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Fluorine in PDB 4bnk: Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol

Enzymatic activity of Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol

All present enzymatic activity of Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol:
1.3.1.10;

Protein crystallography data

The structure of Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol, PDB code: 4bnk was solved by J.Schiebel, A.Chang, G.R.Bommineni, P.J.Tonge, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.11 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 90.610, 95.010, 94.950, 98.12, 97.00, 112.79
R / Rfree (%) 17.998 / 25.006

Other elements in 4bnk:

The structure of Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol (pdb code 4bnk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol, PDB code: 4bnk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4bnk

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Fluorine binding site 1 out of 8 in the Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol


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 S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1258

b:38.0
occ:1.00
F A:FPL1258 0.0 38.0 1.0
C2 A:FPL1258 1.3 37.2 1.0
C1 A:FPL1258 2.3 36.3 1.0
C3 A:FPL1258 2.3 37.4 1.0
O7N A:NAP1257 3.2 37.5 1.0
CZ A:TYR147 3.5 30.1 1.0
CE1 A:PHE204 3.5 25.1 1.0
CE1 A:TYR147 3.5 29.7 1.0
C A:FPL1258 3.6 36.2 1.0
C4 A:FPL1258 3.6 35.8 1.0
CE2 A:TYR147 3.8 28.3 1.0
C4N A:NAP1257 3.8 34.1 1.0
CD1 A:TYR147 3.9 28.7 1.0
C7N A:NAP1257 3.9 35.7 1.0
OH A:TYR147 3.9 27.7 1.0
C3N A:NAP1257 4.0 36.7 1.0
C5 A:FPL1258 4.0 36.0 1.0
CD2 A:TYR147 4.1 26.8 1.0
CG A:TYR147 4.2 27.8 1.0
CD1 A:PHE204 4.4 25.3 1.0
CB A:PRO192 4.4 38.1 1.0
CZ A:PHE204 4.4 22.0 1.0
CA A:PRO192 4.4 37.6 1.0
CE1 A:TYR157 4.5 32.0 1.0
O A:FPL1258 4.7 36.2 1.0
C5N A:NAP1257 4.7 32.0 1.0
CG2 A:VAL201 4.8 35.2 1.0
CG1 A:VAL201 4.9 35.6 1.0
N7N A:NAP1257 5.0 38.2 1.0

Fluorine binding site 2 out of 8 in 4bnk

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Fluorine binding site 2 out of 8 in the Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol


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 S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1258

b:39.8
occ:1.00
F B:FPL1258 0.0 39.8 1.0
C2 B:FPL1258 1.3 42.5 1.0
C1 B:FPL1258 2.3 42.7 1.0
C3 B:FPL1258 2.3 40.3 1.0
O7N B:NAP1257 3.1 39.6 1.0
CE1 B:TYR147 3.5 35.5 1.0
CZ B:TYR147 3.5 36.2 1.0
C4 B:FPL1258 3.6 41.0 1.0
C B:FPL1258 3.6 43.1 1.0
C4N B:NAP1257 3.6 28.8 1.0
CE1 B:PHE204 3.7 47.2 1.0
C7N B:NAP1257 3.8 33.7 1.0
CD1 B:TYR147 3.8 34.5 1.0
CE2 B:TYR147 3.8 33.1 1.0
C3N B:NAP1257 3.8 34.5 1.0
OH B:TYR147 4.0 42.0 1.0
C5 B:FPL1258 4.1 42.6 1.0
CD2 B:TYR147 4.1 30.3 1.0
CG B:TYR147 4.1 31.3 1.0
CA B:PRO192 4.3 34.5 1.0
CB B:PRO192 4.5 36.0 1.0
CD1 B:PHE204 4.6 47.0 1.0
C5N B:NAP1257 4.6 27.8 1.0
CZ B:PHE204 4.6 46.2 1.0
CE1 B:TYR157 4.7 29.6 1.0
O B:FPL1258 4.7 43.6 1.0
N7N B:NAP1257 4.9 36.1 1.0
C2N B:NAP1257 4.9 35.0 1.0
N B:PRO192 5.0 33.8 1.0

Fluorine binding site 3 out of 8 in 4bnk

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Fluorine binding site 3 out of 8 in the Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol


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 S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1258

b:46.5
occ:1.00
F C:FPL1258 0.0 46.5 1.0
C2 C:FPL1258 1.3 42.1 1.0
C1 C:FPL1258 2.3 39.8 1.0
C3 C:FPL1258 2.3 42.0 1.0
O7N C:NAP1257 3.2 44.7 1.0
CE1 C:PHE204 3.4 38.3 1.0
C C:FPL1258 3.6 40.7 1.0
C4 C:FPL1258 3.6 39.3 1.0
CZ C:TYR147 3.6 36.8 1.0
CE1 C:TYR147 3.6 34.0 1.0
CE2 C:TYR147 3.9 30.8 1.0
C7N C:NAP1257 3.9 40.3 1.0
CD1 C:TYR147 4.0 31.7 1.0
OH C:TYR147 4.0 41.3 1.0
C5 C:FPL1258 4.0 40.3 1.0
CD1 C:PHE204 4.1 39.0 1.0
C4N C:NAP1257 4.1 33.4 1.0
C3N C:NAP1257 4.2 37.3 1.0
CD2 C:TYR147 4.2 31.4 1.0
CG C:TYR147 4.3 32.0 1.0
CB C:PRO192 4.3 32.7 1.0
CA C:PRO192 4.3 31.8 1.0
CZ C:PHE204 4.5 39.2 1.0
CE1 C:TYR157 4.6 31.6 1.0
O C:FPL1258 4.7 41.2 1.0
N7N C:NAP1257 4.8 41.9 1.0

