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Chlorine in PDB 3r40: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Apo

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

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

Protein crystallography data

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Apo, PDB code: 3r40 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) 41.41 / 1.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.930, 79.270, 85.080, 90.00, 103.22, 90.00
R / Rfree (%) 14.4 / 16.8

Other elements in 3r40:

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Apo 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/Apo (pdb code 3r40). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Apo, PDB code: 3r40:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 3r40

Go back to Chlorine Binding Sites List in 3r40
Chlorine binding site 1 out of 5 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Apo


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/Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:6.8
occ:0.80
 NE A:ARG114 3.1 6.0 1.0
O A:HOH457 3.2 14.7 1.0
O A:HOH448 3.2 12.0 1.0
NH1 A:ARG114 3.4 6.5 1.0
CG A:ASN110 3.4 5.8 1.0
NH1 A:ARG111 3.5 6.6 1.0
OD1 A:ASN110 3.5 5.7 1.0
ND2 A:ASN110 3.6 8.9 1.0
C A:ASN110 3.7 5.0 1.0
CA A:ASN110 3.7 5.0 1.0
CZ A:ARG114 3.7 6.0 1.0
CD A:ARG111 3.7 5.8 1.0
N A:ARG111 3.8 4.9 1.0
CB A:ASN110 4.1 5.6 1.0
CD A:ARG114 4.1 5.6 1.0
O A:ASN110 4.2 5.3 1.0
CZ2 A:TRP156 4.3 14.1 1.0
CZ A:ARG111 4.4 6.2 1.0
CG2 A:ILE135 4.4 6.9 1.0
NE A:ARG111 4.5 5.9 1.0
CA A:ARG111 4.5 5.1 1.0
OH A:TYR219 4.7 9.5 1.0
CG A:ARG114 4.7 5.5 1.0
CG A:ARG111 4.8 6.0 1.0
CE2 A:TRP156 4.9 10.8 1.0
O A:HOH360 4.9 12.7 1.0
NE1 A:TRP156 5.0 15.3 1.0
O A:HOH531 5.0 17.2 1.0

Chlorine binding site 2 out of 5 in 3r40

Go back to Chlorine Binding Sites List in 3r40
Chlorine binding site 2 out of 5 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Apo


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/Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:11.1
occ:0.70
 O A:HOH360 3.0 12.7 1.0
NH1 A:ARG114 3.1 6.5 1.0
N A:LEU136 3.2 7.6 1.0
O A:LEU136 3.8 7.3 1.0
CA A:ILE135 3.8 6.9 1.0
C A:ILE135 4.0 6.9 1.0
CA A:LEU136 4.0 7.8 1.0
CB A:LEU136 4.1 10.1 1.0
CG2 A:ILE253 4.2 15.4 0.6
CB A:ILE135 4.2 6.9 1.0
CZ A:ARG114 4.3 6.0 1.0
C A:LEU136 4.3 7.2 1.0
CG A:LEU136 4.4 12.6 1.0
NH2 A:ARG114 4.6 6.5 1.0
O A:HOH448 4.7 12.0 1.0
CZ2 A:TRP156 4.7 14.1 1.0
CG2 A:ILE135 4.7 6.9 1.0
O A:ASP134 4.7 7.9 1.0
O A:HOH531 4.9 17.2 1.0
CB A:TYR141 4.9 11.8 1.0
CH2 A:TRP156 5.0 11.9 1.0
N A:ILE135 5.0 6.8 1.0
CD1 A:TYR141 5.0 10.5 0.8

Chlorine binding site 3 out of 5 in 3r40

Go back to Chlorine Binding Sites List in 3r40
Chlorine binding site 3 out of 5 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Apo


