Chlorine in PDB 7avr: The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2

Enzymatic activity of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2

All present enzymatic activity of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2:
3.8.1.5;

Protein crystallography data

The structure of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2, PDB code: 7avr was solved by A.Mazur, P.Kolenko, T.Prudnikova, P.Grinkevich, I.Kuta Smatanova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.44 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 117.385, 155.506, 155.611, 90, 90, 90
R / Rfree (%) 17.6 / 20.6

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Chlorine atom in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 (pdb code 7avr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 18 binding sites of Chlorine where determined in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2, PDB code: 7avr:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 18 in 7avr

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Chlorine binding site 1 out of 18 in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:18.5
occ:1.00
 O A:HOH596 2.9 24.9 1.0
NE1 A:TRP126 3.2 21.8 1.0
NE1 A:TRP165 3.2 20.5 1.0
N A:PRO214 3.5 12.9 1.0
CG A:GLU57 3.6 19.9 1.0
CA A:PRO214 3.7 13.6 1.0
C A:PHE213 3.7 14.4 1.0
CD1 A:TRP126 3.7 20.6 1.0
CG A:PRO214 3.7 11.5 1.0
CB A:GLU57 3.8 20.1 1.0
CD A:PRO214 3.8 10.9 1.0
O A:PHE213 3.9 11.2 1.0
CB A:PHE213 3.9 19.3 1.0
CD1 A:ILE217 4.0 13.4 1.0
CE2 A:TRP165 4.1 19.7 1.0
CB A:PRO214 4.2 13.1 1.0
CD1 A:TRP165 4.3 24.3 1.0
CZ2 A:TRP165 4.3 18.2 1.0
CD A:GLU57 4.4 20.1 1.0
CA A:PHE213 4.4 19.0 1.0
CE2 A:TRP126 4.5 20.3 1.0
CG1 A:ILE217 4.6 14.5 1.0
OE2 A:GLU57 4.6 19.5 1.0
O A:HOH707 4.6 24.8 1.0
CG A:PHE213 4.9 24.5 1.0
OD2 A:ASP125 4.9 19.2 1.0
C A:PRO214 5.0 12.3 1.0

Chlorine binding site 2 out of 18 in 7avr

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Chlorine binding site 2 out of 18 in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:17.8
occ:1.00
 O B:HOH505 3.2 22.5 1.0
NE1 B:TRP126 3.2 21.0 1.0
NE1 B:TRP165 3.3 28.7 1.0
N B:PRO214 3.5 19.7 1.0
CA B:PRO214 3.6 20.4 1.0
C B:PHE213 3.6 20.2 1.0
CG B:GLU57 3.7 22.9 1.0
CG B:PRO214 3.8 22.0 1.0
CD1 B:TRP126 3.8 18.0 1.0
CD B:PRO214 3.8 20.5 1.0
O B:PHE213 3.8 18.0 1.0
CB B:GLU57 3.9 20.5 1.0
CB B:PHE213 3.9 19.0 1.0
CD1 B:ILE217 4.0 22.4 1.0
CE2 B:TRP165 4.1 28.2 1.0
CB B:PRO214 4.2 21.3 1.0
CZ2 B:TRP165 4.2 27.2 1.0
CD1 B:TRP165 4.3 24.9 1.0
O B:HOH681 4.3 31.8 1.0
CA B:PHE213 4.4 17.7 1.0
CD B:GLU57 4.4 21.8 1.0
CE2 B:TRP126 4.5 22.0 1.0
CG1 B:ILE217 4.5 23.1 1.0
OE2 B:GLU57 4.7 18.2 1.0
CG B:PHE213 4.9 21.5 1.0
C B:PRO214 5.0 24.4 1.0
OD1 B:ASP125 5.0 23.0 1.0

