 A:PHE21 3.9 23.8 1.0
C2 A:T6C202 3.9 21.2 0.5
CZ A:PHE21 3.9 25.7 1.0
CD1 A:PHE52 4.0 18.8 1.0
O A:PHE52 4.0 15.7 1.0
N A:THR56 4.1 16.7 1.0
CE1 A:PHE52 4.3 19.4 1.0
CA A:PHE52 4.3 20.1 1.0
C3 A:T6C202 4.4 19.2 0.5
CD2 A:TYR38 4.4 24.8 1.0
C A:HIS55 4.4 17.6 1.0
CA A:HIS55 4.5 19.6 1.0
CG A:HIS55 4.6 25.3 0.5
O A:LYS51 4.6 21.4 1.0
C A:PHE52 4.6 16.9 1.0
CG A:PHE52 4.7 17.0 1.0
CA A:THR56 4.7 19.1 1.0
CE1 A:TYR38 4.7 25.0 1.0
ND1 A:HIS55 4.7 28.4 0.5
CB A:THR56 4.8 17.4 1.0
CG A:PHE21 4.9 19.1 1.0
O1 A:T6C203 4.9 15.6 0.5
CE1 A:PHE21 4.9 25.5 1.0
CL6 A:T6C203 4.9 21.3 0.5
CB A:PHE52 5.0 19.8 1.0

Chlorine binding site 3 out of 9 in 4kn3

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Chlorine binding site 3 out of 9 in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:25.7
occ:0.50
 CL4 A:T6C202 0.0 25.7 0.5
O1 A:T6C203 1.5 15.6 0.5
C4 A:T6C202 1.7 17.9 0.5
C3 A:T6C202 2.6 19.2 0.5
C5 A:T6C202 2.7 18.1 0.5
C1 A:T6C203 2.8 21.1 0.5
FE A:HEM201 3.3 33.2 1.0
ND A:HEM201 3.4 32.4 1.0
CG2 A:VAL59 3.4 19.2 1.0
C2 A:T6C203 3.5 20.6 0.5
CL2 A:T6C203 3.6 21.4 0.5
NC A:HEM201 3.6 33.1 1.0
C1D A:HEM201 3.7 39.5 1.0
C6 A:T6C203 3.9 21.4 0.5
C4C A:HEM201 3.9 31.2 1.0
C2 A:T6C202 3.9 21.2 0.5
C4D A:HEM201 4.0 43.1 1.0
C6 A:T6C202 4.0 20.4 0.5
CHD A:HEM201 4.0 38.1 1.0
NA A:HEM201 4.1 30.5 1.0
CG1 A:VAL59 4.1 20.6 1.0
CL6 A:T6C203 4.2 21.3 0.5
CE1 A:PHE35 4.2 26.3 1.0
CZ A:PHE35 4.2 27.8 1.0
CB A:VAL59 4.3 18.6 1.0
NB A:HEM201 4.3 25.3 1.0
C1C A:HEM201 4.3 33.1 1.0
C1 A:T6C202 4.5 22.5 0.5
CHA A:HEM201 4.5 41.6 1.0
C1A A:HEM201 4.5 39.8 1.0
C2D A:HEM201 4.5 49.9 1.0
CE1 A:PHE21 4.5 25.5 1.0
C3D A:HEM201 4.7 50.3 1.0
C3C A:HEM201 4.7 31.9 1.0
C4B A:HEM201 4.8 25.0 1.0
CZ A:PHE21 4.9 25.7 1.0
C3 A:T6C203 4.9 19.3 0.5
CHC A:HEM201 4.9 29.9 1.0
C2C A:HEM201 4.9 29.4 1.0

