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Chlorine in PDB 3r41: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/Apo

Enzymatic activity of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/Apo

All present enzymatic activity of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/Apo:
3.8.1.3;

Protein crystallography data

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/Apo, PDB code: 3r41 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) 41.39 / 1.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.690, 78.100, 85.100, 90.00, 103.41, 90.00
R / Rfree (%) 14.2 / 16.9

Other elements in 3r41:

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/Apo also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/Apo (pdb code 3r41). 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 - HIS280ASN/Apo, PDB code: 3r41:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 3r41

Go back to Chlorine Binding Sites List in 3r41
Chlorine binding site 1 out of 5 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/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 - HIS280ASN/Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:13.8
occ:1.00
 O A:HOH558 3.1 20.7 1.0
NH1 A:ARG114 3.2 7.5 1.0
N A:LEU136 3.3 7.4 1.0
O A:LEU136 3.9 7.2 1.0
CB A:LEU136 3.9 9.7 1.0
CA A:ILE135 4.0 6.6 1.0
CA A:LEU136 4.1 7.7 1.0
CA A:ALA254 4.1 14.8 1.0
C A:ILE135 4.1 6.8 1.0
CG A:LEU136 4.1 10.5 1.0
CG2 A:ILE253 4.2 18.6 1.0
CZ A:ARG114 4.3 5.8 1.0
C A:LEU136 4.4 7.0 1.0
CB A:ALA254 4.4 14.5 1.0
N A:ALA254 4.5 15.9 1.0
CB A:ILE135 4.6 7.1 1.0
NH2 A:ARG114 4.6 7.0 1.0
CB A:TYR141 4.7 8.5 1.0
CZ2 A:TRP156 4.7 9.1 1.0
CD1 A:TYR141 4.8 11.0 1.0
CD1 A:LEU136 4.8 14.6 1.0
C A:ILE253 4.8 16.0 1.0
O A:HOH551 4.8 17.8 1.0
O A:ASP134 4.8 10.5 1.0
O A:ILE253 4.9 16.4 1.0
CB A:ILE253 5.0 17.7 1.0

Chlorine binding site 2 out of 5 in 3r41

Go back to Chlorine Binding Sites List in 3r41
Chlorine binding site 2 out of 5 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/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 - HIS280ASN/Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:14.2
occ:1.00
 N A:GLN289 3.3 12.2 1.0
N A:ASP288 3.3 12.8 1.0
NE2 A:GLN289 3.3 13.2 1.0
C A:ALA286 3.4 10.4 1.0
CA A:ALA286 3.5 11.4 1.0
N A:PRO287 3.7 11.9 1.0
CG A:GLN289 3.7 12.0 1.0
CB A:ASP288 3.8 17.1 1.0
O A:ALA286 3.8 11.3 1.0
CA A:ASP288 3.9 13.4 1.0
CB A:ALA286 3.9 11.4 1.0
CD A:PRO287 4.0 13.4 1.0
CB A:GLN289 4.0 11.5 1.0
CD A:GLN289 4.0 12.6 1.0
C A:ASP288 4.1 12.0 1.0
C A:PRO287 4.2 12.1 1.0
CA A:GLN289 4.2 11.2 1.0
CG A:ASP288 4.5 24.4 1.0
CA A:PRO287 4.5 12.8 1.0
CG A:PRO287 4.6 16.4 1.0
OD1 A:ASP288 4.7 33.8 1.0
N A:ALA286 4.8 10.6 1.0
O A:HOH463 4.9 16.7 1.0
O A:GLU285 4.9 12.6 1.0

Chlorine binding site 3 out of 5 in 3r41

Go back to Chlorine Binding Sites List in 3r41
Chlorine binding site 3 out of 5 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/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 - HIS280ASN/Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:15.1
occ:0.80
 O A:HOH464 3.1 14.4 1.0
NZ A:LYS90 3.2 19.4 1.0
CG A:ARG86 3.7 7.2 1.0
CB A:ALA87 3.9 7.0 1.0
CA A:ALA87 3.9 5.6 1.0
CE A:LYS90 3.9 14.4 1.0
CD A:LYS90 4.0 11.6 1.0
N A:ALA87 4.0 6.1 1.0
CD A:ARG86 4.1 8.3 1.0
CG2 A:THR81 4.3 12.8 1.0
C A:ARG86 4.4 5.9 1.0
CB A:ARG86 4.5 6.8 1.0
OG1 A:THR84 4.7 7.3 1.0
O A:ARG86 4.8 6.2 1.0
O A:HOH454 4.9 19.2 1.0

