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Fluorine in PDB 3b12: Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate

Enzymatic activity of Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate

All present enzymatic activity of Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate:
3.8.1.3;

Protein crystallography data

The structure of Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate, PDB code: 3b12 was solved by R.Omi, K.Hirotsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.72 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.497, 85.065, 136.354, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 18.5

Other elements in 3b12:

The structure of Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate (pdb code 3b12). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate, PDB code: 3b12:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3b12

Go back to Fluorine Binding Sites List in 3b12
Fluorine binding site 1 out of 3 in the Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:11.1
occ:1.00
 F A:FAH501 0.0 11.1 1.0
CH3 A:FAH501 1.4 10.3 1.0
C A:FAH501 2.4 9.3 1.0
O A:HOH544 2.5 8.1 0.5
OXT A:FAH501 2.6 9.4 1.0
NH2 A:ARG108 3.2 6.6 1.0
CE1 A:HIS271 3.2 4.1 1.0
CG2 A:ILE129 3.5 5.2 1.0
O A:FAH501 3.5 9.1 1.0
CB A:ALA104 3.6 4.3 1.0
CA A:ALA104 3.7 4.0 1.0
NE2 A:HIS271 3.7 4.6 1.0
O A:HOH544 3.8 7.8 0.5
O A:ASP128 3.8 4.6 1.0
O A:HOH328 4.0 5.4 1.0
NE A:ARG108 4.1 5.3 1.0
CZ A:ARG108 4.1 5.8 1.0
ND1 A:HIS271 4.2 4.5 1.0
CE2 A:TYR147 4.2 6.9 1.0
O A:HOH344 4.4 6.4 1.0
OH A:TYR147 4.4 8.0 1.0
C A:ALA104 4.5 4.1 1.0
CB A:ILE129 4.5 4.5 1.0
CA A:ILE129 4.7 4.6 1.0
CZ2 A:TRP150 4.8 5.1 1.0
N A:ALA104 4.8 3.8 1.0
CZ A:TYR147 4.8 6.6 1.0
C A:ASP128 4.8 4.3 1.0
CD2 A:HIS271 4.9 4.6 1.0
N A:ARG105 4.9 3.9 1.0

Fluorine binding site 2 out of 3 in 3b12

Go back to Fluorine Binding Sites List in 3b12
Fluorine binding site 2 out of 3 in the Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:15.0
occ:1.00
 F B:FAH501 0.0 15.0 1.0
CH3 B:FAH501 1.4 13.6 1.0
C B:FAH501 2.3 12.3 1.0
O B:HOH440 2.4 5.7 0.5
OXT B:FAH501 2.6 13.0 1.0
CE1 B:HIS271 3.2 3.8 1.0
O B:HOH440 3.3 12.8 0.5
NH2 B:ARG108 3.4 6.6 1.0
O B:FAH501 3.5 10.0 1.0
CB B:ALA104 3.5 4.6 1.0
CG2 B:ILE129 3.5 5.0 1.0
CA B:ALA104 3.6 4.0 1.0
NE2 B:HIS271 3.7 4.3 1.0
O B:ASP128 3.8 4.9 1.0
O B:HOH318 4.1 5.9 1.0
NE B:ARG108 4.1 5.7 1.0
CZ B:ARG108 4.2 6.0 1.0
ND1 B:HIS271 4.2 4.5 1.0
CE2 B:TYR147 4.3 6.6 1.0
O B:HOH347 4.3 6.8 1.0
OH B:TYR147 4.4 7.2 1.0
C B:ALA104 4.4 3.9 1.0
CB B:ILE129 4.5 4.7 1.0
CA B:ILE129 4.7 5.0 1.0
N B:ALA104 4.8 3.8 1.0
CZ B:TYR147 4.8 6.1 1.0
CZ2 B:TRP150 4.8 4.9 1.0
C B:ASP128 4.9 4.7 1.0
N B:ARG105 4.9 3.7 1.0
CD2 B:HIS271 4.9 4.0 1.0

Fluorine binding site 3 out of 3 in 3b12

Go back to Fluorine Binding Sites List in 3b12
Fluorine binding site 3 out of 3 in the Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Fluoroacetate Dehalogenase D104 Mutant From Burkholderia Sp. FA1 in Complex with Fluoroacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:11.4
occ:1.00
 F B:FAH502 0.0 11.4 1.0
CH3 B:FAH502 1.4 11.0 1.0
C B:FAH502 2.4 11.0 1.0
OXT B:FAH502 2.6 10.4 1.0
CG B:ASP223 3.0 6.0 1.0
O B:HOH358 3.2 7.7 1.0
CB B:ASP223 3.2 6.2 1.0
OD1 B:ASP223 3.3 6.4 1.0
O B:HOH359 3.3 8.0 1.0
CE1 B:HIS111 3.4 9.2 1.0
OD2 B:ASP223 3.5 6.3 1.0
O B:FAH502 3.5 11.5 1.0
CA B:ASP223 3.5 7.0 1.0
ND1 B:HIS111 3.9 8.9 1.0
O B:HOH549 3.9 13.4 1.0
O B:ASP223 4.0 7.5 1.0
CD1 B:LEU115 4.1 8.6 1.0
C B:ASP223 4.2 7.4 1.0
NH2 B:ARG112 4.4 6.9 1.0
NE2 B:HIS111 4.4 8.8 1.0
O B:HOH459 4.5 13.2 1.0
N B:ASP223 4.8 7.3 1.0
CB B:ASP226 4.9 9.9 1.0

Reference:

T.Nakayama, T.Kamachi, K.Jitsumori, R.Omi, K.Hirotsu, N.Esaki, T.Kurihara, K.Yoshizawa. Substrate Specificity of Fluoroacetate Dehalogenase: An Insight From Crystallographic Analysis, Fluorescence Spectroscopy, and Theoretical Computations Chemistry V. 18 8392 2012.
ISSN: ISSN 0947-6539
PubMed: 22674735
DOI: 10.1002/CHEM.201103369
Page generated: Mon Jul 14 15:15:52 2025

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