Fluorine in PDB 8g67: Wildtype PTP1B in Complex with DES4884

Enzymatic activity of Wildtype PTP1B in Complex with DES4884

All present enzymatic activity of Wildtype PTP1B in Complex with DES4884:
3.1.3.48;

Protein crystallography data

The structure of Wildtype PTP1B in Complex with DES4884, PDB code: 8g67 was solved by J.B.Greisman, L.Willmore, C.Y.Yeh, F.Giordanetto, S.Shahamadtar, H.Nisonoff, P.Maragakis, D.E.Shaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.21 / 1.53
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.57, 89.57, 164.31, 90, 90, 90
R / Rfree (%) 15.4 / 22.3

Other elements in 8g67:

The structure of Wildtype PTP1B in Complex with DES4884 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Wildtype PTP1B in Complex with DES4884 (pdb code 8g67). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Wildtype PTP1B in Complex with DES4884, PDB code: 8g67:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8g67

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Fluorine binding site 1 out of 6 in the Wildtype PTP1B in Complex with DES4884


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Wildtype PTP1B in Complex with DES4884 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:54.8
occ:0.95
 FAB A:KB8301 0.0 54.8 0.9
CAU A:KB8301 1.3 32.2 0.9
CAP A:KB8301 2.1 37.5 0.9
FAC A:KB8301 2.1 50.2 0.9
FAD A:KB8301 2.2 49.2 0.9
NAM A:KB8301 2.8 45.2 0.9
CAG A:KB8301 3.0 41.5 0.9
CB A:PHE196 3.3 37.6 1.0
CA A:PHE196 3.3 34.2 1.0
O A:HOH427 3.4 51.9 1.0
N A:PHE196 3.5 30.5 1.0
CD A:ARG199 3.9 33.0 1.0
CD1 A:PHE196 3.9 53.4 1.0
CAR A:KB8301 4.0 53.8 0.9
O A:LEU192 4.0 31.1 1.0
CG A:LEU195 4.1 25.3 1.0
CG A:PHE196 4.1 49.2 1.0
C A:LEU195 4.1 28.3 1.0
CAQ A:KB8301 4.2 40.3 0.9
CD2 A:LEU195 4.3 32.4 1.0
NH1 A:ARG199 4.3 36.4 1.0
NE A:ARG199 4.4 32.4 1.0
CB A:LEU195 4.4 25.1 1.0
O A:LEU195 4.5 30.9 1.0
CAS A:KB8301 4.6 45.0 0.9
CZ A:ARG199 4.6 37.6 1.0
CG A:ARG199 4.8 28.8 1.0
C A:PHE196 4.8 29.7 1.0
CA A:LEU195 4.9 27.7 1.0
CAF A:KB8301 5.0 50.4 0.9

Fluorine binding site 2 out of 6 in 8g67

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Fluorine binding site 2 out of 6 in the Wildtype PTP1B in Complex with DES4884


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Wildtype PTP1B in Complex with DES4884 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:50.2
occ:0.95
 FAC A:KB8301 0.0 50.2 0.9
CAU A:KB8301 1.3 32.2 0.9
FAB A:KB8301 2.1 54.8 0.9
FAD A:KB8301 2.2 49.2 0.9
CAP A:KB8301 2.2 37.5 0.9
NAM A:KB8301 2.6 45.2 0.9
O A:HOH427 3.4 51.9 1.0
CAG A:KB8301 3.5 41.5 0.9
NH1 A:ARG199 3.5 36.4 1.0
CD1 A:LEU232 3.8 33.6 1.0
CAR A:KB8301 3.9 53.8 0.9
CD1 A:ILE281 3.9 72.5 1.0
CZ A:ARG199 4.1 37.6 1.0
CD2 A:LEU195 4.4 32.4 1.0
NE A:ARG199 4.5 32.4 1.0
O A:GLY277 4.6 40.7 1.0
CD A:ARG199 4.6 33.0 1.0
CG1 A:ILE281 4.6 71.4 1.0
CAQ A:KB8301 4.7 40.3 0.9
CAF A:KB8301 4.7 50.4 0.9
NH2 A:ARG199 4.8 37.6 1.0
CAS A:KB8301 4.8 45.0 0.9
CG A:LEU232 4.9 26.0 1.0
CG A:LEU195 4.9 25.3 1.0
CB A:LEU232 5.0 32.9 1.0

Fluorine binding site 3 out of 6 in 8g67

Go back to Fluorine Binding Sites List in 8g67
Fluorine binding site 3 out of 6 in the Wildtype PTP1B in Complex with DES4884


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Wildtype PTP1B in Complex with DES4884 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:49.2
occ:0.95
 FAD A:KB8301 0.0 49.2 0.9
CAU A:KB8301 1.3 32.2 0.9
FAC A:KB8301 2.2 50.2 0.9
FAB A:KB8301 2.2 54.8 0.9
CAP A:KB8301 2.4 37.5 0.9
CAG A:KB8301 2.8 41.5 0.9
O A:LEU192 3.4 31.1 1.0
NAM A:KB8301 3.5 45.2 0.9
CD2 A:LEU192 3.6 31.9 1.0
CB A:LEU192 4.0 34.5 1.0
CA A:LEU192 4.1 32.3 1.0
C A:LEU192 4.1 31.1 1.0
CD2 A:LEU195 4.1 32.4 1.0
CAQ A:KB8301 4.2 40.3 0.9
CD1 A:LEU232 4.3 33.6 1.0
CG A:LEU192 4.4 35.5 1.0
CG A:LEU195 4.5 25.3 1.0
CB A:LEU195 4.5 25.1 1.0
N A:PHE196 4.5 30.5 1.0
CB A:PHE196 4.6 37.6 1.0
CAR A:KB8301 4.7 53.8 0.9
CA A:GLY277 4.8 38.4 1.0
CA A:PHE196 4.9 34.2 1.0

