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Fluorine in PDB 2wm3: Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid

Protein crystallography data

The structure of Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid, PDB code: 2wm3 was solved by C.Bhatia, W.W.Yue, F.Niesen, E.Pilka, E.Ugochukwu, P.Savitsky, V.Hozjan, A.K.Roos, P.Filippakopoulos, F.Von Delft, T.Heightman, C.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.85
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.712, 68.712, 183.789, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.7

Other elements in 2wm3:

The structure of Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid (pdb code 2wm3). 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 Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid, PDB code: 2wm3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 2wm3

Go back to Fluorine Binding Sites List in 2wm3
Fluorine binding site 1 out of 9 in the Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid


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 Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1300

b:27.7
occ:0.50
 F3 A:NFL1300 0.0 27.7 0.5
C15 A:NFL1300 1.4 26.9 0.5
C13 A:NFL1300 1.9 27.5 0.5
F1 A:NFL1300 2.2 29.0 0.5
F2 A:NFL1300 2.2 27.5 0.5
C9 A:NFL1300 2.4 25.7 0.5
C14 A:NFL1300 2.8 26.6 0.5
C14 A:NFL1300 2.8 24.4 0.5
C12 A:NFL1300 2.9 25.7 0.5
CE1 A:HIS162 3.2 26.6 1.0
ND1 A:HIS162 3.3 25.9 1.0
C10 A:NFL1300 3.5 22.7 0.5
NE2 A:HIS162 3.8 30.1 1.0
CG A:HIS162 4.0 18.0 1.0
C9 A:NFL1300 4.1 26.4 0.5
C11 A:NFL1300 4.1 22.7 0.5
C13 A:NFL1300 4.2 21.9 0.5
CD2 A:HIS162 4.2 25.6 1.0
O A:HOH2143 4.6 26.6 1.0
C10 A:NFL1300 4.7 23.9 0.5
C11 A:NFL1300 4.7 21.9 0.5
CB A:HIS162 4.8 15.1 1.0
C12 A:NFL1300 4.9 21.8 0.5

Fluorine binding site 2 out of 9 in 2wm3

Go back to Fluorine Binding Sites List in 2wm3
Fluorine binding site 2 out of 9 in the Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid


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 Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1300

b:27.2
occ:0.50
 F3 A:NFL1300 0.0 27.2 0.5
C15 A:NFL1300 1.4 27.6 0.5
F1 A:NFL1300 2.1 31.6 0.5
F2 A:NFL1300 2.2 27.1 0.5
C9 A:NFL1300 2.4 26.4 0.5
OH A:TYR246 2.8 26.6 1.0
CE1 A:PHE163 2.9 15.3 1.0
C14 A:NFL1300 3.0 26.6 0.5
C13 A:NFL1300 3.1 21.9 0.5
CZ A:PHE163 3.4 16.1 1.0
CB A:HIS162 3.4 15.1 1.0
C14 A:NFL1300 3.5 24.4 0.5
C10 A:NFL1300 3.5 23.9 0.5
CD1 A:PHE163 3.6 16.7 1.0
O A:HIS162 3.8 14.9 1.0
CZ A:TYR246 3.8 27.7 1.0
C A:HIS162 4.1 13.5 1.0
CE1 A:TYR246 4.2 27.2 1.0
CA A:HIS162 4.3 13.1 1.0
O A:HOH2212 4.3 24.5 1.0
CE2 A:PHE163 4.3 14.8 1.0
C12 A:NFL1300 4.3 21.8 0.5
C13 A:NFL1300 4.3 27.5 0.5
CG A:HIS162 4.4 18.0 1.0
CG A:PHE163 4.5 11.9 1.0
CD1 A:LEU257 4.6 20.7 1.0
C11 A:NFL1300 4.7 22.7 0.5
CD2 A:PHE163 4.8 16.0 1.0
N A:PHE163 4.9 11.3 1.0
C9 A:NFL1300 4.9 25.7 0.5
CE2 A:TYR246 4.9 25.9 1.0

