Chlorine in PDB 7m1i: Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol, PDB code: 7m1i was solved by R.A.Ghiladi, V.S.De Serrano, T.Malewschik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.15 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.84, 67.31, 68.03, 90, 90, 90
R / Rfree (%)	18.6 / 24.1

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol (pdb code 7m1i). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol, PDB code: 7m1i:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol


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 in Complex with 2,6- Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:85.6 occ:0.80 CL1 A:DUB202 0.0 85.6 0.8 C02 A:DUB202 1.7 77.5 0.8 CD2 A:HIS55 2.5 24.6 0.2 OH A:TYR38 2.7 38.6 1.0 C08 A:DUB202 2.7 72.5 0.8 C03 A:DUB202 2.7 78.6 0.8 CG A:HIS55 2.8 24.8 0.2 NE2 A:HIS55 2.9 24.1 0.2 O09 A:DUB202 2.9 65.5 0.8 ND1 A:HIS55 3.2 25.3 0.2 CE1 A:HIS55 3.3 25.1 0.2 CB A:HIS55 3.3 29.4 0.8 O2D A:HEM201 3.5 48.9 0.2 ND1 A:HIS55 3.5 33.4 0.8 CB A:HIS55 3.5 25.2 0.2 CZ A:TYR38 3.6 33.5 1.0 CG A:HIS55 3.7 30.9 0.8 CBD A:HEM201 3.8 46.3 1.0 CE2 A:TYR38 3.8 33.4 1.0 C06 A:DUB202 4.0 74.2 0.8 C04 A:DUB202 4.0 76.1 0.8 CGD A:HEM201 4.0 51.5 1.0 CE1 A:PHE35 4.1 32.2 1.0 CD1 A:PHE35 4.2 32.9 1.0 C05 A:DUB202 4.5 75.7 0.8 CE1 A:HIS55 4.6 33.7 0.8 O A:LYS51 4.6 36.1 1.0 CA A:HIS55 4.7 28.3 0.8 CG A:LYS51 4.7 45.2 1.0 CE1 A:TYR38 4.8 33.7 1.0 CD2 A:HIS55 4.9 33.0 0.8

Chlorine binding site 2 out of 4 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol


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 in Complex with 2,6- Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:84.3 occ:0.80 CL2 A:DUB202 0.0 84.3 0.8 C06 A:DUB202 1.7 74.2 0.8 C05 A:DUB202 2.7 75.7 0.8 C08 A:DUB202 2.7 72.5 0.8 OG1 A:THR56 2.9 19.0 0.4 O09 A:DUB202 3.0 65.5 0.8 CD1 A:PHE21 3.1 22.7 0.6 CG A:PHE21 3.1 22.1 0.6 OG1 A:THR56 3.1 22.1 0.6 CE1 A:PHE21 3.1 23.9 0.6 CD2 A:PHE21 3.1 14.3 0.4 CD2 A:PHE21 3.2 23.6 0.6 CZ A:PHE21 3.3 24.0 0.6 CE2 A:PHE21 3.3 24.9 0.6 CA A:THR56 3.3 21.8 0.4 CA A:THR56 3.3 22.2 0.6 CE2 A:PHE21 3.3 14.4 0.4 CG A:PHE21 3.3 14.4 0.4 CD2 A:HIS55 3.5 24.6 0.2 CB A:THR56 3.5 21.6 0.6 CB A:THR56 3.5 21.4 0.4 CD1 A:PHE21 3.6 14.1 0.4 NE2 A:HIS55 3.7 24.1 0.2 CZ A:PHE21 3.7 14.6 0.4 CE1 A:PHE21 3.8 14.2 0.4 CB A:PHE21 3.9 19.1 0.6 C04 A:DUB202 3.9 76.1 0.8 CG2 A:VAL59 4.0 25.1 1.0 C02 A:DUB202 4.0 77.5 0.8 CB A:PHE21 4.0 14.4 0.4 CG2 A:THR56 4.0 21.9 0.4 N A:THR56 4.0 23.6 1.0 CB A:VAL59 4.1 23.0 1.0 O A:HIS55 4.2 25.0 0.8 C A:HIS55 4.3 25.0 0.8 C A:THR56 4.4 20.6 1.0 O A:THR56 4.4 20.3 1.0 CG1 A:VAL59 4.4 24.8 1.0 C03 A:DUB202 4.5 78.6 0.8 CG A:HIS55 4.6 24.8 0.2 C A:HIS55 4.7 24.0 0.2 CE1 A:HIS55 4.8 25.1 0.2 O A:HIS55 5.0 23.7 0.2 CG2 A:THR56 5.0 20.6 0.6