Fluorine binding site 4 out of 6 in 8g67

Go back to Fluorine Binding Sites List in 8g67
Fluorine binding site 4 out of 6 in the Wildtype PTP1B in Complex with DES4884


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Wildtype PTP1B in Complex with DES4884 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:32.8
occ:0.80
 FAB A:KB8302 0.0 32.8 0.8
CAU A:KB8302 1.3 32.3 0.8
FAD A:KB8302 2.2 37.0 0.8
FAC A:KB8302 2.2 35.5 0.8
CAP A:KB8302 2.2 35.3 0.8
CAG A:KB8302 2.9 41.2 0.8
NAM A:KB8302 3.0 32.7 0.8
O A:ALA264 3.5 30.5 1.0
CB A:TRP16 3.5 28.1 1.0
C A:ALA264 3.6 32.4 1.0
N A:ASP265 3.7 25.2 1.0
CA A:ASP265 3.7 28.0 1.0
CG A:TRP16 3.7 31.3 1.0
CB A:ARG268 3.9 33.3 1.0
CD1 A:TRP16 3.9 31.5 1.0
CD A:ARG268 3.9 32.6 1.0
CB A:ALA264 4.1 30.0 1.0
OD1 A:ASP265 4.1 74.6 1.0
CAQ A:KB8302 4.2 37.0 0.8
CAR A:KB8302 4.2 32.1 0.8
CG A:ASP265 4.3 48.4 1.0
O A:HOH547 4.3 53.5 1.0
CA A:ALA264 4.5 29.9 1.0
CG A:ARG268 4.5 34.2 1.0
O A:HOH560 4.5 47.9 1.0
CD2 A:TRP16 4.6 29.7 1.0
CB A:ASP265 4.6 32.9 1.0
C A:ASP265 4.7 32.6 1.0
CAS A:KB8302 4.8 35.5 0.8
OD2 A:ASP265 4.8 54.5 1.0
NE1 A:TRP16 4.8 35.7 1.0
O A:ASP265 4.9 27.9 1.0
O A:HOH418 4.9 43.0 1.0
O A:HOH639 5.0 49.5 1.0

Fluorine binding site 5 out of 6 in 8g67

Go back to Fluorine Binding Sites List in 8g67
Fluorine binding site 5 out of 6 in the Wildtype PTP1B in Complex with DES4884


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Wildtype PTP1B in Complex with DES4884 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:35.5
occ:0.80
 FAC A:KB8302 0.0 35.5 0.8
CAU A:KB8302 1.3 32.3 0.8
FAD A:KB8302 2.1 37.0 0.8
FAB A:KB8302 2.2 32.8 0.8
CAP A:KB8302 2.4 35.3 0.8
NAM A:KB8302 2.8 32.7 0.8
O A:HOH639 3.1 49.5 1.0
O A:HOH560 3.1 47.9 1.0
O A:HOH570 3.2 38.9 1.0
CB A:TRP16 3.6 28.1 1.0
CAG A:KB8302 3.6 41.2 0.8
CAR A:KB8302 4.1 32.1 0.8
CB A:ALA264 4.1 30.0 1.0
CG A:TRP16 4.2 31.3 1.0
CD1 A:TRP16 4.3 31.5 1.0
N A:ALA17 4.7 26.2 1.0
CA A:TRP16 4.8 30.4 1.0
CAQ A:KB8302 4.8 37.0 0.8
C A:ALA264 4.8 32.4 1.0
N A:ASP265 4.9 25.2 1.0
CAF A:KB8302 5.0 35.6 0.8

Fluorine binding site 6 out of 6 in 8g67

Go back to Fluorine Binding Sites List in 8g67
Fluorine binding site 6 out of 6 in the Wildtype PTP1B in Complex with DES4884


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Wildtype PTP1B in Complex with DES4884 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:37.0
occ:0.80
 FAD A:KB8302 0.0 37.0 0.8
CAU A:KB8302 1.3 32.3 0.8
FAC A:KB8302 2.1 35.5 0.8
FAB A:KB8302 2.2 32.8 0.8
CAP A:KB8302 2.3 35.3 0.8
CAG A:KB8302 2.7 41.2 0.8
OD2 A:ASP265 3.2 54.5 1.0
CG A:ASP265 3.3 48.4 1.0
OD1 A:ASP265 3.3 74.6 1.0
NAM A:KB8302 3.5 32.7 0.8
O A:HOH418 3.9 43.0 1.0
CA A:ASP265 4.0 28.0 1.0
N A:ASP265 4.0 25.2 1.0
O A:HOH639 4.1 49.5 1.0
CAQ A:KB8302 4.1 37.0 0.8
CB A:ASP265 4.1 32.9 1.0
C A:ALA264 4.5 32.4 1.0
CAR A:KB8302 4.6 32.1 0.8
CB A:ALA264 4.6 30.0 1.0
CAL A:KB8302 4.8 37.4 0.8
O A:HOH547 4.9 53.5 1.0
O A:ALA264 4.9 30.5 1.0
CAS A:KB8302 5.0 35.5 0.8

Reference:

J.B.Greisman, L.Willmore, C.Y.Yeh, F.Giordanetto, S.Shahamadtar, H.Nisonoff, P.Maragakis, D.E.Shaw. Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1B: From Molecular Dynamics Simulations to X-Ray Crystallography To Be Published.
Page generated: Thu Jul 27 14:24:26 2023

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