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Fluorine in PDB 3gr4: Activator-Bound Structure of Human Pyruvate Kinase M2

Enzymatic activity of Activator-Bound Structure of Human Pyruvate Kinase M2

All present enzymatic activity of Activator-Bound Structure of Human Pyruvate Kinase M2:
2.7.1.40;

Protein crystallography data

The structure of Activator-Bound Structure of Human Pyruvate Kinase M2, PDB code: 3gr4 was solved by B.Hong, S.Dimov, W.Tempel, D.Auld, C.Thomas, M.Boxer, J.-K.Jianq, A.Skoumbourdis, S.Min, N.Southall, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, J.Inglese, H.Park, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.275, 153.206, 93.138, 90.00, 102.91, 90.00
R / Rfree (%) 20.8 / 23.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Activator-Bound Structure of Human Pyruvate Kinase M2 (pdb code 3gr4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Activator-Bound Structure of Human Pyruvate Kinase M2, PDB code: 3gr4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3gr4

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Fluorine binding site 1 out of 8 in the Activator-Bound Structure of Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Activator-Bound Structure of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F550

b:39.9
occ:0.50
FAA A:DYY550 0.0 39.9 0.5
CAD A:DYY550 1.4 38.8 0.5
CAY A:DYY550 2.2 34.5 0.5
CAE A:DYY550 2.4 38.5 0.5
CAC A:DYY550 2.4 38.4 0.5
OAB A:DYY550 2.6 37.8 0.5
CAX A:DYY550 3.0 35.1 0.5
SAF A:DYY550 3.0 38.1 0.5
CAZ A:DYY550 3.1 33.7 0.5
OBD A:DYY550 3.1 36.5 0.5
CAI A:DYY550 3.1 38.9 0.5
SAW A:DYY550 3.3 36.3 0.5
OBA A:DYY550 3.3 34.7 0.5
O A:LEU353 3.5 16.9 1.0
CAH A:DYY550 3.5 35.9 0.5
O A:HOH625 3.6 31.6 1.0
CE1 B:PHE26 3.6 23.0 1.0
CAR A:DYY550 3.7 38.3 0.5
CAP A:DYY550 3.7 37.7 0.5
NAV A:DYY550 3.7 38.0 0.5
O A:HOH573 3.8 22.7 1.0
NAG A:DYY550 3.8 36.8 0.5
CD1 B:PHE26 4.1 23.1 1.0
CAQ A:DYY550 4.2 37.9 0.5
CAK A:DYY550 4.2 34.1 0.5
CAM A:DYY550 4.2 33.4 0.5
OAS A:DYY550 4.3 37.9 0.5
CZ B:PHE26 4.4 24.2 1.0
CAH A:DYY550 4.5 39.9 0.5
C A:LEU353 4.5 16.2 1.0
CAL A:DYY550 4.7 33.0 0.5
FBC A:DYY550 4.7 38.6 0.5
CBB A:DYY550 4.7 34.5 0.5
CAT A:DYY550 4.8 35.4 0.5
OAJ A:DYY550 4.8 35.9 0.5
CAU A:DYY550 4.9 38.2 0.5

Fluorine binding site 2 out of 8 in 3gr4

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Fluorine binding site 2 out of 8 in the Activator-Bound Structure of Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Activator-Bound Structure of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F550

