Fluorine in PDB 3la3: Crystal Structure of Ntca in Complex with 2,2-Difluoropentanedioic Acid

The structure of Crystal Structure of Ntca in Complex with 2,2-Difluoropentanedioic Acid, PDB code: 3la3 was solved by M.X.Zhao, Y.L.Jiang, Y.X.He, Y.F.Chen, Y.B.Teng, Y.X.Chen, C.C.Zhang, C.Z.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.45 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.030, 70.080, 149.730, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.3

The binding sites of Fluorine atom in the Crystal Structure of Ntca in Complex with 2,2-Difluoropentanedioic Acid (pdb code 3la3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Ntca in Complex with 2,2-Difluoropentanedioic Acid, PDB code: 3la3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Ntca in Complex with 2,2-Difluoropentanedioic 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 Ntca in Complex with 2,2-Difluoropentanedioic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F224 b:58.1 occ:1.00 F07 A:2FT224 0.0 58.1 1.0 C06 A:2FT224 1.4 52.9 1.0 F08 A:2FT224 2.1 56.7 1.0 C05 A:2FT224 2.4 47.3 1.0 C09 A:2FT224 2.4 48.7 1.0 O01 A:2FT224 2.4 41.0 1.0 C04 A:2FT224 2.7 45.5 1.0 C02 A:2FT224 2.7 42.8 1.0 O10 A:2FT224 2.8 44.9 1.0 O11 A:2FT224 3.4 44.4 1.0 CD2 B:LEU131 3.5 39.5 1.0 N A:VAL77 3.7 40.8 1.0 N A:LEU78 3.8 42.3 1.0 CG2 A:VAL77 3.8 39.7 1.0 O03 A:2FT224 3.9 43.4 1.0 OE1 B:GLU134 3.9 33.5 1.0 C A:GLY76 4.3 40.9 1.0 CA A:VAL77 4.4 41.4 1.0 C A:VAL77 4.4 42.3 1.0 N A:GLY76 4.4 40.1 1.0 CG B:LEU131 4.5 39.9 1.0 CA A:GLY76 4.5 40.0 1.0 OE2 B:GLU134 4.5 36.0 1.0 CB A:LEU78 4.6 43.0 1.0 CB A:VAL77 4.6 41.3 1.0 CA A:LEU78 4.6 43.6 1.0 CD B:GLU134 4.7 35.8 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Ntca in Complex with 2,2-Difluoropentanedioic 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 Ntca in Complex with 2,2-Difluoropentanedioic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F224 b:56.7 occ:1.00 F08 A:2FT224 0.0 56.7 1.0 C06 A:2FT224 1.4 52.9 1.0 F07 A:2FT224 2.1 58.1 1.0 C05 A:2FT224 2.3 47.3 1.0 C09 A:2FT224 2.4 48.7 1.0 O11 A:2FT224 2.7 44.4 1.0 C04 A:2FT224 2.7 45.5 1.0 OE1 B:GLU134 2.7 33.5 1.0 OE2 B:GLU134 2.9 36.0 1.0 CD B:GLU134 3.2 35.8 1.0 O10 A:2FT224 3.5 44.9 1.0 CD1 A:TYR90 3.5 37.8 1.0 C02 A:2FT224 3.7 42.8 1.0 CE1 A:TYR90 3.9 37.0 1.0 O01 A:2FT224 4.1 41.0 1.0 CD2 B:LEU131 4.2 39.5 1.0 CD1 A:LEU54 4.3 37.7 1.0 CG B:GLU134 4.7 35.8 1.0 CG A:TYR90 4.7 39.1 1.0 O03 A:2FT224 4.8 43.4 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Ntca in Complex with 2,2-Difluoropentanedioic 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 Ntca in Complex with 2,2-Difluoropentanedioic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:F224 b:51.4 occ:1.00 F07 B:2FT224 0.0 51.4 1.0 C06 B:2FT224 1.4 49.1 1.0 F08 B:2FT224 2.2 56.4 1.0 C09 B:2FT224 2.3 46.6 1.0 C05 B:2FT224 2.3 43.8 1.0 O11 B:2FT224 2.6 43.3 1.0 C04 B:2FT224 2.7 40.1 1.0 OE1 A:GLU134 2.9 33.3 1.0 C02 B:2FT224 3.4 38.4 1.0 O10 B:2FT224 3.4 44.1 1.0 OE2 A:GLU134 3.4 35.6 1.0 CD A:GLU134 3.5 35.6 1.0 CD2 A:LEU131 3.8 37.6 1.0 O01 B:2FT224 3.8 33.7 1.0 CD1 B:TYR90 3.8 31.2 1.0 CD1 B:LEU54 4.1 31.0 1.0 CE1 B:TYR90 4.3 26.6 1.0 O03 B:2FT224 4.3 38.0 1.0 CG2 B:VAL77 4.8 36.9 1.0 N B:VAL77 4.9 38.1 1.0 CG2 A:ILE130 5.0 34.5 1.0 CG B:TYR90 5.0 33.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Ntca in Complex with 2,2-Difluoropentanedioic 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 Ntca in Complex with 2,2-Difluoropentanedioic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:F224 b:56.4 occ:1.00 F08 B:2FT224 0.0 56.4 1.0 C06 B:2FT224 1.4 49.1 1.0 O01 B:2FT224 2.1 33.7 1.0 F07 B:2FT224 2.2 51.4 1.0 C05 B:2FT224 2.3 43.8 1.0 C09 B:2FT224 2.4 46.6 1.0 C02 B:2FT224 2.4 38.4 1.0 C04 B:2FT224 2.7 40.1 1.0 O10 B:2FT224 2.8 44.1 1.0 N B:VAL77 2.9 38.1 1.0 N B:LEU78 3.4 40.1 1.0 C B:GLY76 3.4 38.3 1.0 O03 B:2FT224 3.5 38.0 1.0 CA B:GLY76 3.5 37.9 1.0 O11 B:2FT224 3.5 43.3 1.0 CG2 B:VAL77 3.7 36.9 1.0 N B:GLY76 3.7 37.8 1.0 CA B:VAL77 3.9 39.0 1.0 C B:VAL77 4.1 39.7 1.0 CD2 A:LEU131 4.1 37.6 1.0 CB B:LEU78 4.3 40.9 1.0 O B:GLY76 4.3 37.9 1.0 CA B:LEU78 4.4 41.7 1.0 CB B:VAL77 4.4 39.1 1.0 NH1 B:ARG88 4.7 38.0 1.0 OE1 A:GLU134 4.7 33.3 1.0 C B:PHE75 4.9 38.1 1.0

M.X.Zhao, Y.L.Jiang, Y.X.He, Y.F.Chen, Y.B.Teng, Y.X.Chen, C.C.Zhang, C.Z.Zhou. Structural Basis For the Allosteric Control of the Global Transcription Factor Ntca By the Nitrogen Starvation Signal 2-Oxoglutarate. Proc.Natl.Acad.Sci.Usa V. 107 12487 2010.
ISSN: ISSN 0027-8424
PubMed: 20616047
DOI: 10.1073/PNAS.1001556107