Fluorine binding site 4 out of 8 in 4bnk

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Fluorine binding site 4 out of 8 in the Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol


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 S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1258

b:52.0
occ:1.00
F D:FPL1258 0.0 52.0 1.0
C2 D:FPL1258 1.3 51.9 1.0
C1 D:FPL1258 2.3 51.2 1.0
C3 D:FPL1258 2.3 54.0 1.0
O7N D:NAP1257 3.3 54.1 1.0
CZ D:TYR147 3.4 39.1 1.0
CE1 D:TYR147 3.5 39.9 1.0
C D:FPL1258 3.6 51.3 1.0
C4 D:FPL1258 3.6 51.9 1.0
CE2 D:TYR147 3.7 38.0 1.0
CD1 D:TYR147 3.8 39.2 1.0
C4N D:NAP1257 3.9 53.0 1.0
OH D:TYR147 3.9 37.4 1.0
CD2 D:TYR147 4.0 38.1 1.0
C3N D:NAP1257 4.0 54.9 1.0
C7N D:NAP1257 4.0 55.1 1.0
CG D:TYR147 4.0 37.9 1.0
C5 D:FPL1258 4.1 51.1 1.0
CE1 D:PHE204 4.2 57.0 1.0
CE1 D:TYR157 4.3 42.6 1.0
CD1 D:PHE204 4.5 59.6 1.0
O D:FPL1258 4.7 50.8 1.0
CA D:PRO192 4.7 46.9 1.0
C5N D:NAP1257 4.7 52.2 1.0
CB D:PRO192 4.8 47.5 1.0
C2N D:NAP1257 4.9 53.7 1.0
CD1 D:TYR157 4.9 42.9 1.0

Fluorine binding site 5 out of 8 in 4bnk

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Fluorine binding site 5 out of 8 in the Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol


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 S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1259

b:34.4
occ:1.00
F E:FPL1259 0.0 34.4 1.0
C2 E:FPL1259 1.3 37.2 1.0
C1 E:FPL1259 2.3 37.2 1.0
C3 E:FPL1259 2.3 37.4 1.0
O7N E:NAP1258 3.3 36.7 1.0
CZ E:TYR147 3.5 26.9 1.0
C E:FPL1259 3.6 37.6 1.0
C4 E:FPL1259 3.6 36.7 1.0
CE1 E:TYR147 3.6 28.2 1.0
CE1 E:PHE204 3.8 39.0 1.0
CE2 E:TYR147 3.8 25.3 1.0
OH E:TYR147 3.9 26.5 1.0
CD1 E:TYR147 4.0 25.1 1.0
C7N E:NAP1258 4.0 37.2 1.0
C4N E:NAP1258 4.0 34.8 1.0
C5 E:FPL1259 4.1 37.5 1.0
CD2 E:TYR147 4.2 25.1 1.0
C3N E:NAP1258 4.2 38.3 1.0
CG E:TYR147 4.3 26.2 1.0
CB E:PRO192 4.4 33.1 1.0
CD1 E:PHE204 4.5 41.3 1.0
CG2 E:VAL201 4.6 44.4 1.0
CA E:PRO192 4.6 32.5 1.0
CE1 E:TYR157 4.6 30.9 1.0
O E:FPL1259 4.7 38.1 1.0
CZ E:PHE204 4.8 39.1 1.0
C5N E:NAP1258 4.8 32.2 1.0
N7N E:NAP1258 4.9 39.7 1.0

Fluorine binding site 6 out of 8 in 4bnk

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Fluorine binding site 6 out of 8 in the Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol


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 S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1258

