Chlorine in PDB 6vdy: Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol

The structure of Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol, PDB code: 6vdy was solved by R.A.Ghiladi, V.S.De Serrano, A.Mcguire, T.Malewschik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.26 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.227, 67.457, 68.132, 90, 90, 90
R / Rfree (%)	17.9 / 21.4

The structure of Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol (pdb code 6vdy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol, PDB code: 6vdy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:54.2 occ:1.00 CL2 A:T6C202 0.0 54.2 1.0 C2 A:T6C202 1.7 58.0 1.0 C1 A:T6C202 2.7 61.0 1.0 C3 A:T6C202 2.7 56.0 1.0 O1 A:T6C202 2.8 52.9 1.0 OG1 A:THR56 3.0 16.4 0.3 OH A:TYR38 3.3 40.4 1.0 CG2 A:THR56 3.4 20.9 0.7 CE2 A:TYR38 3.4 31.1 1.0 CD1 A:PHE52 3.6 21.1 1.0 CZ A:TYR38 3.7 34.0 1.0 O A:PHE52 3.9 22.7 1.0 CE2 A:PHE21 3.9 34.6 1.0 C6 A:T6C202 4.0 68.4 1.0 CB A:HIS55 4.0 24.1 1.0 C4 A:T6C202 4.0 55.5 1.0 CE1 A:PHE52 4.0 22.5 1.0 CA A:PHE52 4.0 22.3 1.0 N A:THR56 4.1 19.4 1.0 CD2 A:PHE21 4.2 29.3 1.0 CB A:THR56 4.3 20.9 0.3 CG A:PHE52 4.4 21.6 1.0 C A:PHE52 4.4 26.8 1.0 CZ A:PHE21 4.4 32.3 1.0 O A:LYS51 4.5 26.3 0.6 O A:LYS51 4.5 26.5 0.5 C5 A:T6C202 4.5 65.6 1.0 CD2 A:TYR38 4.5 35.9 1.0 CB A:THR56 4.5 18.5 0.7 CA A:THR56 4.5 20.0 0.3 CA A:THR56 4.5 20.5 0.7 C A:HIS55 4.7 21.1 1.0 CB A:PHE52 4.7 24.1 1.0 CE1 A:TYR38 4.9 38.2 1.0 CA A:HIS55 4.9 22.1 1.0 CE1 A:PHE35 4.9 51.1 1.0 CZ A:PHE52 5.0 21.7 1.0 N A:PHE52 5.0 24.7 1.0 CG A:PHE21 5.0 27.3 1.0 CD1 A:PHE35 5.0 49.2 1.0 ND1 A:HIS55 5.0 40.6 1.0 CG A:HIS55 5.0 29.8 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:71.8 occ:1.00 CL6 A:T6C202 0.0 71.8 1.0 C6 A:T6C202 1.8 68.4 1.0 C1 A:T6C202 2.7 61.0 1.0 C5 A:T6C202 2.8 65.6 1.0 O1 A:T6C202 3.0 52.9 1.0 CAD A:HEM201 3.0 61.0 1.0 ND1 A:HIS55 3.3 40.6 1.0 C3D A:HEM201 3.4 67.7 1.0 CE1 A:HIS55 3.9 37.7 1.0 C2D A:HEM201 3.9 61.2 1.0 C4D A:HEM201 4.0 68.0 1.0 C2 A:T6C202 4.0 58.0 1.0 C4 A:T6C202 4.1 55.5 1.0 CG A:HIS55 4.3 29.8 1.0 CMD A:HEM201 4.3 55.6 1.0 CHA A:HEM201 4.4 66.5 1.0 CE1 A:PHE35 4.4 51.1 1.0 C3 A:T6C202 4.6 56.0 1.0 CD1 A:PHE35 4.6 49.2 1.0 CB A:HIS55 4.7 24.1 1.0 ND A:HEM201 4.8 64.0 1.0 C1D A:HEM201 4.8 63.2 1.0 NE2 A:HIS55 5.0 35.5 1.0 O2A A:HEM201 5.0 83.5 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:56.2 occ:1.00 CL4 A:T6C202 0.0 56.2 1.0 C4 A:T6C202 1.8 55.5 1.0 C3 A:T6C202 2.7 56.0 1.0 C5 A:T6C202 2.8 65.6 1.0 NC A:HEM201 3.0 58.1 1.0 C4C A:HEM201 3.2 63.1 1.0 FE A:HEM201 3.2 57.4 1.0 ND A:HEM201 3.3 64.0 1.0 CHD A:HEM201 3.4 65.0 1.0 C1D A:HEM201 3.5 63.2 1.0 CG2 A:VAL59 3.7 21.9 1.0 C1C A:HEM201 3.7 50.0 1.0 CE1 A:PHE21 3.7 35.6 1.0 C3C A:HEM201 3.9 61.1 1.0 CZ A:PHE21 3.9 32.3 1.0 C2 A:T6C202 4.0 58.0 1.0 CZ A:PHE35 4.1 58.9 1.0 C6 A:T6C202 4.1 68.4 1.0 C2C A:HEM201 4.1 47.7 1.0 CE1 A:PHE35 4.2 51.1 1.0 C4D A:HEM201 4.3 68.0 1.0 NB A:HEM201 4.3 58.1 1.0 CHC A:HEM201 4.4 60.4 1.0 CG1 A:VAL59 4.5 24.6 1.0 C2D A:HEM201 4.5 61.2 1.0 C1 A:T6C202 4.6 61.0 1.0 NA A:HEM201 