Fluorine in PDB 3f1o: Crystal Structure of the High Affinity Heterodimer of HIF2 Alpha and Arnt C-Terminal Pas Domains, with An Internally-Bound Artificial Ligand

The structure of Crystal Structure of the High Affinity Heterodimer of HIF2 Alpha and Arnt C-Terminal Pas Domains, with An Internally-Bound Artificial Ligand, PDB code: 3f1o was solved by T.H.Scheuermann, D.R.Tomchick, M.Machius, Y.Guo, R.K.Bruick, K.H.Gardner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.93 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	73.761, 83.019, 41.553, 90.00, 106.36, 90.00
R / Rfree (%)	16.6 / 20.3

The binding sites of Fluorine atom in the Crystal Structure of the High Affinity Heterodimer of HIF2 Alpha and Arnt C-Terminal Pas Domains, with An Internally-Bound Artificial Ligand (pdb code 3f1o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the High Affinity Heterodimer of HIF2 Alpha and Arnt C-Terminal Pas Domains, with An Internally-Bound Artificial Ligand, PDB code: 3f1o:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the High Affinity Heterodimer of HIF2 Alpha and Arnt C-Terminal Pas Domains, with An Internally-Bound Artificial Ligand


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 High Affinity Heterodimer of HIF2 Alpha and Arnt C-Terminal Pas Domains, with An Internally-Bound Artificial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:32.3 occ:1.00 F2 A:2XY1 0.0 32.3 1.0 C9 A:2XY1 1.4 34.1 1.0 F1 A:2XY1 2.2 35.6 1.0 F3 A:2XY1 2.2 44.6 1.0 C8 A:2XY1 2.4 21.7 1.0 HG11 A:VAL302 2.7 36.4 1.0 C10 A:2XY1 2.7 19.9 1.0 HD22 A:LEU296 3.2 21.2 1.0 HB3 A:SER292 3.2 28.5 0.8 HA A:HIS293 3.2 19.4 1.0 HB3 A:SER292 3.3 28.7 0.2 CG1 A:VAL302 3.4 30.3 1.0 HG13 A:VAL302 3.5 36.4 1.0 C7 A:2XY1 3.5 20.2 1.0 OG A:SER292 3.6 24.9 0.2 HB2 A:LEU296 3.6 21.3 1.0 HG12 A:VAL302 3.6 36.4 1.0 HG A:SER292 3.6 29.8 0.2 O A:SER292 3.7 20.9 0.8 C A:SER292 3.7 22.0 0.8 O A:SER292 3.7 22.4 0.2 C A:SER292 3.7 22.6 0.2 N A:HIS293 3.8 21.3 1.0 HD23 A:LEU296 3.9 21.2 1.0 CB A:SER292 3.9 23.9 0.2 HB2 A:SER292 3.9 28.5 0.8 CB A:SER292 3.9 23.8 0.8 CD2 A:LEU296 3.9 17.6 1.0 CA A:HIS293 3.9 16.1 1.0 C11 A:2XY1 4.0 20.8 1.0 CG A:HIS293 4.1 25.4 1.0 HB3 A:LEU296 4.2 21.3 1.0 CD2 A:HIS293 4.2 25.6 1.0 H A:HIS293 4.2 25.6 0.2 H A:HIS293 4.2 25.6 0.8 ND1 A:HIS293 4.3 34.4 1.0 CB A:LEU296 4.3 17.8 1.0 NE2 A:HIS293 4.3 26.1 1.0 CE1 A:HIS293 4.4 36.2 1.0 HE3 A:MET289 4.4 17.1 1.0 HD2 A:HIS293 4.4 30.7 1.0 CA A:SER292 4.5 23.8 0.2 CA A:SER292 4.5 23.4 0.8 HB3 A:SER304 4.5 22.2 0.6 HG21 A:VAL302 4.6 40.2 1.0 HB3 A:SER304 4.6 22.2 0.4 HD21 A:LEU296 4.6 21.2 1.0 CB A:HIS293 4.6 22.4 1.0 HA3 A:GLY323 4.7 18.2 1.0 HB2 A:SER292 4.7 28.7 0.2 CB A:VAL302 4.7 26.7 1.0 CG A:LEU296 4.7 16.5 1.0 C6 A:2XY1 4.8 15.1 1.0 HA A:SER304 4.8 24.5 0.6 HE1 A:MET289 4.8 17.1 1.0 HE1 A:HIS293 4.8 43.4 1.0 C5 A:2XY1 4.9 17.3 1.0 HH A:TYR281 4.9 20.1 1.0 HA A:SER292 4.9 28.6 0.2 HA A:SER292 5.0 28.1 0.8 O2 A:2XY1 5.0 33.8 1.0 H A:LEU296 5.0 22.1 1.0 HB A:VAL302 5.0 32.1 1.0 HD13 A:LEU296 5.0 22.4 1.0 N3 A:2XY1 5.0 28.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the High Affinity Heterodimer of HIF2 Alpha and Arnt C-Terminal Pas Domains, with An Internally-Bound Artificial Ligand