b:43.5
occ:1.00
F F:FPL1258 0.0 43.5 1.0
C2 F:FPL1258 1.4 41.3 1.0
C1 F:FPL1258 2.3 40.8 1.0
C3 F:FPL1258 2.4 37.5 1.0
O7N F:NAP1257 3.0 41.9 1.0
CE1 F:TYR147 3.5 35.8 1.0
CZ F:TYR147 3.6 37.0 1.0
C F:FPL1258 3.6 41.0 1.0
C4 F:FPL1258 3.6 37.9 1.0
C4N F:NAP1257 3.6 31.9 1.0
C7N F:NAP1257 3.8 39.2 1.0
CD1 F:TYR147 3.8 31.4 1.0
CE2 F:TYR147 3.8 31.2 1.0
CE1 F:PHE204 3.8 43.0 1.0
C3N F:NAP1257 3.9 37.3 1.0
CG F:TYR147 4.0 32.2 1.0
CD2 F:TYR147 4.0 29.2 1.0
OH F:TYR147 4.1 45.4 1.0
C5 F:FPL1258 4.1 40.9 1.0
CA F:PRO192 4.2 38.3 1.0
CB F:PRO192 4.4 38.8 1.0
C5N F:NAP1257 4.5 31.2 1.0
CD1 F:PHE204 4.7 43.6 1.0
O F:FPL1258 4.7 41.2 1.0
CZ F:PHE204 4.8 41.8 1.0
CE1 F:TYR157 4.8 36.8 1.0
N7N F:NAP1257 4.9 38.9 1.0
N F:PRO192 4.9 37.8 1.0
C2N F:NAP1257 4.9 35.6 1.0

Fluorine binding site 7 out of 8 in 4bnk

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Fluorine binding site 7 out of 8 in the Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol


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 S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F1258

b:41.2
occ:1.00
F G:FPL1258 0.0 41.2 1.0
C2 G:FPL1258 1.4 39.2 1.0
C1 G:FPL1258 2.3 38.7 1.0
C3 G:FPL1258 2.3 37.8 1.0
O7N G:NAP1257 3.1 37.0 1.0
CE1 G:PHE204 3.5 30.8 1.0
C G:FPL1258 3.6 39.5 1.0
C4 G:FPL1258 3.6 37.7 1.0
CE1 G:TYR147 3.6 36.9 1.0
CZ G:TYR147 3.7 40.9 1.0
CD1 G:TYR147 3.8 34.6 1.0
C7N G:NAP1257 3.9 34.0 1.0
C4N G:NAP1257 4.0 31.7 1.0
CE2 G:TYR147 4.1 36.4 1.0
C5 G:FPL1258 4.1 39.4 1.0
C3N G:NAP1257 4.1 34.3 1.0
CG G:TYR147 4.2 33.9 1.0
OH G:TYR147 4.2 48.1 1.0
CD1 G:PHE204 4.3 31.2 1.0
CD2 G:TYR147 4.3 33.8 1.0
CA G:PRO192 4.3 33.5 1.0
CB G:PRO192 4.3 34.5 1.0
CZ G:PHE204 4.5 32.5 1.0
CE1 G:TYR157 4.6 32.7 1.0
O G:FPL1258 4.7 39.8 1.0
N7N G:NAP1257 4.8 37.1 1.0
C5N G:NAP1257 4.9 33.5 1.0

Fluorine binding site 8 out of 8 in 4bnk

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Fluorine binding site 8 out of 8 in the Crystal Structure of S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol


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 S. Aureus Fabi in Complex with Nadp and 5-Fluoro-2-Phenoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F1258

b:58.0
occ:1.00
F H:FPL1258 0.0 58.0 1.0
C2 H:FPL1258 1.4 58.9 1.0
C3 H:FPL1258 2.3 59.9 1.0
C1 H:FPL1258 2.3 58.4 1.0
O7N H:NAP1257 3.6 56.2 1.0
C4 H:FPL1258 3.6 59.8 1.0
C H:FPL1258 3.6 58.7 1.0
CZ H:TYR147 3.6 50.2 1.0
CE1 H:TYR147 3.7 49.4 1.0
CE2 H:TYR147 3.7 48.0 1.0
CE1 H:PHE204 3.8 58.7 1.0
CD1 H:TYR147 4.0 48.7 1.0
CD2 H:TYR147 4.0 46.4 1.0
C5 H:FPL1258 4.1 58.9 1.0
CG H:TYR147 4.1 44.4 1.0
OH H:TYR147 4.1 53.3 1.0
C4N H:NAP1257 4.1 50.5 1.0
C3N H:NAP1257 4.2 53.9 1.0
C7N H:NAP1257 4.3 54.8 1.0
CE1 H:TYR157 4.4 40.0 1.0
CD1 H:PHE204 4.4 60.7 1.0
O H:FPL1258 4.7 58.4 1.0
CZ H:PHE204 4.8 59.3 1.0
CD1 H:TYR157 4.9 41.6 1.0
CD1 H:ILE207 4.9 64.9 1.0
C5N H:NAP1257 4.9 49.6 1.0
CA H:PRO192 4.9 43.4 1.0
CG2 H:VAL201 5.0 59.0 1.0

Reference:

A.Chang, J.Schiebel, W.Yu, G.R.Bommineni, P.Pan, M.V.Baxter, A.Khanna, C.A.Sotriffer, C.F.Kisker, P.J.Tonge. Rational Optimization of Drug-Target Residence Time: Insights From Inhibitor Binding to the S. Aureus Fabi Enzyme-Product Complex. Biochemistry V. 52 4217 2013.
ISSN: ISSN 0006-2960
PubMed: 23697754
DOI: 10.1021/BI400413C
Page generated: Thu Aug 1 00:17:56 2024

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