Chlorine in PDB 4kmw: Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol

The structure of Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol, PDB code: 4kmw 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)	47.78 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.553, 67.259, 67.890, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 23.2

The structure of Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Chlorine atom in the Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol (pdb code 4kmw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol, PDB code: 4kmw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A 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 Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:46.8 occ:1.00 CL2 A:T6C202 0.0 46.8 1.0 C2 A:T6C202 1.8 43.3 1.0 C1 A:T6C202 2.7 43.9 1.0 CAD A:HEM201 2.7 56.2 1.0 C3 A:T6C202 2.7 40.5 1.0 O1 A:T6C202 2.9 41.0 1.0 C3D A:HEM201 3.1 51.9 1.0 O A:HOH402 3.3 43.5 1.0 CGD A:HEM201 3.3 78.1 0.8 O1D A:HEM201 3.3 67.7 0.8 CBD A:HEM201 3.4 69.0 1.0 ND1 A:HIS55 3.5 43.0 1.0 C2D A:HEM201 3.8 48.0 1.0 C4D A:HEM201 3.9 53.4 1.0 O2D A:HEM201 3.9 67.3 0.8 C6 A:T6C202 4.0 37.3 1.0 C4 A:T6C202 4.0 37.0 1.0 CE1 A:HIS55 4.1 44.7 1.0 CHA A:HEM201 4.1 54.8 1.0 CMD A:HEM201 4.2 48.8 1.0 CG A:HIS55 4.5 34.8 1.0 CE1 A:PHE35 4.5 28.9 1.0 C5 A:T6C202 4.5 31.4 1.0 CD1 A:PHE35 4.6 31.4 1.0 C1D A:HEM201 4.7 44.4 1.0 ND A:HEM201 4.8 45.0 1.0 CB A:HIS55 4.9 23.9 1.0 O2A A:HEM201 5.0 50.2 0.7 CBA A:HEM201 5.0 35.9 1.0

Chlorine binding site 2 out of 6 in the Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A 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 Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:37.7 occ:1.00 CL6 A:T6C202 0.0 37.7 1.0 C6 A:T6C202 1.8 37.3 1.0 C5 A:T6C202 2.7 31.4 1.0 C1 A:T6C202 2.7 43.9 1.0 O1 A:T6C202 3.0 41.0 1.0 OH A:TYR38 3.1 30.2 1.0 CE2 A:TYR38 3.2 26.4 1.0 CG2 A:THR56 3.5 22.2 1.0 CZ A:TYR38 3.5 27.8 1.0 CB A:HIS55 3.6 23.9 1.0 CE2 A:PHE21 3.9 33.9 1.0 O A:PHE52 3.9 18.1 1.0 CD1 A:PHE52 3.9 25.6 1.0 C4 A:T6C202 3.9 37.0 1.0 N A:THR56 4.0 19.2 1.0 C2 A:T6C202 4.0 43.3 1.0 CZ A:PHE21 4.2 27.2 1.0 CE1 A:PHE52 4.3 21.8 1.0 CD2 A:PHE21 4.3 28.7 1.0 C A:HIS55 4.3 18.7 1.0 CA A:PHE52 4.3 22.2 1.0 CD2 A:TYR38 4.4 25.1 1.0 C3 A:T6C202 4.5 40.5 1.0 CA A:THR56 4.5 19.9 1.0 CA A:HIS55 4.5 19.3 1.0 O A:LYS51 4.6 22.3 1.0 C A:PHE52 4.6 19.6 1.0 CB A:THR56 4.6 22.1 1.0 CG A:HIS55 4.7 34.8 1.0 CG A:PHE52 4.7 19.0 1.0 CE1 A:TYR38 4.8 24.2 1.0 ND1 A:HIS55 4.8 43.0 1.0 CD1 A:PHE35 5.0 31.4 1.0 CE1 A:PHE21 5.0 38.2 1.0 CE1 A:PHE35 5.0 28.9 1.0

Chlorine binding site 3 out of 6 in the Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A 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 Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:39.4 occ:1.00 CL4 A:T6C202 0.0 39.4 1.0 C4 A:T6C202 1.8 37.0 1.0 C3 A:T6C202 2.7 40.5 1.0 C5 A:T6C202 2.8 31.4 1.0 FE A:HEM201 3.3 41.6 1.0 NC A:HEM201 3.3 40.6 1.0 ND A:HEM201 3.4 45.0 1.0 CG2 A:VAL59 3.5 23.5 1.0 C4C A:HEM201 3.5 42.9 1.0 C1D A:HEM201 3.7 44.4 1.0 CHD A:HEM201 3.7 37.3 1.0 CE1 A:PHE21 3.8 38.2 1.0 C1C A:HEM201 3.9 39.1 1.0 C6 A:T6C202 4.0 37.3 1.0 C2 A:T6C202 4.0 43.3 1.0 CZ A:PHE35 4.1 29.4 1.0 CE1 A:PHE35 4.1 28.9 1.0 CG1 A:VAL59 4.2 20.8 1.0 C4D A:HEM201 4.2 53.4 1.0 C3C A:HEM201 4.2 41.0 1.0 NB A:HEM201 4.2 33.0 1.0 CZ A:PHE21 4.3 27.2 1.0 NA A:HEM201 4.3 34.9 1.0 CB A:VAL59 4.4 22.6 1.0 C2C A:HEM201 4.4 32.4 1.0 CHC A:HEM201 4.5 35.4 1.0 C1 A:T6C202 4.6 43.9 1.0 C2D A:HEM201 4.6 48.0 1.0 C4B A:HEM201 4.7 27.6 1.0 CD1 A:PHE21 4.7 31.3 1.0 CHA A:HEM201 4.8 54.8 1.0 C1A A:HEM201 4.8 46.0 1.0 C3D A:HEM201 4.9 51.9 1.0