Fluorine binding site 3 out of 9 in 2wm3

Go back to Fluorine Binding Sites List in 2wm3
Fluorine binding site 3 out of 9 in the Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid


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 Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1300

b:29.0
occ:0.50
 F1 A:NFL1300 0.0 29.0 0.5
C15 A:NFL1300 1.3 26.9 0.5
F3 A:NFL1300 2.2 27.7 0.5
F2 A:NFL1300 2.2 27.5 0.5
C9 A:NFL1300 2.4 25.7 0.5
C13 A:NFL1300 2.7 27.5 0.5
C12 A:NFL1300 2.8 25.7 0.5
C10 A:NFL1300 2.8 22.7 0.5
CD2 A:TRP82 3.0 19.4 1.0
CE3 A:TRP82 3.1 21.7 1.0
CE2 A:TRP82 3.2 20.0 1.0
CZ3 A:TRP82 3.5 23.2 1.0
CG A:TRP82 3.6 15.7 1.0
CZ2 A:TRP82 3.6 21.6 1.0
CH2 A:TRP82 3.7 24.6 1.0
C14 A:NFL1300 3.7 24.4 0.5
NE1 A:TRP82 3.8 18.4 1.0
C14 A:NFL1300 4.0 26.6 0.5
CD1 A:TRP82 4.0 18.4 1.0
C11 A:NFL1300 4.1 22.7 0.5
C11 A:NFL1300 4.2 21.9 0.5
CE1 A:HIS162 4.4 26.6 1.0
CB A:TRP82 4.4 12.9 1.0
NE2 A:HIS162 4.5 30.1 1.0
N2 A:NFL1300 4.7 20.3 0.5
C13 A:NFL1300 4.8 21.9 0.5
ND1 A:HIS162 4.9 25.9 1.0
N2 A:NFL1300 5.0 18.5 0.5

Fluorine binding site 4 out of 9 in 2wm3

Go back to Fluorine Binding Sites List in 2wm3
Fluorine binding site 4 out of 9 in the Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid


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 Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1300

b:31.6
occ:0.50
 F1 A:NFL1300 0.0 31.6 0.5
C15 A:NFL1300 1.3 27.6 0.5
F2 A:NFL1300 2.1 27.1 0.5
F3 A:NFL1300 2.1 27.2 0.5
C9 A:NFL1300 2.3 26.4 0.5
CD1 A:LEU257 2.5 20.7 1.0
C14 A:NFL1300 2.8 26.6 0.5
OH A:TYR246 3.0 26.6 1.0
CE1 A:TYR246 3.1 27.2 1.0
C13 A:NFL1300 3.2 21.9 0.5
CZ A:TYR246 3.3 27.7 1.0
C14 A:NFL1300 3.3 24.4 0.5
C10 A:NFL1300 3.5 23.9 0.5
CG A:LEU257 3.6 10.7 1.0
CD2 A:LEU257 3.8 17.6 1.0
CB A:LEU257 4.1 11.9 1.0
CD1 A:TYR246 4.1 25.4 1.0
C13 A:NFL1300 4.1 27.5 0.5
C12 A:NFL1300 4.3 21.8 0.5
CE2 A:TYR246 4.4 25.9 1.0
CE1 A:PHE163 4.4 15.3 1.0
C9 A:NFL1300 4.5 25.7 0.5
C11 A:NFL1300 4.6 22.7 0.5
CZ A:PHE163 4.6 16.1 1.0
C12 A:NFL1300 4.9 25.7 0.5
F2 A:NFL1300 4.9 27.5 0.5

Fluorine binding site 5 out of 9 in 2wm3

Go back to Fluorine Binding Sites List in 2wm3
Fluorine binding site 5 out of 9 in the Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid


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 Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1300

b:27.5
occ:0.50
 F2 A:NFL1300 0.0 27.5 0.5
C15 A:NFL1300 1.4 26.9 0.5
F1 A:NFL1300 2.2 29.0 0.5
F3 A:NFL1300 2.2 27.7 0.5
C9 A:NFL1300 2.4 25.7 0.5
C13 A:NFL1300 2.4 27.5 0.5
C14 A:NFL1300 3.0 26.6 0.5
C14 A:NFL1300 3.1 24.4 0.5
C12 A:NFL1300 3.2 25.7 0.5
CZ3 A:TRP82 3.3 23.2 1.0
CH2 A:TRP82 3.4 24.6 1.0
C10 A:NFL1300 3.4 22.7 0.5
CE3 A:TRP82 3.7 21.7 1.0
CZ2 A:TRP82 3.9 21.6 1.0
CD1 A:LEU257 4.1 20.7 1.0
C9 A:NFL1300 4.1 26.4 0.5
CD2 A:TRP82 4.3 19.4 1.0
C11 A:NFL1300 4.3 22.7 0.5
CE2 A:TRP82 4.3 20.0 1.0
C13 A:NFL1300 4.3 21.9 0.5
C11 A:NFL1300 4.6 21.9 0.5
C10 A:NFL1300 4.7 23.9 0.5
CD2 A:LEU257 4.7 17.6 1.0
CG A:LEU257 4.9 10.7 1.0
F1 A:NFL1300 4.9 31.6 0.5
C12 A:NFL1300 5.0 21.8 0.5

Fluorine binding site 6 out of 9 in 2wm3

Go back to Fluorine Binding Sites List in 2wm3
Fluorine binding site 6 out of 9 in the Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid


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 Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1300

b:27.1
occ:0.50
 F2 A:NFL1300 0.0 27.1 0.5
C15 A:NFL1300 1.3 27.6 0.5
F1 A:NFL1300 2.1 31.6 0.5
F3 A:NFL1300 2.2 27.2 0.5
C9 A:NFL1300 2.4 26.4 0.5
CZ A:PHE163 2.8 16.1 1.0
C10 A:NFL1300 2.8 23.9 0.5
C13 A:NFL1300 2.8 21.9 0.5
CE1 A:PHE163 2.9 15.3 1.0
OH A:TYR246 3.1 26.6 1.0
C12 A:NFL1300 3.5 21.8 0.5
CE2 A:PHE261 3.6 15.1 1.0
C14 A:NFL1300 3.6 26.6 0.5
CZ A:TYR246 3.6 27.7 1.0
C14 A:NFL1300 3.7 24.4 0.5
CD2 A:LEU257 4.0 17.6 1.0
CD1 A:LEU257 4.0 20.7 1.0
CE2 A:PHE163 4.0 14.8 1.0
CE1 A:TYR246 4.1 27.2 1.0
CZ A:PHE261 4.2 15.6 1.0
CD1 A:PHE163 4.2 16.7 1.0
C11 A:NFL1300 4.2 22.7 0.5
CE2 A:TYR246 4.3 25.9 1.0
CE A:MET260 4.3 7.0 1.0
CG A:LEU257 4.3 10.7 1.0
N1 A:NFL1300 4.5 14.2 0.5
CB A:LEU257 4.6 11.9 1.0
CD2 A:PHE261 4.7 15.2 1.0
C13 A:NFL1300 4.8 27.5 0.5
C11 A:NFL1300 4.8 21.9 0.5
C9 A:NFL1300 5.0 25.7 0.5

Fluorine binding site 7 out of 9 in 2wm3

Go back to Fluorine Binding Sites List in 2wm3
Fluorine binding site 7 out of 9 in the Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid