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 High Affinity Heterodimer of HIF2 Alpha and Arnt C-Terminal Pas Domains, with An Internally-Bound Artificial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:44.6 occ:1.00 F3 A:2XY1 0.0 44.6 1.0 C9 A:2XY1 1.4 34.1 1.0 F1 A:2XY1 2.2 35.6 1.0 F2 A:2XY1 2.2 32.3 1.0 C8 A:2XY1 2.4 21.7 1.0 HG13 A:VAL302 2.5 36.4 1.0 HG11 A:VAL302 2.9 36.4 1.0 CG1 A:VAL302 3.0 30.3 1.0 HG12 A:VAL302 3.1 36.4 1.0 HB3 A:SER304 3.1 22.2 0.6 C7 A:2XY1 3.1 20.2 1.0 C10 A:2XY1 3.3 19.9 1.0 HB3 A:SER304 3.3 22.2 0.4 HA3 A:GLY323 3.4 18.2 1.0 HG22 A:THR321 3.5 16.9 1.0 H A:GLY323 3.7 18.8 1.0 HB A:THR321 3.7 16.4 1.0 HD22 A:LEU296 3.7 21.2 1.0 HG21 A:THR321 3.8 16.9 1.0 HG A:SER292 3.8 29.8 0.2 H A:SER304 3.9 23.8 0.4 HA A:SER304 4.0 24.5 0.6 N A:GLY323 4.0 15.6 1.0 CB A:SER304 4.0 18.5 0.6 CG2 A:THR321 4.0 14.1 1.0 O A:THR321 4.0 17.5 1.0 HB3 A:SER292 4.1 28.5 0.8 OG A:SER292 4.1 24.9 0.2 CA A:GLY323 4.1 15.1 1.0 O A:VAL302 4.2 21.2 1.0 CB A:SER304 4.2 18.4 0.4 N A:SER304 4.2 19.8 0.4 H A:SER304 4.2 23.3 0.6 HB2 A:SER304 4.3 22.2 0.6 N A:SER304 4.3 19.4 0.6 CA A:SER304 4.3 20.4 0.6 CB A:THR321 4.4 13.7 1.0 CB A:VAL302 4.4 26.7 1.0 C11 A:2XY1 4.4 20.8 1.0 HB2 A:LEU296 4.5 21.3 1.0 C6 A:2XY1 4.5 15.1 1.0 HA A:SER304 4.5 24.3 0.4 CA A:SER304 4.6 20.2 0.4 C A:VAL302 4.6 22.0 1.0 C A:THR321 4.6 17.2 1.0 HB2 A:SER304 4.6 22.2 0.4 HA2 A:GLY323 4.6 18.2 1.0 HB3 A:SER292 4.7 28.7 0.2 HG22 A:VAL302 4.7 40.2 1.0 CD2 A:LEU296 4.7 17.6 1.0 C A:GLN322 4.8 18.1 1.0 HE1 A:MET289 4.8 17.1 1.0 HA A:VAL303 4.8 22.4 1.0 HD13 A:LEU296 4.8 22.4 1.0 HA A:GLN322 4.8 17.1 1.0 HG21 A:VAL302 4.8 40.2 1.0 C A:VAL303 4.9 23.3 1.0 HG23 A:THR321 4.9 16.9 1.0 CG2 A:VAL302 4.9 33.5 1.0 C5 A:2XY1 4.9 17.3 1.0 HB A:VAL302 5.0 32.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the High Affinity Heterodimer of HIF2 Alpha and Arnt C-Terminal Pas Domains, with An Internally-Bound Artificial Ligand