b:44.6
occ:0.50
FAA A:DYY550 0.0 44.6 0.5
CAD A:DYY550 1.4 43.0 0.5
CAY A:DYY550 1.9 27.9 0.5
CAC A:DYY550 2.4 42.6 0.5
CAE A:DYY550 2.4 42.8 0.5
CAX A:DYY550 2.7 30.7 0.5
CAI A:DYY550 2.8 35.6 0.5
OBD A:DYY550 2.9 35.1 0.5
CAZ A:DYY550 2.9 26.2 0.5
OAB A:DYY550 3.0 43.5 0.5
SAF A:DYY550 3.1 43.1 0.5
SAW A:DYY550 3.1 34.8 0.5
OBA A:DYY550 3.2 26.1 0.5
CAH A:DYY550 3.3 39.9 0.5
NAV A:DYY550 3.4 35.2 0.5
CE1 A:PHE26 3.6 23.1 1.0
O A:HOH695 3.6 36.4 1.0
CAR A:DYY550 3.6 42.0 0.5
CAP A:DYY550 3.7 41.9 0.5
O B:LEU353 3.7 17.7 1.0
NAG A:DYY550 3.7 41.5 0.5
O B:HOH631 3.9 32.4 1.0
CAK A:DYY550 4.0 27.3 0.5
CD1 A:PHE26 4.0 22.2 1.0
CAM A:DYY550 4.1 25.9 0.5
CAQ A:DYY550 4.1 42.0 0.5
CAH A:DYY550 4.2 35.9 0.5
O B:HOH667 4.4 19.8 1.0
OAS A:DYY550 4.4 43.0 0.5
CAL A:DYY550 4.5 25.8 0.5
OAJ A:DYY550 4.5 34.9 0.5
CZ A:PHE26 4.5 23.8 1.0
CBB A:DYY550 4.6 26.7 0.5
CAU A:DYY550 4.7 35.5 0.5
C B:LEU353 4.7 15.7 1.0
FBC A:DYY550 4.7 43.0 0.5
CAT A:DYY550 4.7 39.8 0.5
CAI A:DYY550 4.8 38.9 0.5

Fluorine binding site 3 out of 8 in 3gr4

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Fluorine binding site 3 out of 8 in the Activator-Bound Structure of Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Activator-Bound Structure of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F550

b:38.6
occ:0.50
FBC A:DYY550 0.0 38.6 0.5
CAR A:DYY550 1.3 38.3 0.5
CAK A:DYY550 1.5 34.1 0.5
OAJ A:DYY550 1.6 35.9 0.5
CAX A:DYY550 1.9 35.1 0.5
SAW A:DYY550 2.1 36.3 0.5
CAE A:DYY550 2.4 38.5 0.5
CAQ A:DYY550 2.4 37.9 0.5
OAS A:DYY550 2.6 37.9 0.5
CAL A:DYY550 2.8 33.0 0.5
SAF A:DYY550 3.0 38.1 0.5
CG A:GLN393 3.1 20.3 1.0
CAU A:DYY550 3.2 38.2 0.5
NAV A:DYY550 3.2 38.0 0.5
CAY A:DYY550 3.3 34.5 0.5
CD A:GLN393 3.4 20.2 1.0
OBD A:DYY550 3.4 36.5 0.5
CAT A:DYY550 3.4 35.4 0.5
CB A:GLN393 3.5 20.4 1.0
CAP A:DYY550 3.6 37.7 0.5
CAD A:DYY550 3.6 38.8 0.5
NE2 A:GLN393 3.6 22.2 1.0
N A:LEU394 3.8 20.6 1.0
NAG A:DYY550 3.8 36.8 0.5
CAM A:DYY550 3.9 33.4 0.5
OE1 A:GLN393 3.9 22.1 1.0
C A:GLN393 4.0 18.4 1.0
CAZ A:DYY550 4.1 33.7 0.5
CA A:LEU394 4.1 20.6 1.0
CAC A:DYY550 4.1 38.4 0.5
OE1 A:GLU397 4.2 24.1 1.0
OAB A:DYY550 4.3 37.8 0.5
CAI A:DYY550 4.3 38.9 0.5
O A:GLN393 4.3 19.9 1.0
CA A:GLN393 4.4 19.5 1.0
CD A:GLU397 4.4 26.7 1.0
OE2 A:GLU397 4.5 23.7 1.0
CB B:PHE26 4.5 19.0 1.0
CD1 B:PHE26 4.5 23.1 1.0
CB A:LEU394 4.6 19.6 1.0
O A:TYR390 4.6 16.7 1.0
CAT A:DYY550 4.7 39.8 0.5
FAA A:DYY550 4.7 39.9 0.5
CG B:PHE26 4.8 22.1 1.0
CAU A:DYY550 4.9 35.5 0.5
CAH A:DYY550 4.9 35.9 0.5
CD2 A:TYR390 4.9 17.7 1.0

