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Fluorine in PDB 5k3c: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan

Enzymatic activity of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan

All present enzymatic activity of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan:
3.8.1.3;

Protein crystallography data

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan, PDB code: 5k3c was solved by P.Mehrabi, T.H.Kim, S.R.Prosser, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.14 / 1.54
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.890, 79.460, 85.240, 90.00, 103.02, 90.00
R / Rfree (%) 17.4 / 21.1

Other elements in 5k3c:

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan (pdb code 5k3c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan, PDB code: 5k3c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 5k3c

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Fluorine binding site 1 out of 18 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan


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 RPA1163 - Wt/5- Fluorotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F15

b:47.0
occ:1.00
 F A:FTR15 0.0 47.0 1.0
CZ3 A:FTR15 1.3 34.6 1.0
CE3 A:FTR15 2.3 24.6 1.0
CH2 A:FTR15 2.4 25.3 1.0
CD2 A:FTR15 3.6 26.2 1.0
CZ2 A:FTR15 3.6 24.2 1.0
CE2 A:FTR15 4.0 19.3 1.0
O A:HOH655 4.2 35.2 1.0
O A:HOH700 4.7 32.2 1.0
CG A:FTR15 4.8 19.6 1.0
CE1 A:PHE24 4.9 10.3 1.0

Fluorine binding site 2 out of 18 in 5k3c

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Fluorine binding site 2 out of 18 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan


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 RPA1163 - Wt/5- Fluorotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F47

b:23.7
occ:1.00
 F A:FTR47 0.0 23.7 1.0
CZ3 A:FTR47 1.3 10.9 1.0
CH2 A:FTR47 2.3 9.8 1.0
CE3 A:FTR47 2.3 7.8 1.0
CG A:PRO283 3.5 9.3 1.0
CD1 A:LEU294 3.5 13.5 1.0
CD2 A:FTR47 3.5 9.6 1.0
CZ2 A:FTR47 3.6 7.7 1.0
CD2 A:LEU133 3.7 8.1 1.0
CB A:PRO283 4.0 9.0 1.0
CE2 A:FTR47 4.0 8.0 1.0
CG2 A:VAL50 4.0 15.4 1.0
CG2 A:THR290 4.2 13.7 1.0
CD2 A:LEU36 4.7 10.8 1.0
CG A:FTR47 4.8 7.4 1.0
CG A:LEU294 4.8 13.8 1.0
CD A:PRO283 4.9 12.0 1.0
CB A:ALA107 4.9 6.9 1.0
CG A:LEU133 5.0 7.8 1.0
CD1 A:LEU133 5.0 13.0 1.0

Fluorine binding site 3 out of 18 in 5k3c

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Fluorine binding site 3 out of 18 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan


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 RPA1163 - Wt/5- Fluorotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F70

b:33.0
occ:1.00
 F A:FTR70 0.0 33.0 1.0
CZ3 A:FTR70 1.5 17.6 1.0
CH2 A:FTR70 2.5 18.7 1.0
CE3 A:FTR70 2.6 17.1 1.0
CZ A:PHE24 3.0 14.0 1.0
CE2 A:PHE24 3.1 12.5 1.0
O A:HOH525 3.2 12.4 1.0
O A:HOH654 3.8 31.3 1.0
CD2 A:FTR70 3.8 16.0 1.0
CZ2 A:FTR70 3.8 16.9 1.0
CE1 A:PHE24 4.0 10.3 1.0
CE1 A:HIS44 4.1 7.6 1.0
CD2 A:PHE24 4.2 11.1 1.0
CE2 A:FTR70 4.2 14.8 1.0
NE2 A:HIS44 4.3 8.9 1.0
CD A:ARG26 4.5 9.8 1.0
CD1 A:PHE24 4.9 9.9 1.0
NH2 A:ARG26 4.9 11.9 1.0
CG A:PHE24 4.9 9.8 1.0
O A:HOH590 5.0 11.4 1.0
OG A:SER13 5.0 26.4 1.0

