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Chlorine in PDB 3r3w: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate

Enzymatic activity of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate

All present enzymatic activity of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate:
3.8.1.3;

Protein crystallography data

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate, PDB code: 3r3w was solved by P.W.Y.Chan, A.F.Yakunin, E.A.Edwards, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.69 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.030, 79.770, 85.180, 90.00, 103.22, 90.00
R / Rfree (%) 17.9 / 22.3

Other elements in 3r3w:

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate (pdb code 3r3w). 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 the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate, PDB code: 3r3w:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3r3w

Go back to Chlorine Binding Sites List in 3r3w
Chlorine binding site 1 out of 6 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate


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 the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:10.7
occ:0.70
 CL1 A:R3W305 0.0 10.7 0.7
C2 A:R3W305 1.8 8.2 0.7
C1 A:R3W305 2.8 11.6 0.7
O1 A:R3W305 3.0 7.7 0.7
O A:HOH413 3.1 33.4 1.0
ND2 A:ASN110 3.3 11.1 1.0
NE2 A:HIS155 3.4 9.2 1.0
OH A:TYR219 3.4 8.6 1.0
CE1 A:HIS155 3.4 8.0 1.0
CL A:CL307 3.6 8.4 0.3
CD1 A:ILE253 3.6 16.0 1.0
CH2 A:TRP185 3.7 9.0 1.0
CZ3 A:TRP185 3.9 9.9 1.0
O2 A:R3W305 3.9 12.6 0.7
NE1 A:TRP156 4.0 12.1 1.0
CG A:ASN110 4.2 4.5 1.0
CZ2 A:TRP185 4.2 7.5 1.0
NE2 A:HIS280 4.5 6.2 1.0
OD1 A:ASN110 4.6 7.3 1.0
CZ A:TYR219 4.6 8.7 1.0
CE3 A:TRP185 4.7 8.6 1.0
CD2 A:HIS155 4.7 12.0 1.0
ND1 A:HIS155 4.7 11.6 1.0
CD1 A:TRP156 4.8 10.7 1.0
CE1 A:HIS280 4.8 6.1 1.0
O A:HOH415 4.9 16.1 1.0
CE1 A:TYR219 5.0 7.4 1.0
CE2 A:TRP156 5.0 9.6 1.0
CE2 A:TRP185 5.0 10.6 1.0

Chlorine binding site 2 out of 6 in 3r3w

Go back to Chlorine Binding Sites List in 3r3w
Chlorine binding site 2 out of 6 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate


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 the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:8.4
occ:0.30
 O2 A:R3W305 0.5 12.6 0.7
C1 A:R3W305 0.9 11.6 0.7
O1 A:R3W305 1.8 7.7 0.7
C2 A:R3W305 2.2 8.2 0.7
NE A:ARG114 3.0 6.4 1.0
NH1 A:ARG114 3.1 8.4 1.0
CG A:ASN110 3.5 4.5 1.0
CZ A:ARG114 3.5 7.8 1.0
OD1 A:ASN110 3.6 7.3 1.0
CA A:ASN110 3.6 4.0 1.0
CL1 A:R3W305 3.6 10.7 0.7
C A:ASN110 3.6 5.8 1.0
NH1 A:ARG111 3.6 10.5 1.0
N A:ARG111 3.8 5.1 1.0
ND2 A:ASN110 3.8 11.1 1.0
CD A:ARG111 3.8 6.0 1.0
CD A:ARG114 4.0 5.3 1.0
CB A:ASN110 4.1 4.9 1.0
O A:ASN110 4.2 6.3 1.0
CZ2 A:TRP156 4.2 14.2 1.0
CG2 A:ILE135 4.4 7.0 1.0
OH A:TYR219 4.4 8.6 1.0
O A:HOH415 4.4 16.1 1.0
CA A:ARG111 4.5 4.6 1.0
CZ A:ARG111 4.6 10.2 1.0
NE A:ARG111 4.6 8.2 1.0
O A:HOH413 4.7 33.4 1.0
CG A:ARG114 4.7 5.8 1.0
NH2 A:ARG114 4.8 8.0 1.0
CE2 A:TRP156 4.9 9.6 1.0
NE1 A:TRP156 4.9 12.1 1.0
CG A:ARG111 4.9 5.5 1.0
N A:ASN110 5.0 6.6 1.0

Chlorine binding site 3 out of 6 in 3r3w

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Chlorine binding site 3 out of 6 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate


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 the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:18.2
occ:1.00
 O A:HOH415 2.9 16.1 1.0
N A:LEU136 3.1 6.9 1.0
NH1 A:ARG114 3.1 8.4 1.0
O A:LEU136 3.7 8.4 1.0
CA A:ILE135 3.7 7.9 1.0
C A:ILE135 3.9 8.1 1.0
CB A:LEU136 3.9 9.5 1.0
CA A:LEU136 3.9 7.8 1.0
CZ A:ARG114 4.1 7.8 1.0
CG A:LEU136 4.1 13.1 1.0
C A:LEU136 4.2 7.0 1.0
CB A:ILE135 4.2 5.3 1.0
CA A:ALA254 4.3 23.7 1.0
NH2 A:ARG114 4.3 8.0 1.0
CB A:ALA254 4.3 22.6 1.0
CG2 A:ILE253 4.6 23.3 1.0
CB A:TYR141 4.6 11.4 1.0
O A:HOH413 4.7 33.4 1.0
CD1 A:LEU136 4.7 18.2 1.0
CZ2 A:TRP156 4.8 14.2 1.0
CD1 A:TYR141 4.8 21.3 1.0
CG2 A:ILE135 4.8 7.0 1.0
O A:ASP134 4.8 9.6 1.0
N A:ALA254 4.8 23.5 1.0
N A:ILE135 4.9 7.5 1.0
O A:ILE253 5.0 25.7 1.0