Chlorine binding site 4 out of 9 in 4kn3

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Chlorine binding site 4 out of 9 in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:21.4
occ:0.50
 CL2 A:T6C203 0.0 21.4 0.5
C2 A:T6C203 1.7 20.6 0.5
C3 A:T6C203 2.5 19.3 0.5
C1 A:T6C203 2.7 21.1 0.5
O1 A:T6C203 3.1 15.6 0.5
C2C A:HEM201 3.2 29.4 1.0
C3C A:HEM201 3.3 31.9 1.0
CE2 A:PHE24 3.4 18.9 1.0
CL4 A:T6C202 3.6 25.7 0.5
C1C A:HEM201 3.6 33.1 1.0
CMC A:HEM201 3.6 34.0 1.0
CE1 A:PHE21 3.7 25.5 1.0
C4C A:HEM201 3.7 31.2 1.0
CAC A:HEM201 3.7 36.4 1.0
C4 A:T6C203 3.8 22.3 0.5
NC A:HEM201 3.8 33.1 1.0
CBC A:HEM201 3.9 40.4 1.0
C6 A:T6C203 3.9 21.4 0.5
CD2 A:PHE24 3.9 14.8 1.0
CZ A:PHE24 4.0 22.3 1.0
CD1 A:LEU100 4.1 29.6 1.0
CZ A:PHE35 4.1 27.8 1.0
CD1 A:PHE21 4.1 24.6 1.0
CHC A:HEM201 4.3 29.9 1.0
C5 A:T6C203 4.4 19.3 0.5
CHD A:HEM201 4.4 38.1 1.0
CE2 A:PHE35 4.7 26.2 1.0
CZ A:PHE21 4.7 25.7 1.0
C4 A:T6C202 4.8 17.9 0.5
CG A:PHE24 4.9 14.7 1.0
CB A:LEU100 4.9 22.1 1.0
CE1 A:PHE24 5.0 17.1 1.0
CG A:LEU100 5.0 29.0 1.0

Chlorine binding site 5 out of 9 in 4kn3

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Chlorine binding site 5 out of 9 in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:21.3
occ:0.50
 CL6 A:T6C203 0.0 21.3 0.5
C6 A:T6C203 1.7 21.4 0.5
C1 A:T6C203 2.6 21.1 0.5
C5 A:T6C203 2.6 19.3 0.5
O1 A:T6C203 3.0 15.6 0.5
CE2 A:PHE60 3.5 29.2 1.0
CG2 A:THR56 3.6 18.9 1.0
CA A:THR56 3.6 19.1 1.0
CG A:PHE21 3.6 19.1 1.0
CB A:VAL59 3.7 18.6 1.0
CG1 A:VAL59 3.7 20.6 1.0
CB A:PHE21 3.7 15.1 1.0
C5 A:T6C202 3.7 18.1 0.5
CD1 A:PHE21 3.7 24.6 1.0
CB A:THR56 3.7 17.4 1.0
CD2 A:PHE60 3.8 21.1 1.0
C2 A:T6C203 3.9 20.6 0.5
C4 A:T6C203 3.9 22.3 0.5
O A:THR56 4.1 17.8 1.0
CG2 A:VAL59 4.1 19.2 1.0
CD2 A:PHE21 4.1 23.8 1.0
CL4 A:T6C202 4.2 25.7 0.5
C4 A:T6C202 4.3 17.9 0.5
C A:THR56 4.4 18.5 1.0
CE1 A:PHE21 4.4 25.5 1.0
C3 A:T6C203 4.4 19.3 0.5
N A:THR56 4.5 16.7 1.0
O A:ALA17 4.6 15.5 1.0
O A:HIS55 4.7 18.3 1.0
CE2 A:PHE21 4.7 26.0 1.0
C6 A:T6C202 4.8 20.4 0.5
CZ A:PHE60 4.8 21.5 1.0
CZ A:PHE21 4.8 25.7 1.0
CA A:PHE21 4.8 12.2 1.0
C A:HIS55 4.9 17.6 1.0
CL6 A:T6C202 4.9 21.6 0.5

