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

Protein crystallography data

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

Other elements in 6vdy:

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

Chlorine Binding Sites:

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 6vdy

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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 6vdy

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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 6vdy

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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 6vdy

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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 6vdy

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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 6vdy

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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

Reference:

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.
Page generated: Sun Jan 24 10:59:48 2021

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