Chlorine binding site 4 out of 6 in the Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A 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 Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:51.5 occ:1.00 CL2 B:T6C202 0.0 51.5 1.0 C2 B:T6C202 1.8 43.3 1.0 C1 B:T6C202 2.7 39.1 1.0 C3 B:T6C202 2.8 51.0 1.0 O1 B:T6C202 2.9 33.2 1.0 ND1 B:HIS55 3.1 45.0 1.0 CAD B:HEM201 3.3 51.5 1.0 C3D B:HEM201 3.6 35.3 1.0 CE1 B:HIS55 3.7 50.0 1.0 C2D B:HEM201 3.9 37.1 1.0 CMD B:HEM201 4.0 34.2 1.0 C6 B:T6C202 4.1 31.4 1.0 C4 B:T6C202 4.1 36.7 1.0 CG B:HIS55 4.2 38.7 1.0 CE2 B:PHE35 4.2 40.0 1.0 O1A B:HEM201 4.3 59.1 0.7 C4D B:HEM201 4.4 35.8 1.0 CD2 B:PHE35 4.5 36.3 1.0 CB B:HIS55 4.6 32.9 1.0 C5 B:T6C202 4.7 28.0 1.0 C1D B:HEM201 4.8 34.4 1.0 NE2 B:HIS55 4.8 39.7 1.0 CHA B:HEM201 4.9 35.1 1.0

Chlorine binding site 5 out of 6 in the Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A 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 Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:35.0 occ:1.00 CL6 B:T6C202 0.0 35.0 1.0 C6 B:T6C202 1.8 31.4 1.0 C5 B:T6C202 2.7 28.0 1.0 C1 B:T6C202 2.7 39.1 1.0 O1 B:T6C202 3.0 33.2 1.0 OH B:TYR38 3.3 33.2 1.0 CG2 B:THR56 3.3 23.3 1.0 CE2 B:TYR38 3.5 33.2 1.0 CD1 B:PHE52 3.6 28.4 1.0 CZ B:TYR38 3.7 33.6 1.0 O B:PHE52 3.7 23.4 1.0 CB B:HIS55 3.8 32.9 1.0 CE2 B:PHE21 3.9 23.5 1.0 C4 B:T6C202 3.9 36.7 1.0 CE1 B:PHE52 4.0 28.4 1.0 C2 B:T6C202 4.0 43.3 1.0 CA B:PHE52 4.0 30.8 1.0 N B:THR56 4.0 23.5 1.0 CD2 B:PHE21 4.1 27.1 1.0 CG B:PHE52 4.3 25.2 1.0 C B:PHE52 4.4 27.5 1.0 C3 B:T6C202 4.5 51.0 1.0 O B:LYS51 4.5 36.8 1.0 C B:HIS55 4.5 23.6 1.0 CB B:THR56 4.5 22.6 1.0 CA B:THR56 4.6 24.5 1.0 CD2 B:TYR38 4.6 31.5 1.0 CZ B:PHE21 4.6 20.5 1.0 CB B:PHE52 4.6 26.9 1.0 CA B:HIS55 4.8 26.9 1.0 CG B:HIS55 4.8 38.7 1.0 ND1 B:HIS55 4.9 45.0 1.0 CE1 B:TYR38 4.9 31.0 1.0 CZ B:PHE52 4.9 25.0 1.0 CG B:PHE21 4.9 23.6 1.0 N B:PHE52 5.0 41.2 1.0

Chlorine binding site 6 out of 6 in the Structure of the Y34N Mutant of Dehaloperoxidase-Hemoglobin A 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 Y34N Mutant of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata with 2,4,6-Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:34.6 occ:1.00 CL4 B:T6C202 0.0 34.6 1.0 C4 B:T6C202 1.8 36.7 1.0 C5 B:T6C202 2.7 28.0 1.0 C3 B:T6C202 2.7 51.0 1.0 NC B:HEM201 3.3 29.4 1.0 C4C B:HEM201 3.4 28.1 1.0 CG2 B:VAL59 3.6 26.5 1.0 CE1 B:PHE21 3.7 28.9 1.0 CHD B:HEM201 3.8 29.5 1.0 CZ B:PHE21 3.8 20.5 1.0 FE B:HEM201 3.8 32.8 1.0 C1C B:HEM201 3.8 26.4 1.0 C1D B:HEM201 3.9 34.4 1.0 C3C B:HEM201 3.9 27.3 1.0 ND B:HEM201 3.9 37.6 1.0 C6 B:T6C202 4.0 31.4 1.0 C2 B:T6C202 4.0 43.3 1.0 C2C B:HEM201 4.1 27.0 1.0 CG1 B:VAL59 4.4 22.4 1.0 CHC B:HEM201 4.5 27.7 1.0 C1 B:T6C202 4.5 39.1 1.0 CZ B:PHE35 4.5 37.2 1.0 CB B:VAL59 4.6 21.3 1.0 NB B:HEM201 4.6 28.8 1.0 CAC B:HEM201 4.6 31.2 1.0 CD1 B:PHE21 4.7 27.2 1.0 C4D B:HEM201 4.7 35.8 1.0 C4B B:HEM201 4.8 23.6 1.0 CE2 B:PHE35 4.8 40.0 1.0 CE2 B:PHE21 4.8 23.5 1.0 C2D B:HEM201 4.8 37.1 1.0

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