Chlorine binding site 6 out of 9 in 4kn3

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Chlorine binding site 6 out of 9 in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:22.7
occ:0.50
 CL4 A:T6C203 0.0 22.7 0.5
C4 A:T6C203 1.7 22.3 0.5
C3 A:T6C203 2.7 19.3 0.5
C5 A:T6C203 2.7 19.3 0.5
CG A:LEU100 3.2 29.0 1.0
CG2 A:ILE20 3.6 14.3 1.0
CB A:PHE24 3.7 15.8 1.0
O A:ILE20 3.7 13.9 1.0
CD1 A:LEU100 3.8 29.6 1.0
CA A:PHE21 3.9 12.2 1.0
C2 A:T6C203 3.9 20.6 0.5
C A:ILE20 4.0 13.4 1.0
CZ A:PHE60 4.0 21.5 1.0
C6 A:T6C203 4.0 21.4 0.5
CB A:LEU100 4.1 22.1 1.0
N A:PHE21 4.1 11.9 1.0
CD2 A:LEU100 4.1 37.8 1.0
CG A:PHE24 4.2 14.7 1.0
O A:LEU100 4.2 17.4 1.0
CE2 A:PHE60 4.3 29.2 1.0
CA A:LEU100 4.4 20.6 1.0
CD1 A:PHE21 4.5 24.6 1.0
CD2 A:PHE24 4.5 14.8 1.0
C1 A:T6C203 4.6 21.1 0.5
CB A:ILE20 4.6 12.8 1.0
CB A:PHE21 4.6 15.1 1.0
C A:LEU100 4.7 19.7 1.0
CD1 A:PHE24 4.8 17.2 1.0
CA A:ILE20 4.9 12.5 1.0
C A:PHE21 5.0 14.1 1.0

Chlorine binding site 7 out of 9 in 4kn3

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Chlorine binding site 7 out of 9 in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:42.7
occ:1.00
 CL2 B:T6C202 0.0 42.7 1.0
C2 B:T6C202 1.7 41.4 1.0
C1 B:T6C202 2.6 41.2 1.0
C3 B:T6C202 2.7 38.1 1.0
O1 B:T6C202 2.8 39.8 1.0
CAD B:HEM201 3.2 51.5 1.0
O B:HOH413 3.2 43.1 1.0
CBD B:HEM201 3.3 66.8 1.0
C3D B:HEM201 3.3 44.1 1.0
ND1 B:HIS55 3.3 33.4 1.0
C2D B:HEM201 3.5 40.9 1.0
O B:HOH389 3.6 47.0 1.0
O1D B:HEM201 3.6 52.1 1.0
CMD B:HEM201 3.7 38.9 1.0
CGD B:HEM201 3.7 73.7 1.0
CE1 B:HIS55 3.9 39.7 1.0
C6 B:T6C202 3.9 35.4 1.0
C4 B:T6C202 4.0 26.1 1.0
CE1 B:PHE35 4.1 40.5 1.0
C4D B:HEM201 4.2 41.8 1.0
CG B:HIS55 4.3 35.6 1.0
CD1 B:PHE35 4.3 34.5 1.0
C1D B:HEM201 4.4 37.7 1.0
C5 B:T6C202 4.5 29.0 1.0
CB B:HIS55 4.7 25.7 1.0
ND B:HEM201 4.8 39.1 1.0
CHA B:HEM201 4.8 34.9 1.0
O2D B:HEM201 4.8 82.4 1.0
NE2 B:HIS55 5.0 44.9 1.0