Chlorine binding site 3 out of 4 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol


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 in Complex with 2,6- Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:76.2 occ:0.85 CL1 B:DUB202 0.0 76.2 0.8 C02 B:DUB202 1.7 51.5 0.8 C03 B:DUB202 2.7 49.7 0.8 C08 B:DUB202 2.7 48.0 0.8 CG2 B:THR56 2.8 18.6 0.6 CE1 B:PHE21 2.9 19.0 0.6 OG1 B:THR56 2.9 21.9 0.4 CD1 B:PHE21 2.9 18.5 0.6 O09 B:DUB202 3.0 28.7 0.8 CZ B:PHE21 3.0 19.9 0.6 CD2 B:PHE21 3.1 15.8 0.4 CG B:PHE21 3.1 18.3 0.6 CE2 B:PHE21 3.1 20.6 0.6 CE2 B:PHE21 3.1 16.2 0.4 CG B:PHE21 3.2 15.4 0.4 CD2 B:PHE21 3.2 19.9 0.6 CZ B:PHE21 3.3 16.5 0.4 CD1 B:PHE21 3.3 15.4 0.4 CE1 B:PHE21 3.4 16.2 0.4 CA B:THR56 3.5 19.8 0.6 CA B:THR56 3.5 20.9 0.4 CB B:THR56 3.6 20.2 0.4 CB B:THR56 3.6 18.2 0.6 CG2 B:THR56 3.8 20.4 0.4 C04 B:DUB202 3.9 47.8 0.8 C06 B:DUB202 4.0 49.9 0.8 CB B:PHE21 4.0 14.9 0.4 CB B:PHE21 4.0 16.6 0.6 N B:THR56 4.0 20.0 1.0 CG2 B:VAL59 4.4 24.7 1.0 C B:HIS55 4.4 23.4 1.0 C05 B:DUB202 4.4 52.4 0.8 O B:HIS55 4.5 22.5 1.0 CB B:VAL59 4.7 22.3 1.0 C B:THR56 4.7 20.7 1.0 OG1 B:THR56 4.9 17.0 0.6 O B:THR56 4.9 20.8 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol


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 in Complex with 2,6- Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:63.6 occ:0.85 CL2 B:DUB202 0.0 63.6 0.8 C06 B:DUB202 1.7 49.9 0.8 ND1 B:HIS55 2.6 40.6 1.0 C08 B:DUB202 2.7 48.0 0.8 OH B:TYR38 2.7 30.7 1.0 C05 B:DUB202 2.7 52.4 0.8 O1D B:HEM201 2.9 56.5 1.0 O09 B:DUB202 2.9 28.7 0.8 CGD B:HEM201 3.1 55.2 1.0 CG B:HIS55 3.4 35.6 1.0 CB B:HIS55 3.4 30.1 1.0 O2D B:HEM201 3.5 56.6 0.2 CZ B:TYR38 3.6 28.9 1.0 CE1 B:HIS55 3.6 41.1 1.0 CE2 B:TYR38 3.8 28.3 1.0 CBD B:HEM201 3.9 54.5 1.0 C02 B:DUB202 4.0 51.5 0.8 C04 B:DUB202 4.0 47.8 0.8 CD2 B:PHE35 4.2 35.9 1.0 ND2 B:ASN37 4.2 32.1 0.5 CE2 B:PHE35 4.3 36.3 1.0 C03 B:DUB202 4.5 49.7 0.8 CD2 B:HIS55 4.5 38.7 1.0 NE2 B:HIS55 4.6 38.9 1.0 CE1 B:TYR38 4.7 27.9 1.0 O B:LYS51 4.8 28.9 1.0 CAD B:HEM201 4.9 49.9 1.0 CA B:HIS55 4.9 26.0 1.0

T.Malewschik, L.M.Carey, V.De Serrano, R.A.Ghiladi. Bridging the Functional Gap Between Reactivity and Inhibition in Dehaloperoxidase B From Amphitrite Ornata: Mechanistic and Structural Studies with 2,4- and 2,6-Dihalophenols. J.Inorg.Biochem. V. 236 11944 2022.
ISSN: ISSN 0162-0134
PubMed: 35969974
DOI: 10.1016/J.JINORGBIO.2022.111944