Fluorine binding site 4 out of 8 in 3gr4

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Fluorine binding site 4 out of 8 in the Activator-Bound Structure of Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Activator-Bound Structure of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F550

b:43.0
occ:0.50
FBC A:DYY550 0.0 43.0 0.5
CAK A:DYY550 1.1 27.3 0.5
CAR A:DYY550 1.3 42.0 0.5
CAX A:DYY550 2.0 30.7 0.5
CAL A:DYY550 2.2 25.8 0.5
OAS A:DYY550 2.2 43.0 0.5
CAE A:DYY550 2.3 42.8 0.5
CAQ A:DYY550 2.4 42.0 0.5
OAJ A:DYY550 2.5 34.9 0.5
SAW A:DYY550 2.7 34.8 0.5
SAF A:DYY550 2.9 43.1 0.5
CG B:GLN393 3.2 21.4 1.0
CAY A:DYY550 3.3 27.9 0.5
CAM A:DYY550 3.4 25.9 0.5
CD B:GLN393 3.5 21.9 1.0
NE2 B:GLN393 3.5 20.2 1.0
OE1 B:GLU397 3.5 22.6 1.0
CAD A:DYY550 3.6 43.0 0.5
CAP A:DYY550 3.6 41.9 0.5
CB B:GLN393 3.7 19.6 1.0
CAU A:DYY550 3.7 35.5 0.5
N B:LEU394 3.7 18.1 1.0
NAV A:DYY550 3.8 35.2 0.5
C B:GLN393 3.8 18.1 1.0
CAZ A:DYY550 3.8 26.2 0.5
CD B:GLU397 3.8 23.5 1.0
CAT A:DYY550 3.8 39.8 0.5
CA B:LEU394 3.9 18.4 1.0
OBD A:DYY550 4.0 35.1 0.5
NAG A:DYY550 4.0 41.5 0.5
O B:GLN393 4.0 18.2 1.0
OAB A:DYY550 4.0 43.5 0.5
CAC A:DYY550 4.1 42.6 0.5
OE2 B:GLU397 4.1 21.9 1.0
CB A:PHE26 4.2 19.1 1.0
OE1 B:GLN393 4.3 22.3 1.0
CA B:GLN393 4.4 17.7 1.0
CD1 A:PHE26 4.4 22.2 1.0
CB B:LEU394 4.5 18.9 1.0
CG B:GLU397 4.5 22.2 1.0
OAN A:DYY550 4.5 25.0 0.5
CAI A:DYY550 4.7 35.6 0.5
CG A:PHE26 4.7 21.7 1.0
FAA A:DYY550 4.7 44.6 0.5
CD1 B:LEU394 4.9 19.7 1.0

Fluorine binding site 5 out of 8 in 3gr4

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Fluorine binding site 5 out of 8 in the Activator-Bound Structure of Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Activator-Bound Structure of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F550

b:46.0
occ:0.50
FAA D:DYY550 0.0 46.0 0.5
CAD D:DYY550 1.4 45.2 0.5
CAY D:DYY550 2.2 32.4 0.5
CAC D:DYY550 2.4 44.9 0.5
CAE D:DYY550 2.4 44.5 0.5
OAB D:DYY550 2.6 43.3 0.5
CAZ D:DYY550 3.0 30.7 0.5
SAF D:DYY550 3.0 43.5 0.5
CAI D:DYY550 3.1 37.0 0.5
OBA D:DYY550 3.1 30.8 0.5
CAX D:DYY550 3.2 33.8 0.5
O C:LEU353 3.3 17.1 1.0
OBD D:DYY550 3.5 35.6 0.5
SAW D:DYY550 3.6 35.4 0.5
CE1 D:PHE26 3.6 24.9 1.0
O C:HOH650 3.6 30.0 1.0
O D:HOH655 3.7 33.0 1.0
CAP D:DYY550 3.7 44.8 0.5
CAH D:DYY550 3.7 39.7 0.5
CAR D:DYY550 3.7 44.5 0.5
O C:HOH660 3.7 22.5 1.0
NAV D:DYY550 3.8 36.4 0.5
NAG D:DYY550 3.9 41.4 0.5
CD1 D:PHE26 4.1 23.3 1.0
CAQ D:DYY550 4.2 44.4 0.5
CAM D:DYY550 4.3 31.0 0.5
OAS D:DYY550 4.3 42.8 0.5
C C:LEU353 4.3 18.2 1.0
CAK D:DYY550 4.4 31.0 0.5
CAH D:DYY550 4.4 37.7 0.5
CZ D:PHE26 4.5 24.4 1.0
CBB D:DYY550 4.5 29.8 0.5
CAL D:DYY550 4.8 30.5 0.5
FBC D:DYY550 4.8 44.3 0.5
CAT D:DYY550 4.9 39.7 0.5
CA C:ASP354 4.9 15.1 1.0
SD D:MET30 5.0 27.1 1.0
N C:ASP354 5.0 16.3 1.0