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/Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:15.4
occ:1.00
 N A:ASP288 3.3 14.3 1.0
N A:GLN289 3.3 13.0 1.0
NE2 A:GLN289 3.3 14.3 1.0
C A:ALA286 3.4 11.2 1.0
CA A:ALA286 3.5 11.1 1.0
N A:PRO287 3.6 12.0 1.0
CG A:GLN289 3.7 13.4 1.0
CB A:ASP288 3.7 18.1 1.0
O A:ALA286 3.8 11.4 1.0
CA A:ASP288 3.8 16.9 1.0
CB A:ALA286 3.9 12.3 1.0
CD A:PRO287 3.9 13.3 1.0
CB A:GLN289 3.9 12.8 1.0
CD A:GLN289 4.0 14.1 1.0
C A:ASP288 4.1 14.3 1.0
C A:PRO287 4.2 12.8 1.0
CA A:GLN289 4.3 12.3 1.0
CA A:PRO287 4.5 12.7 1.0
CG A:ASP288 4.5 24.9 1.0
CG A:PRO287 4.5 16.6 1.0
N A:ALA286 4.8 11.1 1.0
OD1 A:ASP288 4.8 36.8 1.0
O A:HOH534 4.9 17.7 1.0
O A:GLU285 5.0 13.0 1.0

Chlorine binding site 4 out of 5 in 3r40

Go back to Chlorine Binding Sites List in 3r40
Chlorine binding site 4 out of 5 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Apo


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/Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:13.0
occ:0.60
 O A:HOH520 2.8 32.7 1.0
O A:HOH406 3.0 14.1 1.0
NZ A:LYS90 3.1 18.3 1.0
CG A:ARG86 3.7 7.5 1.0
CE A:LYS90 3.8 14.2 1.0
CD A:LYS90 3.8 11.3 1.0
CB A:ALA87 3.9 6.9 1.0
CA A:ALA87 3.9 5.8 1.0
N A:ALA87 4.0 5.6 1.0
CD A:ARG86 4.1 8.2 1.0
CG2 A:THR81 4.4 12.8 1.0
C A:ARG86 4.5 6.1 1.0
CB A:ARG86 4.5 7.0 1.0
OG1 A:THR84 4.7 6.4 1.0
O A:ARG86 4.7 6.4 1.0
O A:HOH480 4.9 36.8 1.0

Chlorine binding site 5 out of 5 in 3r40

Go back to Chlorine Binding Sites List in 3r40
Chlorine binding site 5 out of 5 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - ASP110ASN/Apo


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/Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:12.5
occ:0.80
 O B:HOH312 3.0 11.6 1.0
NE B:ARG114 3.0 9.4 1.0
CG B:ASN110 3.4 8.6 1.0
NH1 B:ARG114 3.5 11.9 1.0
OD1 B:ASN110 3.5 8.6 1.0
ND2 B:ASN110 3.5 11.8 1.0
C B:ASN110 3.5 8.1 1.0
NH1 B:ARG111 3.6 9.8 1.0
CA B:ASN110 3.6 8.6 1.0
CZ B:ARG114 3.7 9.1 1.0
N B:ARG111 3.7 7.2 1.0
CD B:ARG111 3.7 8.0 1.0
CD B:ARG114 4.0 9.3 1.0
CB B:ASN110 4.0 8.5 1.0
O B:ASN110 4.0 7.7 1.0
CZ2 B:TRP156 4.3 11.7 1.0
CA B:ARG111 4.3 6.8 1.0
CG2 B:ILE135 4.4 12.1 1.0
CZ B:ARG111 4.5 7.7 1.0
NE B:ARG111 4.5 7.9 1.0
CG B:ARG114 4.6 8.4 1.0
CG B:ARG111 4.7 8.2 1.0
NE1 B:TRP156 4.8 9.9 1.0
OH B:TYR219 4.8 11.1 1.0
CE2 B:TRP156 4.9 9.2 1.0
N B:ASN110 4.9 9.0 1.0
NH2 B:ARG114 5.0 10.1 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: Fri Jul 11 09:41:26 2025

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