Chlorine binding site 3 out of 18 in 7avr

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Chlorine binding site 3 out of 18 in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:21.7
occ:1.00
 O C:HOH643 2.8 11.2 1.0
NE1 C:TRP165 3.1 19.1 1.0
NE1 C:TRP126 3.2 16.9 1.0
N C:PRO214 3.6 16.9 1.0
CG C:GLU57 3.7 17.0 1.0
CA C:PRO214 3.7 18.4 1.0
CD1 C:TRP126 3.8 15.7 1.0
C C:PHE213 3.8 18.1 1.0
CG C:PRO214 3.8 18.5 1.0
CB C:GLU57 3.9 15.6 1.0
CD C:PRO214 4.0 18.6 1.0
CD1 C:ILE217 4.0 27.7 1.0
O C:PHE213 4.0 21.0 1.0
CE2 C:TRP165 4.0 19.7 1.0
CB C:PHE213 4.1 16.2 1.0
CD1 C:TRP165 4.1 16.9 1.0
CZ2 C:TRP165 4.2 21.1 1.0
CB C:PRO214 4.2 18.7 1.0
O C:HOH703 4.4 35.6 1.0
CE2 C:TRP126 4.5 17.1 1.0
CD C:GLU57 4.5 15.1 1.0
CG1 C:ILE217 4.5 29.6 1.0
CA C:PHE213 4.6 16.7 1.0
OE2 C:GLU57 4.7 16.9 1.0
OD2 C:ASP125 4.9 24.0 1.0
CG C:PHE213 5.0 13.8 1.0

Chlorine binding site 4 out of 18 in 7avr

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Chlorine binding site 4 out of 18 in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:34.5
occ:1.00
 N C:ARG7 2.9 25.9 1.0
O C:ARG7 3.4 26.1 1.0
CA C:LEU6 3.6 28.3 1.0
C C:LEU6 3.8 25.9 1.0
CA C:ARG7 3.8 23.4 1.0
O C:HOH514 3.8 22.1 1.0
CD2 C:LEU6 3.9 36.9 1.0
CB C:ARG7 3.9 25.3 1.0
C C:ARG7 4.0 24.5 1.0
CB C:LEU6 4.1 31.2 1.0
O C:ALA5 4.6 29.8 1.0
CG C:LEU6 4.6 30.4 1.0
O C:HOH713 4.7 48.3 1.0
N C:LEU6 4.8 28.0 1.0
O C:LEU6 5.0 22.2 1.0

Chlorine binding site 5 out of 18 in 7avr

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Chlorine binding site 5 out of 18 in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:47.1
occ:1.00
 O C:HOH650 2.6 13.8 1.0
N C:THR8 2.6 23.2 1.0
O C:SER89 3.1 18.3 1.0
O C:ARG88 3.3 16.7 1.0
OG1 C:THR8 3.4 17.0 1.0
CB C:THR8 3.4 18.9 1.0
NZ C:LYS91 3.5 15.7 1.0
CA C:THR8 3.5 20.2 1.0
C C:ARG7 3.5 24.5 1.0
CA C:ARG7 3.6 23.4 1.0
C C:ARG88 3.6 17.2 1.0
CG C:ARG7 3.7 23.3 1.0
C C:SER89 3.8 17.4 1.0
O C:THR8 3.9 26.8 1.0
O C:HOH555 3.9 18.1 1.0
CA C:ARG88 4.1 16.9 1.0
C C:THR8 4.2 19.6 1.0
CB C:ARG7 4.2 25.3 1.0
N C:SER89 4.2 14.7 1.0
OD1 C:ASP90 4.4 20.5 1.0
O C:GLY87 4.4 18.4 1.0
N C:ASP90 4.5 19.5 1.0
CA C:ASP90 4.6 17.3 1.0
CA C:SER89 4.6 17.0 1.0
O C:LEU6 4.6 22.2 1.0
O C:ARG7 4.7 26.1 1.0
CE C:LYS91 4.8 15.6 1.0
N C:ARG7 4.8 25.9 1.0
CG2 C:THR8 4.8 18.5 1.0
O C:HOH515 4.9 26.4 1.0
CE2 C:PHE13 4.9 18.7 1.0
O C:HOH513 5.0 18.5 1.0