Chlorine binding site 4 out of 5 in 3r41

Go back to Chlorine Binding Sites List in 3r41
Chlorine binding site 4 out of 5 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/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 - HIS280ASN/Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl306

b:15.8
occ:0.90
 OD2 B:ASP110 2.3 13.0 0.8
NE B:ARG114 3.0 6.9 1.0
CG B:ASP110 3.2 8.9 0.8
NH1 B:ARG111 3.3 7.5 1.0
NH1 B:ARG114 3.4 9.0 1.0
O B:HOH308 3.5 11.0 1.0
O B:HOH402 3.5 20.8 1.0
O B:HOH312 3.5 18.7 1.0
CD B:ARG111 3.6 7.4 1.0
OD2 B:ASP110 3.6 10.8 0.2
OD1 B:ASP110 3.6 9.2 0.8
CZ B:ARG114 3.6 6.8 1.0
OD1 B:ASP110 3.7 8.4 0.2
CG B:ASP110 3.7 9.4 0.2
O B:HOH403 3.8 21.0 1.0
C B:ASP110 3.9 7.9 0.2
CD B:ARG114 4.0 6.7 1.0
OH B:TYR219 4.0 12.1 0.5
CZ2 B:TRP156 4.1 9.2 1.0
N B:ARG111 4.1 6.2 1.0
C B:ASP110 4.1 6.3 0.8
CA B:ASP110 4.2 7.5 0.2
CA B:ASP110 4.2 6.8 0.8
O B:ASP110 4.3 9.6 0.2
CB B:ASP110 4.3 7.6 0.8
CZ B:ARG111 4.3 7.5 1.0
NE B:ARG111 4.4 7.1 1.0
CB B:ASP110 4.6 8.2 0.2
OH B:TYR219 4.6 11.0 0.5
NE1 B:TRP156 4.6 8.9 1.0
CA B:ARG111 4.6 5.8 1.0
O B:ASP110 4.6 5.2 0.8
CG2 B:ILE135 4.6 7.9 1.0
CE2 B:TRP156 4.7 8.2 1.0
CG B:ARG111 4.7 7.5 1.0
CG B:ARG114 4.8 6.1 1.0
NH2 B:ARG114 4.9 7.5 1.0
CZ B:TYR219 5.0 8.0 0.5

Chlorine binding site 5 out of 5 in 3r41

Go back to Chlorine Binding Sites List in 3r41
Chlorine binding site 5 out of 5 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - HIS280ASN/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 - HIS280ASN/Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl307

b:18.4
occ:0.30
 CZ B:TYR141 1.1 11.1 0.7
OH B:TYR141 1.3 14.3 0.7
CE2 B:TYR141 1.8 11.4 0.7
CE1 B:TYR141 2.1 11.2 0.7
NH1 B:ARG114 2.8 9.0 1.0
CD2 B:TYR141 2.9 11.9 0.7
O B:HOH402 3.0 20.8 1.0
N B:LEU136 3.1 8.0 1.0
CD1 B:TYR141 3.1 9.7 0.7
CE2 B:TYR141 3.2 14.3 0.3
CZ B:TYR141 3.2 17.9 0.3
CD2 B:TYR141 3.3 12.1 0.3
CE1 B:TYR141 3.3 17.7 0.3
CG B:TYR141 3.4 8.2 0.7
CG B:TYR141 3.5 12.2 0.3
CD1 B:TYR141 3.5 13.1 0.3
O B:LEU136 3.6 8.4 1.0
CA B:ILE135 3.8 7.4 1.0
OH B:TYR141 3.9 22.1 0.3
C B:ILE135 3.9 7.5 1.0
CZ B:ARG114 3.9 6.8 1.0
CA B:LEU136 4.0 8.2 1.0
CB B:LEU136 4.1 9.9 1.0
CB B:ILE135 4.1 7.0 1.0
C B:LEU136 4.2 8.3 1.0
NH2 B:ARG114 4.3 7.5 1.0
CG B:LEU136 4.3 11.9 1.0
CB B:TYR141 4.4 10.7 0.3
O B:ASP134 4.5 16.6 0.4
CG2 B:ILE253 4.5 26.2 1.0
CA B:ALA254 4.6 15.1 1.0
OH B:TYR149 4.6 18.8 0.7
CG2 B:ILE135 4.6 7.9 1.0
O B:ASP134 4.7 6.7 0.6
CG1 B:ILE253 4.7 19.1 1.0
CB B:ALA254 4.7 15.5 1.0
CZ2 B:TRP156 4.8 9.2 1.0
CB B:TYR141 4.9 8.2 0.7
N B:ALA254 4.9 16.0 1.0
N B:ILE135 5.0 7.9 1.0
CD1 B:LEU136 5.0 15.3 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 03:26:02 2024

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