Fluorine binding site 4 out of 18 in 5k3c

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Fluorine binding site 4 out of 18 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F142

b:19.2
occ:1.00
 F A:FTR142 0.0 19.2 1.0
CZ3 A:FTR142 1.3 10.1 1.0
CE3 A:FTR142 2.3 11.7 1.0
CH2 A:FTR142 2.3 9.0 1.0
OG A:SER157 3.0 15.7 1.0
CB B:ALA150 3.3 9.7 1.0
CD2 A:FTR142 3.5 9.2 1.0
CZ2 A:FTR142 3.6 9.1 1.0
CE A:MET145 3.8 8.5 1.0
O A:HOH615 3.9 14.8 1.0
O B:ARG147 4.0 11.1 1.0
CA B:ARG147 4.0 10.1 1.0
CE2 A:FTR142 4.0 9.4 1.0
CG A:MET145 4.1 18.9 1.0
CG B:LEU151 4.4 9.7 1.0
CB A:SER157 4.4 10.1 1.0
CG B:ARG147 4.4 10.6 1.0
C B:ARG147 4.5 11.8 1.0
CB B:ARG147 4.5 10.4 1.0
CE1 A:TYR141 4.5 22.3 1.0
SD A:MET145 4.5 20.2 1.0
CA B:ALA150 4.5 9.9 1.0
N B:LEU151 4.6 10.6 1.0
C B:ALA150 4.7 11.7 1.0
CD2 B:LEU151 4.7 9.6 1.0
CG A:FTR142 4.8 7.2 1.0
CB A:MET145 4.8 13.6 1.0
O B:ASN146 4.9 10.3 1.0
CA A:SER157 4.9 8.6 1.0
N A:SER157 4.9 7.3 1.0
N B:ARG147 5.0 9.0 1.0
CD1 B:LEU151 5.0 11.3 1.0
OH A:TYR141 5.0 23.4 1.0

Fluorine binding site 5 out of 18 in 5k3c

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Fluorine binding site 5 out of 18 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F156

b:25.1
occ:1.00
 F A:FTR156 0.0 25.1 1.0
CZ3 A:FTR156 1.3 11.7 1.0
CH2 A:FTR156 2.3 9.9 1.0
CE3 A:FTR156 2.4 12.8 1.0
CG2 A:THR138 3.1 9.3 1.0
NE1 A:FTR142 3.1 9.7 1.0
O A:HOH553 3.1 26.1 1.0
CD1 A:FTR142 3.4 9.4 1.0
O A:THR138 3.4 9.4 1.0
CA A:THR138 3.5 8.6 1.0
CD1 A:TYR141 3.5 15.2 1.0
CZ2 A:FTR156 3.5 10.9 1.0
CD2 A:FTR156 3.6 13.7 1.0
CB A:THR138 3.6 8.3 1.0
OG1 A:THR138 3.7 7.8 1.0
CB A:TYR141 3.7 12.5 1.0
CG A:TYR141 3.8 17.4 1.0
C A:THR138 3.9 11.0 1.0
CE2 A:FTR142 3.9 9.4 1.0
O A:HOH712 3.9 10.8 1.0
CE2 A:FTR156 4.0 10.5 1.0
O A:GLY222 4.0 10.6 1.0
CG A:FTR142 4.1 7.2 1.0
CE1 A:TYR141 4.4 22.3 1.0
CD2 A:FTR142 4.5 9.2 1.0
CZ2 A:FTR142 4.6 9.1 1.0
N A:FTR142 4.7 8.8 1.0
NH2 A:ARG114 4.7 8.9 1.0
N A:THR138 4.8 6.5 1.0
CD2 A:TYR141 4.8 26.7 1.0
CG A:FTR156 4.8 9.0 1.0
CA A:TYR141 4.9 11.6 1.0
C A:GLY222 4.9 8.7 1.0
CZ A:ARG114 5.0 6.2 1.0

