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

Protein crystallography data

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

Other elements in 7m1i:

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

Iron (Fe) 2 atoms

Chlorine Binding Sites:

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 7m1i

Go back to Chlorine Binding Sites List in 7m1i
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 7m1i

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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 7m1i

Go back to Chlorine Binding Sites List in 7m1i
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 7m1i

Go back to Chlorine Binding Sites List in 7m1i
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

Reference:

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
Page generated: Tue Jul 30 00:21:59 2024

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