Chlorine binding site 4 out of 6 in 3r3w

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Chlorine binding site 4 out of 6 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate


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 the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:20.7
occ:1.00
 N A:GLN289 3.3 13.2 1.0
N A:ASP288 3.3 14.1 1.0
NE2 A:GLN289 3.4 14.5 1.0
C A:ALA286 3.4 11.1 1.0
CA A:ALA286 3.5 10.7 1.0
CB A:ASP288 3.6 16.6 1.0
N A:PRO287 3.6 11.8 1.0
CA A:ASP288 3.8 15.0 1.0
CD A:PRO287 3.8 14.0 1.0
O A:ALA286 3.8 10.1 1.0
CG A:GLN289 3.8 14.6 1.0
CB A:GLN289 4.0 12.9 1.0
CB A:ALA286 4.0 12.2 1.0
C A:ASP288 4.0 12.6 1.0
CD A:GLN289 4.1 13.1 1.0
C A:PRO287 4.2 11.5 1.0
CA A:GLN289 4.2 12.7 1.0
CG A:ASP288 4.3 21.7 1.0
OD1 A:ASP288 4.4 29.9 1.0
CA A:PRO287 4.5 12.6 1.0
CG A:PRO287 4.7 15.7 1.0
N A:ALA286 4.8 10.5 1.0
O A:HOH492 4.8 15.4 1.0

Chlorine binding site 5 out of 6 in 3r3w

Go back to Chlorine Binding Sites List in 3r3w
Chlorine binding site 5 out of 6 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate


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 the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:16.6
occ:0.50
 OH B:TYR141 1.2 27.4 0.5
CZ B:TYR141 1.4 25.5 0.5
CE2 B:TYR141 1.7 26.1 0.5
CE1 B:TYR141 2.7 24.9 0.5
NH1 B:ARG114 2.8 10.0 1.0
N B:LEU136 3.0 10.8 1.0
CD2 B:TYR141 3.0 25.0 0.5
CZ B:TYR141 3.3 16.9 0.5
CE1 B:TYR141 3.4 13.5 0.5
O B:LEU136 3.5 11.3 1.0
CE2 B:TYR141 3.5 13.6 0.5
CA B:ILE135 3.5 10.4 1.0
CD1 B:TYR141 3.6 15.4 0.5
CD1 B:TYR141 3.6 23.7 0.5
CD2 B:TYR141 3.7 15.5 0.5
CG B:TYR141 3.8 19.4 0.5
C B:ILE135 3.8 10.7 1.0
CG B:TYR141 3.8 15.3 0.5
CB B:ILE135 3.8 10.9 1.0
CA B:LEU136 3.9 11.0 1.0
OH B:TYR141 3.9 17.7 0.5
CZ B:ARG114 4.0 9.4 1.0
CB B:LEU136 4.1 12.1 1.0
C B:LEU136 4.1 10.4 1.0
CG2 B:ILE135 4.3 9.9 1.0
NH2 B:ARG114 4.3 8.1 1.0
O B:ASP134 4.5 12.4 1.0
CG B:LEU136 4.6 13.8 1.0
N B:ILE135 4.8 11.0 1.0
CB B:TYR141 4.8 15.0 0.5
CZ2 B:TRP156 4.9 11.9 1.0

Chlorine binding site 6 out of 6 in 3r3w

Go back to Chlorine Binding Sites List in 3r3w
Chlorine binding site 6 out of 6 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate


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 the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Chloroacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl306

b:13.1
occ:0.50
 NE B:ARG114 3.0 9.4 1.0
NH1 B:ARG114 3.4 10.0 1.0
CG B:ASN110 3.4 10.7 1.0
OD1 B:ASN110 3.5 8.7 1.0
C B:ASN110 3.6 8.7 1.0
CZ B:ARG114 3.6 9.4 1.0
ND2 B:ASN110 3.6 11.6 1.0
CA B:ASN110 3.6 8.5 1.0
NH1 B:ARG111 3.7 11.7 1.0
N B:ARG111 3.7 8.4 1.0
CD B:ARG111 3.8 8.5 1.0
CD B:ARG114 4.0 9.2 1.0
O B:ASN110 4.1 7.9 1.0
CB B:ASN110 4.1 9.6 1.0
CG2 B:ILE135 4.2 9.9 1.0
CZ2 B:TRP156 4.3 11.9 1.0
CA B:ARG111 4.4 8.6 1.0
CZ B:ARG111 4.6 9.4 1.0
NE B:ARG111 4.6 9.1 1.0
CG B:ARG114 4.6 7.4 1.0
NE1 B:TRP156 4.7 12.7 1.0
CG B:ARG111 4.8 7.8 1.0
OH B:TYR219 4.8 16.2 1.0
CE2 B:TRP156 4.9 12.2 1.0
NH2 B:ARG114 4.9 8.1 1.0
N B:ASN110 5.0 7.6 1.0

Reference:

P.W.Chan, A.F.Yakunin, E.A.Edwards, E.F.Pai. Mapping the Reaction Coordinates of Enzymatic Defluorination. J.Am.Chem.Soc. V. 133 7461 2011.
ISSN: ISSN 0002-7863
PubMed: 21510690
DOI: 10.1021/JA200277D
Page generated: Sun Jul 21 03:23:52 2024

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