Fluorine binding site 6 out of 18 in 5k3c

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Fluorine binding site 6 out of 18 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F185

b:28.8
occ:1.00
 F A:FTR185 0.0 28.8 1.0
CZ3 A:FTR185 1.3 28.0 1.0
CE3 A:FTR185 2.3 14.2 1.0
CH2 A:FTR185 2.3 20.6 1.0
O A:HOH518 2.6 18.4 1.0
O A:PHE40 3.2 10.8 1.0
CD A:PRO41 3.3 7.8 1.0
CD2 A:FTR185 3.5 16.9 1.0
CZ2 A:FTR185 3.6 18.6 1.0
CD1 A:PHE40 3.6 7.3 1.0
CE1 A:PHE40 3.9 8.2 1.0
C A:PHE40 3.9 10.7 1.0
CE2 A:FTR185 4.0 19.2 1.0
N A:PRO41 4.1 5.5 1.0
CB A:LYS181 4.3 11.9 1.0
CG A:PRO41 4.3 8.0 1.0
CZ A:PHE281 4.4 15.6 1.0
O A:HOH763 4.4 23.3 1.0
O A:LYS181 4.6 14.8 1.0
CG A:FTR185 4.7 19.2 1.0
O A:HOH558 4.7 11.0 1.0
CG A:PHE40 4.7 6.4 1.0
CD A:LYS181 4.8 17.9 1.0
C A:LYS181 4.8 12.9 1.0
CG A:LYS181 4.8 14.1 1.0
CE1 A:PHE281 4.9 12.6 1.0
O A:HOH515 4.9 24.4 1.0

Fluorine binding site 7 out of 18 in 5k3c

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Fluorine binding site 7 out of 18 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F248

b:29.6
occ:1.00
 F A:FTR248 0.0 29.6 1.0
CZ3 A:FTR248 1.3 19.4 1.0
CH2 A:FTR248 2.3 20.6 1.0
CE3 A:FTR248 2.4 14.4 1.0
O A:ALA246 3.0 13.8 1.0
CA A:GLY273 3.1 19.1 1.0
N A:ALA274 3.2 12.0 1.0
C A:GLY273 3.4 15.2 1.0
CB A:ALA246 3.6 12.6 1.0
CD2 A:FTR248 3.6 12.1 1.0
CZ2 A:FTR248 3.6 16.7 1.0
C A:ALA246 3.7 13.7 1.0
CB A:LEU261 3.9 23.5 1.0
CE2 A:FTR248 4.0 14.4 1.0
N A:LEU261 4.1 16.9 1.0
CD1 A:LEU261 4.1 24.4 1.0
CA A:LEU261 4.1 16.8 1.0
CA A:ALA274 4.2 14.3 1.0
O A:ALA274 4.2 11.7 1.0
CA A:ALA246 4.2 11.8 1.0
O A:GLY273 4.3 17.3 1.0
C A:ALA274 4.3 11.9 1.0
N A:GLY273 4.3 17.1 1.0
CG A:LEU261 4.5 25.1 1.0
N A:LEU247 4.6 9.8 1.0
C A:PRO260 4.7 21.6 1.0
CD2 A:LEU261 4.7 27.0 1.0
CB A:PRO260 4.7 21.6 1.0
O A:GLN272 4.8 16.2 1.0
N A:ALA246 4.8 11.2 1.0
CG A:FTR248 4.9 13.5 1.0
C A:GLN272 4.9 19.2 1.0
CA A:LEU247 5.0 11.9 1.0