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 Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:45.2
occ:1.00
 F3 A:NFL1301 0.0 45.2 1.0
C15 A:NFL1301 1.3 41.9 1.0
F1 A:NFL1301 2.2 45.7 1.0
F2 A:NFL1301 2.2 43.2 1.0
C9 A:NFL1301 2.3 36.6 1.0
C10 A:NFL1301 2.9 30.9 1.0
C14 A:NFL1301 3.3 30.4 1.0
O4 A:PO41303 3.5 86.3 1.0
C11 A:NFL1301 4.1 34.2 1.0
O2 A:PO41303 4.3 86.9 1.0
C13 A:NFL1301 4.4 32.2 1.0
P A:PO41303 4.5 86.9 1.0
N1 A:NFL1301 4.7 36.9 1.0
C12 A:NFL1301 4.8 30.5 1.0
O A:LEU120 4.9 14.9 1.0

Fluorine binding site 8 out of 9 in 2wm3

Go back to Fluorine Binding Sites List in 2wm3
Fluorine binding site 8 out of 9 in the Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid


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 Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:45.7
occ:1.00
 F1 A:NFL1301 0.0 45.7 1.0
C15 A:NFL1301 1.3 41.9 1.0
F2 A:NFL1301 2.2 43.2 1.0
F3 A:NFL1301 2.2 45.2 1.0
C9 A:NFL1301 2.4 36.6 1.0
C14 A:NFL1301 2.7 30.4 1.0
O4 A:PO41303 3.0 86.3 1.0
CD1 A:LEU266 3.5 9.9 1.0
C10 A:NFL1301 3.6 30.9 1.0
C13 A:NFL1301 4.1 32.2 1.0
CB A:LEU266 4.2 8.1 1.0
P A:PO41303 4.5 86.9 1.0
CG A:LEU266 4.5 8.8 1.0
CG2 A:THR121 4.6 11.7 1.0
C11 A:NFL1301 4.8 34.2 1.0
C12 A:NFL1301 4.9 30.5 1.0
O2 A:PO41303 4.9 86.9 1.0
CE1 A:PHE263 5.0 16.0 1.0
NH2 A:ARG124 5.0 18.1 1.0

Fluorine binding site 9 out of 9 in 2wm3

Go back to Fluorine Binding Sites List in 2wm3
Fluorine binding site 9 out of 9 in the Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid


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 Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:43.2
occ:1.00
 F2 A:NFL1301 0.0 43.2 1.0
C15 A:NFL1301 1.3 41.9 1.0
F1 A:NFL1301 2.2 45.7 1.0
F3 A:NFL1301 2.2 45.2 1.0
C9 A:NFL1301 2.4 36.6 1.0
C10 A:NFL1301 2.9 30.9 1.0
O4 A:PO41303 3.3 86.3 1.0
C14 A:NFL1301 3.5 30.4 1.0
O A:LEU120 3.5 14.9 1.0
CG2 A:THR121 3.8 11.7 1.0
C A:LEU120 3.8 14.6 1.0
CB A:LEU120 3.9 14.1 1.0
C11 A:NFL1301 4.2 34.2 1.0
O2 A:PO41303 4.2 86.9 1.0
N A:THR121 4.3 13.8 1.0
P A:PO41303 4.3 86.9 1.0
CA A:THR121 4.5 14.3 1.0
CA A:LEU120 4.5 13.9 1.0
C13 A:NFL1301 4.6 32.2 1.0
CB A:THR121 4.8 14.2 1.0
CE1 A:PHE263 4.8 16.0 1.0
O3 A:PO41303 4.9 86.2 1.0
C12 A:NFL1301 4.9 30.5 1.0
CG A:LEU120 4.9 16.6 1.0
N1 A:NFL1301 4.9 36.9 1.0

Reference:

C.Bhatia, W.W.Yue, E.Pilka, E.Ugochukwu, P.Savitsky, V.Hozjan, A.K.Roos, P.Filippakopoulos, F.Von Delft, T.Heightman, C.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, U.Oppermann. Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid To Be Published.
Page generated: Wed Jul 31 16:26:02 2024

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