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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

Protein crystallography data

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

Fluorine Binding Sites:

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 3f1o

Go back to Fluorine Binding Sites List in 3f1o
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 3f1o

Go back to Fluorine Binding Sites List in 3f1o
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 3f1o

Go back to Fluorine Binding Sites List in 3f1o
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

Reference:

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
Page generated: Sun Dec 13 11:45:45 2020

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