Fluorine binding site 8 out of 18 in 5k3c

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Fluorine binding site 8 out of 18 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F264

b:19.2
occ:1.00
 F A:FTR264 0.0 19.2 1.0
CZ3 A:FTR264 1.3 11.2 1.0
CH2 A:FTR264 2.4 9.3 1.0
CE3 A:FTR264 2.4 12.5 1.0
CE A:MET244 3.4 18.8 1.0
CD1 A:ILE240 3.5 11.8 1.0
CD2 A:FTR264 3.6 9.1 1.0
CZ2 A:FTR264 3.6 11.5 1.0
CB A:FTR267 3.6 11.4 1.0
CB A:TYR117 3.6 6.8 1.0
CG A:TYR117 3.9 6.3 1.0
CE2 A:FTR264 4.1 12.2 1.0
CD1 A:TYR117 4.1 6.7 1.0
CG A:PRO137 4.3 12.2 1.0
SD A:MET244 4.3 22.0 1.0
CG A:FTR267 4.4 10.8 1.0
O A:FTR267 4.5 14.0 1.0
CD2 A:TYR117 4.6 7.0 1.0
CE3 A:FTR267 4.7 13.4 1.0
CD2 A:FTR267 4.8 8.3 1.0
CG1 A:ILE240 4.8 13.1 1.0
C A:FTR267 4.8 11.2 1.0
CG A:FTR264 4.8 9.9 1.0
CA A:FTR267 4.9 14.7 1.0
CE1 A:TYR117 5.0 9.6 1.0
CA A:TYR117 5.0 7.2 1.0

Fluorine binding site 9 out of 18 in 5k3c

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Fluorine binding site 9 out of 18 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F267

b:22.8
occ:1.00
 F A:FTR267 0.0 22.8 1.0
CZ3 A:FTR267 1.3 10.4 1.0
CH2 A:FTR267 2.3 14.0 1.0
CE3 A:FTR267 2.4 13.4 1.0
CD1 A:LEU121 3.4 11.4 1.0
CZ2 A:FTR267 3.5 13.5 1.0
CD2 A:FTR267 3.6 8.3 1.0
CB A:ASP233 3.6 9.8 1.0
O A:ASP230 3.7 8.6 1.0
CA A:ASP230 3.8 7.8 1.0
O A:HOH526 3.9 23.8 1.0
CG A:ASP230 3.9 8.8 1.0
CB A:ASP230 4.0 7.6 1.0
CE2 A:FTR267 4.0 14.3 1.0
OD1 A:ASP230 4.0 7.2 1.0
NH2 A:ARG118 4.1 8.3 1.0
OD2 A:ASP233 4.1 9.8 1.0
C A:ASP230 4.2 7.0 1.0
CG A:ASP233 4.3 12.6 1.0
OD2 A:ASP230 4.3 9.9 1.0
CE1 A:TYR117 4.4 9.6 1.0
N A:VAL234 4.6 9.4 1.0
CG A:LEU121 4.7 10.5 1.0
CD2 A:LEU121 4.7 12.2 1.0
CA A:ASP233 4.8 9.0 1.0
CG A:FTR267 4.8 10.8 1.0
CD1 A:TYR117 4.9 6.7 1.0
C A:ASP233 4.9 10.8 1.0

Fluorine binding site 10 out of 18 in 5k3c

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Fluorine binding site 10 out of 18 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/5- Fluorotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F15

b:60.7
occ:1.00
 F B:FTR15 0.0 60.7 1.0
CZ3 B:FTR15 1.4 40.3 1.0
CH2 B:FTR15 2.4 46.1 1.0
CE3 B:FTR15 2.4 32.2 1.0
CD2 B:FTR15 3.6 35.0 1.0
CZ2 B:FTR15 3.7 42.6 1.0
CE2 B:FTR15 4.1 36.3 1.0
CG B:FTR15 4.8 29.4 1.0
CE1 B:PHE24 4.9 25.2 1.0
O B:HOH671 5.0 34.0 1.0

Reference:

T.H.Kim, P.Mehrabi, Z.Ren, A.Sljoka, C.Ing, A.Bezginov, L.Ye, R.Pomes, R.S.Prosser, E.F.Pai. The Role of Dimer Asymmetry and Protomer Dynamics in Enzyme Catalysis. Science V. 355 2017.
ISSN: ESSN 1095-9203
PubMed: 28104837
DOI: 10.1126/SCIENCE.AAG2355
Page generated: Thu Aug 1 10:50:03 2024

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