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 High Affinity Heterodimer of HIF2 Alpha and Arnt C-Terminal Pas Domains, with An Internally-Bound Artificial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:35.6 occ:1.00 F1 A:2XY1 0.0 35.6 1.0 C9 A:2XY1 1.3 34.1 1.0 F2 A:2XY1 2.2 32.3 1.0 F3 A:2XY1 2.2 44.6 1.0 C8 A:2XY1 2.3 21.7 1.0 HG A:SER292 2.5 29.8 0.2 HB3 A:SER304 2.6 22.2 0.6 HB3 A:SER304 2.6 22.2 0.4 C7 A:2XY1 2.7 20.2 1.0 HB3 A:SER292 2.8 28.5 0.8 HB2 A:SER304 2.9 22.2 0.6 OG A:SER292 2.9 24.9 0.2 HB3 A:SER292 3.0 28.7 0.2 HE1 A:MET289 3.0 17.1 1.0 HA A:SER304 3.1 24.5 0.6 CB A:SER304 3.1 18.5 0.6 HE3 A:MET289 3.2 17.1 1.0 HB2 A:SER304 3.2 22.2 0.4 CB A:SER304 3.3 18.4 0.4 HB2 A:SER292 3.4 28.5 0.8 CB A:SER292 3.4 23.9 0.2 CB A:SER292 3.5 23.8 0.8 CE A:MET289 3.5 14.2 1.0 HA A:SER304 3.6 24.3 0.4 CA A:SER304 3.6 20.4 0.6 C10 A:2XY1 3.6 19.9 1.0 HG11 A:VAL302 3.7 36.4 1.0 HG13 A:VAL302 3.7 36.4 1.0 CA A:SER304 3.9 20.2 0.4 HG A:SER292 3.9 27.9 0.8 HB2 A:SER292 3.9 28.7 0.2 HB A:THR321 4.1 16.4 1.0 CG1 A:VAL302 4.1 30.3 1.0 C6 A:2XY1 4.2 15.1 1.0 OG A:SER292 4.2 23.3 0.8 H A:SER304 4.2 23.8 0.4 HE2 A:MET289 4.3 17.1 1.0 N A:SER304 4.3 19.8 0.4 N A:SER304 4.3 19.4 0.6 OG A:SER304 4.4 16.6 0.6 H A:SER304 4.5 23.3 0.6 OG A:SER304 4.5 17.4 0.4 SD A:MET289 4.6 21.5 1.0 HG A:SER304 4.6 21.0 0.4 HG12 A:VAL302 4.6 36.4 1.0 C A:SER292 4.6 22.0 0.8 C A:SER292 4.7 22.6 0.2 CA A:SER292 4.7 23.8 0.2 CA A:SER292 4.7 23.4 0.8 C11 A:2XY1 4.7 20.8 1.0 HA A:MET289 4.7 22.0 1.0 HH A:TYR281 4.7 20.1 1.0 C A:SER304 4.8 22.2 0.6 HG21 A:THR321 4.9 16.9 1.0 O A:SER304 4.9 24.4 0.6 HD2 A:HIS293 4.9 30.7 1.0 N A:HIS293 4.9 21.3 1.0 CD2 A:HIS293 4.9 25.6 1.0 HG21 A:VAL302 4.9 40.2 1.0 HG22 A:THR321 4.9 16.9 1.0 C5 A:2XY1 4.9 17.3 1.0 O A:SER292 4.9 20.9 0.8 O A:SER292 4.9 22.4 0.2 HG22 A:VAL302 5.0 40.2 1.0 NE2 A:HIS293 5.0 26.1 1.0 CB A:THR321 5.0 13.7 1.0 HG A:SER304 5.0 19.9 0.6

T.H.Scheuermann, D.R.Tomchick, M.Machius, Y.Guo, R.K.Bruick, K.H.Gardner. Artificial Ligand Binding Within the HIF2ALPHA Pas-B Domain of the HIF2 Transcription Factor. Proc.Natl.Acad.Sci.Usa V. 106 450 2009.
ISSN: ISSN 0027-8424
PubMed: 19129502
DOI: 10.1073/PNAS.0808092106