Chlorine binding site 8 out of 9 in 4kn3

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Chlorine binding site 8 out of 9 in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:28.1
occ:1.00
 CL6 B:T6C202 0.0 28.1 1.0
C6 B:T6C202 1.7 35.4 1.0
C5 B:T6C202 2.7 29.0 1.0
C1 B:T6C202 2.7 41.2 1.0
O1 B:T6C202 3.1 39.8 1.0
OH B:TYR38 3.3 30.0 1.0
CE2 B:TYR38 3.5 28.8 1.0
CG2 B:THR56 3.5 22.9 1.0
CZ B:TYR38 3.7 30.0 1.0
CE2 B:PHE21 3.7 19.8 1.0
CD1 B:PHE52 3.7 24.4 1.0
CB B:HIS55 3.8 25.7 1.0
O B:PHE52 3.9 26.5 1.0
C4 B:T6C202 3.9 26.1 1.0
C2 B:T6C202 3.9 41.4 1.0
CD2 B:PHE21 3.9 24.2 1.0
N B:THR56 4.1 19.1 1.0
CE1 B:PHE52 4.1 25.4 1.0
CA B:PHE52 4.2 29.9 1.0
CG B:PHE52 4.4 20.2 1.0
C3 B:T6C202 4.4 38.1 1.0
CZ B:PHE21 4.5 25.8 1.0
C B:PHE52 4.5 27.9 1.0
CD2 B:TYR38 4.6 26.0 1.0
C B:HIS55 4.6 20.9 1.0
CA B:THR56 4.6 20.4 1.0
O B:LYS51 4.6 37.7 1.0
CB B:THR56 4.7 20.3 1.0
CG B:HIS55 4.8 35.6 1.0
CA B:HIS55 4.8 22.2 1.0
CG B:PHE21 4.8 19.1 1.0
ND1 B:HIS55 4.8 33.4 1.0
CB B:PHE52 4.8 25.7 1.0
CE1 B:TYR38 4.9 31.5 1.0
CZ B:PHE52 5.0 17.3 1.0

Chlorine binding site 9 out of 9 in 4kn3

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Chlorine binding site 9 out of 9 in the Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of the Y34NS91G Double Mutant of Dehaloperoxidase From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:33.4
occ:1.00
 CL4 B:T6C202 0.0 33.4 1.0
C4 B:T6C202 1.7 26.1 1.0
C3 B:T6C202 2.6 38.1 1.0
C5 B:T6C202 2.6 29.0 1.0
NC B:HEM201 3.4 33.4 1.0
C4C B:HEM201 3.5 29.6 1.0
CG2 B:VAL59 3.7 19.9 1.0
CE1 B:PHE21 3.8 21.8 1.0
C1C B:HEM201 3.8 26.8 1.0
FE B:HEM201 3.8 33.9 1.0
C2 B:T6C202 3.9 41.4 1.0
C6 B:T6C202 3.9 35.4 1.0
CHD B:HEM201 3.9 29.1 1.0
C3C B:HEM201 3.9 30.2 1.0
CZ B:PHE21 4.0 25.8 1.0
ND B:HEM201 4.0 39.1 1.0
C1D B:HEM201 4.0 37.7 1.0
C2C B:HEM201 4.1 27.9 1.0
CG1 B:VAL59 4.3 20.8 1.0
C1 B:T6C202 4.4 41.2 1.0
CHC B:HEM201 4.4 28.0 1.0
CB B:VAL59 4.5 17.7 1.0
CD1 B:PHE21 4.6 26.1 1.0
NB B:HEM201 4.6 31.0 1.0
CZ B:PHE35 4.6 33.1 1.0
CE1 B:PHE35 4.7 40.5 1.0
C4B B:HEM201 4.7 29.7 1.0
CAC B:HEM201 4.7 30.5 1.0
C4D B:HEM201 4.8 41.8 1.0
CE2 B:PHE21 4.9 19.8 1.0
C2D B:HEM201 5.0 40.9 1.0

Reference:

C.Wang, L.L.Lovelace, S.Sun, J.H.Dawson, L.Lebioda. Complexes of Dual-Function Hemoglobin/Dehaloperoxidase with Substrate 2,4,6-Trichlorophenol Are Inhibitory and Indicate Binding of Halophenol to Compound I. Biochemistry V. 52 6203 2013.
ISSN: ISSN 0006-2960
PubMed: 23952341
DOI: 10.1021/BI400627W
Page generated: Sun Jul 21 18:17:22 2024

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