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Fluorine in PDB 4nir: Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol

Enzymatic activity of Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol

All present enzymatic activity of Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol:
2.5.1.15;

Protein crystallography data

The structure of Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol, PDB code: 4nir was solved by D.I.Hammoudeh, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.19 / 1.77
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 98.338, 98.338, 263.415, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 22

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol (pdb code 4nir). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol, PDB code: 4nir:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 4nir

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Fluorine binding site 1 out of 9 in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol


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 B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F307

b:74.8
occ:1.00
 F01 A:6DH307 0.0 74.8 1.0
C01 A:6DH307 1.3 68.2 1.0
F A:6DH307 2.2 81.6 1.0
F02 A:6DH307 2.2 71.9 1.0
C07 A:6DH307 2.3 44.8 1.0
C08 A:6DH307 2.9 36.7 1.0
C06 A:6DH307 3.5 34.3 1.0
NE1 A:TRP123 4.1 19.1 1.0
C10 A:6DH307 4.2 38.9 1.0
CE2 A:TRP123 4.4 19.3 1.0
OH A:TYR103 4.5 31.2 1.0
CZ A:TYR103 4.6 27.8 1.0
CZ2 A:TRP123 4.6 18.5 1.0
C09 A:6DH307 4.6 40.3 1.0
CE1 A:TYR103 4.7 28.4 1.0
CD1 A:TRP123 4.7 19.0 1.0
C A:6DH307 4.9 43.2 1.0

Fluorine binding site 2 out of 9 in 4nir

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Fluorine binding site 2 out of 9 in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol


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 B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F307

b:71.9
occ:1.00
 F02 A:6DH307 0.0 71.9 1.0
C01 A:6DH307 1.3 68.2 1.0
F01 A:6DH307 2.2 74.8 1.0
F A:6DH307 2.2 81.6 1.0
C07 A:6DH307 2.3 44.8 1.0
C06 A:6DH307 2.6 34.3 1.0
C08 A:6DH307 3.6 36.7 1.0
C09 A:6DH307 4.0 40.3 1.0
O A:HOH518 4.3 37.4 1.0
C10 A:6DH307 4.7 38.9 1.0
C A:6DH307 4.8 43.2 1.0
CE1 A:TYR103 4.9 28.4 1.0
OH A:TYR103 5.0 31.2 1.0

Fluorine binding site 3 out of 9 in 4nir

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Fluorine binding site 3 out of 9 in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol


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 B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F307

b:81.6
occ:1.00
 F A:6DH307 0.0 81.6 1.0
C01 A:6DH307 1.3 68.2 1.0
F01 A:6DH307 2.2 74.8 1.0
F02 A:6DH307 2.2 71.9 1.0
C07 A:6DH307 2.3 44.8 1.0
C08 A:6DH307 3.0 36.7 1.0
C06 A:6DH307 3.3 34.3 1.0
C10 A:6DH307 4.3 38.9 1.0
C09 A:6DH307 4.5 40.3 1.0
C A:6DH307 4.9 43.2 1.0

Fluorine binding site 4 out of 9 in 4nir

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Fluorine binding site 4 out of 9 in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol


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 B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F308

b:32.5
occ:0.44
 F01 A:6DH308 0.0 32.5 0.4
C01 A:6DH308 1.3 33.5 0.4
F A:6DH308 2.2 33.4 0.4
F02 A:6DH308 2.2 33.9 0.4
C07 A:6DH308 2.3 34.6 0.4
C06 A:6DH308 2.9 34.0 0.4
C08 A:6DH308 3.4 35.0 0.4
O A:LEU235 3.6 21.0 1.0
CA A:GLU236 3.6 23.6 1.0
C A:LEU235 3.7 20.3 1.0
N A:GLU236 3.7 23.7 1.0
CG A:GLU236 4.1 24.6 1.0
CB A:LEU235 4.2 28.7 1.0
C09 A:6DH308 4.2 34.9 0.4
SD A:MET264 4.3 36.0 1.0
CB A:GLU236 4.4 20.4 1.0
C10 A:6DH308 4.6 35.4 0.4
CA A:LEU235 4.6 25.6 1.0
C A:GLU236 4.7 25.5 1.0
CD A:GLU236 4.8 30.9 1.0
O A:GLU236 4.8 24.6 1.0
C A:6DH308 4.9 37.1 0.4
CE A:MET261 4.9 43.3 1.0

Fluorine binding site 5 out of 9 in 4nir

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Fluorine binding site 5 out of 9 in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol


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 B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F308

b:33.9
occ:0.44
 F02 A:6DH308 0.0 33.9 0.4
C01 A:6DH308 1.3 33.5 0.4
F A:6DH308 2.2 33.4 0.4
F01 A:6DH308 2.2 32.5 0.4
C07 A:6DH308 2.3 34.6 0.4
C08 A:6DH308 2.7 35.0 0.4
C06 A:6DH308 3.6 34.0 0.4
C10 A:6DH308 4.1 35.4 0.4
SD A:MET264 4.1 36.0 1.0
CG A:MET264 4.4 35.2 1.0
CE A:MET264 4.7 50.9 1.0
C09 A:6DH308 4.8 34.9 0.4
C A:6DH308 4.9 37.1 0.4