Fluorine binding site 6 out of 8 in 3gr4

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Fluorine binding site 6 out of 8 in the Activator-Bound Structure of Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Activator-Bound Structure of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F550

b:41.0
occ:0.50
FAA D:DYY550 0.0 41.0 0.5
CAD D:DYY550 1.4 40.3 0.5
CAY D:DYY550 1.9 32.9 0.5
CAC D:DYY550 2.4 39.5 0.5
CAE D:DYY550 2.4 40.0 0.5
CAZ D:DYY550 2.8 30.8 0.5
OAB D:DYY550 2.8 41.1 0.5
CAX D:DYY550 2.9 34.1 0.5
OBA D:DYY550 2.9 31.2 0.5
CAI D:DYY550 3.0 39.1 0.5
SAF D:DYY550 3.1 40.7 0.5
OBD D:DYY550 3.3 36.9 0.5
O D:LEU353 3.4 16.2 1.0
SAW D:DYY550 3.4 36.9 0.5
O D:HOH653 3.6 32.4 1.0
CE1 C:PHE26 3.6 23.1 1.0
CAP D:DYY550 3.7 39.4 0.5
CAR D:DYY550 3.7 38.9 0.5
CAH D:DYY550 3.7 37.7 0.5
NAV D:DYY550 3.8 38.0 0.5
O D:HOH595 3.9 28.0 1.0
NAG D:DYY550 3.9 39.0 0.5
O D:HOH670 4.0 19.9 1.0
CD1 C:PHE26 4.0 21.5 1.0
CAM D:DYY550 4.0 31.1 0.5
CAK D:DYY550 4.1 31.3 0.5
CAQ D:DYY550 4.2 38.5 0.5
CBB D:DYY550 4.3 30.6 0.5
CAH D:DYY550 4.3 39.7 0.5
C D:LEU353 4.4 16.6 1.0
OAS D:DYY550 4.4 41.2 0.5
CZ C:PHE26 4.5 24.0 1.0
CAL D:DYY550 4.6 30.3 0.5
FBC D:DYY550 4.8 38.9 0.5
CAT D:DYY550 4.8 37.7 0.5
OAJ D:DYY550 4.9 36.5 0.5
CAU D:DYY550 4.9 38.8 0.5
SD C:MET30 4.9 25.6 1.0

Fluorine binding site 7 out of 8 in 3gr4

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Fluorine binding site 7 out of 8 in the Activator-Bound Structure of Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Activator-Bound Structure of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F550

b:44.3
occ:0.50
FBC D:DYY550 0.0 44.3 0.5
CAR D:DYY550 1.3 44.5 0.5
OAJ D:DYY550 1.4 35.0 0.5
CAK D:DYY550 1.6 31.0 0.5
CAX D:DYY550 1.8 33.8 0.5
SAW D:DYY550 1.9 35.4 0.5
CAQ D:DYY550 2.4 44.4 0.5
CAE D:DYY550 2.4 44.5 0.5
OAS D:DYY550 2.7 42.8 0.5
CAL D:DYY550 3.0 30.5 0.5
SAF D:DYY550 3.0 43.5 0.5
OBD D:DYY550 3.1 35.6 0.5
NAV D:DYY550 3.1 36.4 0.5
CAU D:DYY550 3.1 36.8 0.5
CAY D:DYY550 3.2 32.4 0.5
CG C:GLN393 3.2 18.7 1.0
CAT D:DYY550 3.3 39.7 0.5
CD C:GLN393 3.3 16.9 1.0
CB C:GLN393 3.5 18.4 1.0
NE2 C:GLN393 3.6 18.9 1.0
CAP D:DYY550 3.6 44.8 0.5
CAD D:DYY550 3.7 45.2 0.5
NAG D:DYY550 3.7 41.4 0.5
OE1 C:GLN393 3.9 21.2 1.0
N C:LEU394 4.0 19.6 1.0
CAM D:DYY550 4.0 31.0 0.5
CAZ D:DYY550 4.1 30.7 0.5
C C:GLN393 4.1 19.0 1.0
CAI D:DYY550 4.1 37.0 0.5
CAC D:DYY550 4.1 44.9 0.5
CB D:PHE26 4.3 20.4 1.0
CA C:LEU394 4.3 18.4 1.0
OE1 C:GLU397 4.4 21.9 1.0
OAB D:DYY550 4.4 43.3 0.5
CA C:GLN393 4.4 18.4 1.0
O C:GLN393 4.4 18.3 1.0
CD1 D:PHE26 4.4 23.3 1.0
CD C:GLU397 4.5 24.1 1.0
OE2 C:GLU397 4.6 21.9 1.0
CG D:PHE26 4.6 22.0 1.0
CAT D:DYY550 4.7 37.7 0.5
O C:TYR390 4.7 17.4 1.0
CAU D:DYY550 4.7 38.8 0.5
CB C:LEU394 4.8 18.8 1.0
FAA D:DYY550 4.8 46.0 0.5
CAH D:DYY550 4.9 39.7 0.5
CD2 C:TYR390 5.0 20.3 1.0