Chlorine binding site 6 out of 18 in 7avr

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Chlorine binding site 6 out of 18 in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:17.3
occ:1.00
 NE1 D:TRP126 3.1 18.3 1.0
O D:HOH540 3.1 20.0 1.0
NE1 D:TRP165 3.2 17.9 1.0
N D:PRO214 3.5 21.2 1.0
CD1 D:TRP126 3.6 20.2 1.0
CA D:PRO214 3.7 20.5 1.0
C D:PHE213 3.7 21.6 1.0
O D:PHE213 3.8 19.6 1.0
CG D:GLU57 3.8 16.5 1.0
CG D:PRO214 3.9 22.5 1.0
CD D:PRO214 3.9 20.9 1.0
CB D:GLU57 3.9 17.6 1.0
CB D:PHE213 4.0 18.5 1.0
CD1 D:ILE217 4.0 22.3 1.0
CE2 D:TRP165 4.1 16.9 1.0
CD1 D:TRP165 4.2 19.4 1.0
CB D:PRO214 4.3 24.1 1.0
CE2 D:TRP126 4.3 19.7 1.0
CZ2 D:TRP165 4.3 17.6 1.0
CG1 D:ILE217 4.4 23.4 1.0
CA D:PHE213 4.5 20.9 1.0
O D:HOH682 4.5 26.9 1.0
CD D:GLU57 4.6 15.2 1.0
O D:HOH686 4.7 30.8 1.0
OE2 D:GLU57 4.8 16.7 1.0
OD2 D:ASP125 4.9 15.6 1.0
CG D:PHE213 4.9 17.8 1.0
CZ2 D:TRP126 4.9 25.0 1.0
C D:PRO214 4.9 23.5 1.0
CG D:TRP126 5.0 20.9 1.0

Chlorine binding site 7 out of 18 in 7avr

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Chlorine binding site 7 out of 18 in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:24.2
occ:1.00
 NE1 E:TRP126 3.2 20.1 1.0
O E:HOH537 3.3 34.1 1.0
NE1 E:TRP165 3.3 29.1 1.0
N E:PRO214 3.6 21.0 1.0
CG E:GLU57 3.7 28.5 1.0
CA E:PRO214 3.7 22.1 1.0
CD1 E:TRP126 3.7 20.2 1.0
C E:PHE213 3.8 22.9 1.0
CB E:GLU57 3.8 27.0 1.0
CG E:PRO214 3.9 20.9 1.0
O E:PHE213 3.9 21.6 1.0
CD E:PRO214 3.9 23.7 1.0
CD1 E:ILE217 4.0 27.6 1.0
CB E:PHE213 4.0 23.6 1.0
CE2 E:TRP165 4.2 24.3 1.0
CZ2 E:TRP165 4.3 27.9 1.0
CB E:PRO214 4.3 19.1 1.0
CD1 E:TRP165 4.3 24.3 1.0
CE2 E:TRP126 4.5 21.5 1.0
CG1 E:ILE217 4.5 30.8 1.0
CD E:GLU57 4.5 27.6 1.0
CA E:PHE213 4.5 25.4 1.0
OE2 E:GLU57 4.7 31.6 1.0
CG E:PHE213 4.9 25.4 1.0
OD1 E:ASP125 4.9 31.4 1.0
O E:HOH712 4.9 57.2 1.0
OD2 E:ASP125 5.0 30.6 1.0