Fluorine binding site 6 out of 9 in 4nir

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Fluorine binding site 6 out of 9 in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol


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 B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F308

b:33.4
occ:0.44
 F A:6DH308 0.0 33.4 0.4
C01 A:6DH308 1.3 33.5 0.4
F02 A:6DH308 2.2 33.9 0.4
F01 A:6DH308 2.2 32.5 0.4
C07 A:6DH308 2.3 34.6 0.4
C06 A:6DH308 2.9 34.0 0.4
C08 A:6DH308 3.4 35.0 0.4
CG A:GLU236 3.9 24.6 1.0
C09 A:6DH308 4.2 34.9 0.4
C10 A:6DH308 4.5 35.4 0.4
CA A:GLU236 4.6 23.6 1.0
CB A:GLU236 4.7 20.4 1.0
C A:6DH308 4.9 37.1 0.4
CD A:GLU236 4.9 30.9 1.0

Fluorine binding site 7 out of 9 in 4nir

Go back to Fluorine Binding Sites List in 4nir
Fluorine binding site 7 out of 9 in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol


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 B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F306

b:42.1
occ:0.45
 F01 B:6DH306 0.0 42.1 0.5
C01 B:6DH306 1.3 43.7 0.5
F B:6DH306 2.2 40.2 0.5
F02 B:6DH306 2.2 43.4 0.5
C07 B:6DH306 2.3 43.5 0.5
C08 B:6DH306 2.9 44.1 0.5
C06 B:6DH306 3.4 43.5 0.5
C10 B:6DH306 4.2 47.5 0.5
SD B:MET264 4.6 32.9 1.0
C09 B:6DH306 4.6 46.3 0.5
CE B:MET264 4.9 47.2 1.0
C B:6DH306 4.9 49.1 0.5
CG B:MET264 4.9 35.3 1.0

Fluorine binding site 8 out of 9 in 4nir

Go back to Fluorine Binding Sites List in 4nir
Fluorine binding site 8 out of 9 in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol


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 B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F306

b:43.4
occ:0.45
 F02 B:6DH306 0.0 43.4 0.5
C01 B:6DH306 1.3 43.7 0.5
F B:6DH306 2.2 40.2 0.5
F01 B:6DH306 2.2 42.1 0.5
C07 B:6DH306 2.3 43.5 0.5
C06 B:6DH306 2.7 43.5 0.5
CG B:GLU236 3.5 23.6 1.0
CA B:GLU236 3.6 23.5 1.0
C08 B:6DH306 3.6 44.1 0.5
N B:GLU236 3.9 22.1 1.0
CB B:GLU236 4.0 20.6 1.0
C09 B:6DH306 4.1 46.3 0.5
C B:LEU235 4.3 25.0 1.0
O B:LEU235 4.3 22.1 1.0
CD B:GLU236 4.3 30.6 1.0
OE2 B:GLU236 4.7 30.0 1.0
C10 B:6DH306 4.7 47.5 0.5
C B:GLU236 4.7 24.2 1.0
SD B:MET264 4.8 32.9 1.0
CB B:LEU235 4.8 26.2 1.0
O B:GLU236 4.9 21.6 1.0
C B:6DH306 4.9 49.1 0.5

Fluorine binding site 9 out of 9 in 4nir

Go back to Fluorine Binding Sites List in 4nir
Fluorine binding site 9 out of 9 in the Crystal Structure of B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol


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 B. Anthracis Dhps with Compound 6: 3-[6- (Trifluoromethyl)-1H-Benzimidazol-2-Yl]Propan-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F306

b:40.2
occ:0.45
 F B:6DH306 0.0 40.2 0.5
C01 B:6DH306 1.3 43.7 0.5
F01 B:6DH306 2.2 42.1 0.5
F02 B:6DH306 2.2 43.4 0.5
C07 B:6DH306 2.3 43.5 0.5
C08 B:6DH306 2.9 44.1 0.5
C06 B:6DH306 3.4 43.5 0.5
CE B:MET261 3.6 29.9 1.0
CB B:GLU260 4.0 21.6 1.0
CD2 B:LEU235 4.0 44.6 1.0
SD B:MET264 4.0 32.9 1.0
C10 B:6DH306 4.2 47.5 0.5
CG B:MET264 4.4 35.3 1.0
CG B:GLU260 4.5 24.1 1.0
O B:LEU235 4.5 22.1 1.0
CD1 B:LEU235 4.6 44.2 1.0
C09 B:6DH306 4.6 46.3 0.5
CG B:LEU235 4.7 39.4 1.0
C B:LEU235 4.8 25.0 1.0
CB B:LEU235 4.8 26.2 1.0
C B:6DH306 4.9 49.1 0.5
O B:GLU260 4.9 19.2 1.0
CA B:GLU260 5.0 21.5 1.0

Reference:

D.I.Hammoudeh, M.Date, M.K.Yun, W.Zhang, V.A.Boyd, A.Viacava Follis, E.Griffith, R.E.Lee, D.Bashford, S.W.White. Identification and Characterization of An Allosteric Inhibitory Site on Dihydropteroate Synthase. Acs Chem.Biol. V. 9 1294 2014.
ISSN: ISSN 1554-8929
PubMed: 24650357
DOI: 10.1021/CB500038G
Page generated: Thu Aug 1 04:19:34 2024

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