4.6 67.3 1.0 CB A:VAL59 4.7 25.5 1.0 C4B A:HEM201 4.7 57.5 1.0 CD1 A:PHE21 4.8 35.4 1.0 CAC A:HEM201 4.8 64.2 1.0 C3D A:HEM201 4.9 67.7 1.0 CHA A:HEM201 4.9 66.5 1.0 C1A A:HEM201 4.9 70.2 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:54.2 occ:1.00 CL2 B:T6C403 0.0 54.2 1.0 C2 B:T6C403 1.8 52.5 1.0 C1 B:T6C403 2.7 56.6 1.0 C3 B:T6C403 2.8 43.5 1.0 O1 B:T6C403 2.9 44.4 1.0 OH B:TYR38 3.1 35.8 1.0 OG1 B:THR56 3.2 18.6 0.2 CE2 B:TYR38 3.2 31.0 1.0 CG2 B:THR56 3.4 19.6 0.8 CZ B:TYR38 3.5 35.3 1.0 CD1 B:PHE52 3.7 21.3 1.0 CB B:HIS55 3.8 21.1 1.0 CE2 B:PHE21 3.9 36.3 1.0 C6 B:T6C403 4.0 59.8 1.0 O B:PHE52 4.0 19.1 1.0 C4 B:T6C403 4.0 44.2 1.0 N B:THR56 4.1 18.9 1.0 CE1 B:PHE52 4.1 28.8 1.0 CD2 B:PHE21 4.2 32.4 1.0 CA B:PHE52 4.3 21.8 1.0 CZ B:PHE21 4.4 30.7 1.0 CD2 B:TYR38 4.4 30.0 1.0 CB B:THR56 4.4 18.2 0.2 C5 B:T6C403 4.5 56.0 1.0 CG B:PHE52 4.5 20.5 1.0 CB B:THR56 4.6 16.7 0.8 CA B:THR56 4.6 18.2 0.2 CA B:THR56 4.6 17.8 0.8 C B:HIS55 4.6 23.0 1.0 C B:PHE52 4.6 21.4 1.0 O B:LYS51 4.7 27.3 1.0 CA B:HIS55 4.8 22.9 1.0 CE1 B:TYR38 4.8 32.9 1.0 CG B:HIS55 4.8 32.3 1.0 ND1 B:HIS55 4.8 43.3 1.0 CB B:PHE52 4.9 20.8 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:63.7 occ:1.00 CL6 B:T6C403 0.0 63.7 1.0 C6 B:T6C403 1.8 59.8 1.0 C1 B:T6C403 2.7 56.6 1.0 C5 B:T6C403 2.8 56.0 1.0 O1 B:T6C403 2.9 44.4 1.0 CAD B:HEM402 3.0 80.4 1.0 C3D B:HEM402 3.3 77.3 1.0 ND1 B:HIS55 3.4 43.3 1.0 C2D B:HEM402 3.9 72.2 1.0 C4D B:HEM402 3.9 73.3 1.0 CE1 B:HIS55 4.0 43.5 1.0 C2 B:T6C403 4.0 52.5 1.0 C4 B:T6C403 4.0 44.2 1.0 CMD B:HEM402 4.3 65.3 1.0 CHA B:HEM402 4.4 73.0 1.0 CG B:HIS55 4.4 32.3 1.0 O2A B:HEM402 4.5 84.4 1.0 C3 B:T6C403 4.5 43.5 1.0 CE1 B:PHE35 4.6 41.0 1.0 CD1 B:PHE35 4.7 37.2 1.0 C1D B:HEM402 4.7 69.4 1.0 ND B:HEM402 4.7 65.2 1.0 CB B:HIS55 4.8 21.1 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Dehaloperoxidase B Wild Type in Complex with Substrate Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:49.1 occ:1.00 CL4 B:T6C403 0.0 49.1 1.0 C4 B:T6C403 1.8 44.2 1.0 C5 B:T6C403 2.7 56.0 1.0 C3 B:T6C403 2.8 43.5 1.0 NC B:HEM402 3.1 65.0 1.0 FE B:HEM402 3.2 58.4 1.0 C4C B:HEM402 3.2 70.1 1.0 ND B:HEM402 3.3 65.2 1.0 CG2 B:VAL59 3.5 23.5 1.0 CHD B:HEM402 3.5 68.5 1.0 C1D B:HEM402 3.5 69.4 1.0 C1C B:HEM402 3.6 59.6 1.0 CE1 B:PHE21 3.9 36.9 1.0 C3C B:HEM402 3.9 67.9 1.0 C6 B:T6C403 4.0 59.8 1.0 C2 B:T6C403 4.1 52.5 1.0 C2C B:HEM402 4.1 56.8 1.0 CG1 B:VAL59 4.2 23.1 1.0 CZ B:PHE21 4.2 30.7 1.0 C4D B:HEM402 4.2 73.3 1.0 NB B:HEM402 4.2 56.9 1.0 CB B:VAL59 4.3 21.0 1.0 CHC B:HEM402 4.3 57.4 1.0 CE1 B:PHE35 4.4 41.0 1.0 CZ B:PHE35 4.5 47.0 1.0 NA B:HEM402 4.6 62.4 1.0 C1 B:T6C403 4.6 56.6 1.0 C2D B:HEM402 4.6 72.2 1.0 C4B B:HEM402 4.6 56.8 1.0 CAC B:HEM402 4.8 72.7 1.0 CHA B:HEM402 4.8 73.0 1.0 CD1 B:PHE21 4.9 32.0 1.0 C1A B:HEM402 4.9 68.6 1.0 C3D B:HEM402 4.9 77.3 1.0

A.H.Mcguire, A.R.Petit, J.Kang, T.Malewschik, V.De Serrano, L.M.Carey, R.A.Ghiladi. Nonnative Heme Incorporation Into Multifunctional Globin Increases Peroxygenase Activity An Order and Magnitude Compared to Native Enzyme To Be Published.