Chlorine binding site 8 out of 18 in 7avr

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Chlorine binding site 8 out of 18 in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl402

b:54.0
occ:1.00
 N E:GLU48 2.9 51.1 1.0
O E:HOH534 3.0 47.0 1.0
CA E:SER47 3.1 46.4 1.0
O E:GLY75 3.2 37.9 1.0
C E:SER47 3.5 48.7 1.0
O E:HOH612 3.6 34.1 1.0
CB E:SER47 3.6 45.0 1.0
O E:HOH502 4.0 34.6 1.0
CB E:GLU48 4.0 54.8 1.0
CA E:GLU48 4.1 52.6 1.0
OG E:SER47 4.1 38.7 1.0
N E:SER47 4.4 55.3 1.0
C E:GLY75 4.4 37.5 1.0
O E:ASP46 4.4 56.3 1.0
O E:SER47 4.7 50.4 1.0
C E:ASP46 4.8 55.5 1.0

Chlorine binding site 9 out of 18 in 7avr

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Chlorine binding site 9 out of 18 in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl401

b:58.0
occ:1.00
 O F:MET136 3.1 37.5 1.0
N F:GLN139 3.2 40.6 1.0
C F:ASP137 3.5 39.8 1.0
N F:MET138 3.5 44.9 1.0
CB F:GLN139 3.5 41.6 1.0
CA F:ASP137 3.7 36.9 1.0
C F:MET136 3.8 30.8 1.0
O F:ASP137 3.9 35.3 1.0
CA F:GLN139 4.0 42.1 1.0
CA F:MET138 4.0 42.1 1.0
N F:ASP137 4.1 33.0 1.0
C F:MET138 4.1 44.2 1.0
O F:HOH666 4.2 38.1 1.0
O F:PRO135 4.4 28.3 1.0
CG F:GLN139 4.7 49.0 1.0
OE1 F:GLN139 4.7 50.2 1.0
CD F:GLN139 4.8 54.6 1.0
CA F:MET136 4.9 35.2 1.0

Chlorine binding site 10 out of 18 in 7avr

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Chlorine binding site 10 out of 18 in the The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of The Tetrameric Structure of Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl402

b:19.9
occ:1.00
 O F:HOH629 2.7 24.4 1.0
NE1 F:TRP126 3.2 23.4 1.0
NE1 F:TRP165 3.2 20.6 1.0
N F:PRO214 3.5 18.4 1.0
CG F:GLU57 3.6 17.1 1.0
CA F:PRO214 3.7 21.9 1.0
C F:PHE213 3.7 15.8 1.0
CD1 F:TRP126 3.7 24.7 1.0
CG F:PRO214 3.8 18.5 1.0
CB F:GLU57 3.8 17.6 1.0
CD F:PRO214 3.8 18.4 1.0
O F:PHE213 3.9 14.1 1.0
CB F:PHE213 3.9 16.3 1.0
O F:HOH657 4.1 17.9 1.0
CE2 F:TRP165 4.1 18.1 1.0
CD1 F:ILE217 4.1 26.0 1.0
CB F:PRO214 4.2 21.2 1.0
CZ2 F:TRP165 4.3 20.2 1.0
O F:HOH665 4.3 34.4 1.0
CD1 F:TRP165 4.3 21.1 1.0
CD F:GLU57 4.4 16.0 1.0
CA F:PHE213 4.4 16.8 1.0
CE2 F:TRP126 4.5 22.8 1.0
CG1 F:ILE217 4.6 25.0 1.0
OE2 F:GLU57 4.6 19.4 1.0
CG F:PHE213 4.9 15.2 1.0
OD2 F:ASP125 4.9 20.6 1.0
C F:PRO214 5.0 21.6 1.0

Reference:

A.Mazur, T.Prudnikova, P.Grinkevich, J.R.Mesters, D.Mrazova, R.Chaloupkova, J.Damborsky, M.Kuty, P.Kolenko, I.Kuta Smatanova. The Tetrameric Structure of the Novel Haloalkane Dehalogenase Dpaa From Paraglaciecola Agarilytica NO2. Acta Crystallogr D Struct V. 77 347 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 33645538
DOI: 10.1107/S2059798321000486
Page generated: Sat Apr 3 14:23:03 2021

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