Fluorine binding site 8 out of 8 in 3gr4

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Fluorine binding site 8 out of 8 in the Activator-Bound Structure of Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Activator-Bound Structure of Human Pyruvate Kinase M2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F550

b:38.9
occ:0.50
FBC D:DYY550 0.0 38.9 0.5
CAK D:DYY550 1.3 31.3 0.5
CAR D:DYY550 1.3 38.9 0.5
OAJ D:DYY550 1.9 36.5 0.5
CAX D:DYY550 1.9 34.1 0.5
SAW D:DYY550 2.3 36.9 0.5
CAE D:DYY550 2.3 40.0 0.5
CAQ D:DYY550 2.4 38.5 0.5
OAS D:DYY550 2.4 41.2 0.5
CAL D:DYY550 2.6 30.3 0.5
SAF D:DYY550 2.9 40.7 0.5
CG D:GLN393 3.1 17.6 1.0
CAY D:DYY550 3.3 32.9 0.5
CAU D:DYY550 3.3 38.8 0.5
NAV D:DYY550 3.3 38.0 0.5
CD D:GLN393 3.3 20.0 1.0
NE2 D:GLN393 3.4 20.7 1.0
CAT D:DYY550 3.4 37.7 0.5
CB D:GLN393 3.5 18.1 1.0
OBD D:DYY550 3.5 36.9 0.5
CAP D:DYY550 3.6 39.4 0.5
CAD D:DYY550 3.6 40.3 0.5
NAG D:DYY550 3.7 39.0 0.5
CAM D:DYY550 3.7 31.1 0.5
N D:LEU394 3.9 18.1 1.0
CAZ D:DYY550 4.0 30.8 0.5
OE1 D:GLN393 4.0 23.3 1.0
C D:GLN393 4.0 16.8 1.0
OE1 D:GLU397 4.1 22.4 1.0
CAC D:DYY550 4.1 39.5 0.5
CD D:GLU397 4.1 23.2 1.0
OAB D:DYY550 4.2 41.1 0.5
CA D:LEU394 4.2 16.6 1.0
CB C:PHE26 4.2 19.0 1.0
OE2 D:GLU397 4.3 21.2 1.0
CAI D:DYY550 4.3 39.1 0.5
O D:GLN393 4.3 16.5 1.0
CD1 C:PHE26 4.4 21.5 1.0
CA D:GLN393 4.4 17.8 1.0
CG C:PHE26 4.6 21.2 1.0
CB D:LEU394 4.7 18.6 1.0
FAA D:DYY550 4.8 41.0 0.5
CAT D:DYY550 4.8 39.7 0.5
CAU D:DYY550 4.8 36.8 0.5
CG D:GLU397 4.9 19.8 1.0
O D:TYR390 4.9 16.4 1.0
CAH D:DYY550 4.9 37.7 0.5
OAN D:DYY550 4.9 30.6 0.5

Reference:

B.Hong, S.Dimov, W.Tempel, D.Auld, C.Thomas, M.Boxer, J.-K.Jianq, A.Skoumbourdis, S.Min, N.Southall, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, J.Inglese, H.Park. Activator-Bound Structures of Human Pyruvate Kinase M2 To Be Published.
Page generated: Sun Dec 13 11:47:13 2020

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