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Fluorine in PDB 3pp0: Crystal Structure of the Kinase Domain of Human HER2 (ERBB2).

Enzymatic activity of Crystal Structure of the Kinase Domain of Human HER2 (ERBB2).

All present enzymatic activity of Crystal Structure of the Kinase Domain of Human HER2 (ERBB2).:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of the Kinase Domain of Human HER2 (ERBB2)., PDB code: 3pp0 was solved by R.J.Skene, K.Aertgeerts, S.Sogabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.705, 78.951, 152.675, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 26

Other elements in 3pp0:

The structure of Crystal Structure of the Kinase Domain of Human HER2 (ERBB2). also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Kinase Domain of Human HER2 (ERBB2). (pdb code 3pp0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Kinase Domain of Human HER2 (ERBB2)., PDB code: 3pp0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3pp0

Go back to Fluorine Binding Sites List in 3pp0
Fluorine binding site 1 out of 6 in the Crystal Structure of the Kinase Domain of Human HER2 (ERBB2).


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 Kinase Domain of Human HER2 (ERBB2). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:45.2
occ:1.00
 F28 A:03Q1 0.0 45.2 1.0
C27 A:03Q1 1.4 41.5 1.0
F30 A:03Q1 2.2 47.6 1.0
F29 A:03Q1 2.3 55.0 1.0
C25 A:03Q1 2.4 43.3 1.0
C26 A:03Q1 2.8 35.0 1.0
OE2 A:GLU770 3.5 47.2 1.0
CD1 A:LEU796 3.5 31.1 1.0
CB A:GLU770 3.5 35.2 1.0
C24 A:03Q1 3.7 36.6 1.0
C21 A:03Q1 4.1 35.4 1.0
O A:HOH137 4.3 34.8 1.0
C A:GLU770 4.3 39.0 1.0
CD A:GLU770 4.4 43.3 1.0
CG A:GLU770 4.4 36.4 1.0
N A:ALA771 4.4 38.7 1.0
CB A:PHE864 4.5 36.2 1.0
O A:ASP863 4.5 38.7 1.0
O A:GLU770 4.5 40.7 1.0
CD2 A:LEU796 4.6 35.6 1.0
CG A:LEU796 4.6 35.7 1.0
CA A:GLU770 4.6 37.2 1.0
O A:ILE767 4.7 40.8 1.0
C23 A:03Q1 4.8 41.1 1.0
CD1 A:LEU785 4.8 26.6 1.0
CA A:ALA771 4.9 38.9 1.0
O20 A:03Q1 4.9 39.9 1.0
CD2 A:PHE864 5.0 37.9 1.0
C22 A:03Q1 5.0 37.4 1.0

Fluorine binding site 2 out of 6 in 3pp0

Go back to Fluorine Binding Sites List in 3pp0
Fluorine binding site 2 out of 6 in the Crystal Structure of the Kinase Domain of Human HER2 (ERBB2).


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 Kinase Domain of Human HER2 (ERBB2). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:55.0
occ:1.00
 F29 A:03Q1 0.0 55.0 1.0
C27 A:03Q1 1.4 41.5 1.0
F28 A:03Q1 2.3 45.2 1.0
F30 A:03Q1 2.3 47.6 1.0
C25 A:03Q1 2.3 43.3 1.0
C24 A:03Q1 2.8 36.6 1.0
CD2 A:LEU785 3.4 31.6 1.0
CB A:MET774 3.4 37.7 1.0
O A:GLU770 3.5 40.7 1.0
C26 A:03Q1 3.5 35.0 1.0
CB A:LEU785 3.5 24.2 1.0
CD1 A:LEU785 3.6 26.6 1.0
CG A:LEU785 3.6 30.4 1.0
CA A:ALA771 3.7 38.9 1.0
C A:GLU770 3.8 39.0 1.0
N A:ALA771 3.9 38.7 1.0
C23 A:03Q1 4.1 41.1 1.0
CG A:MET774 4.2 44.7 1.0
CB A:GLU770 4.4 35.2 1.0
CB A:ALA771 4.4 39.4 1.0
C21 A:03Q1 4.6 35.4 1.0
CA A:MET774 4.6 37.5 1.0
CA A:LEU785 4.7 28.2 1.0
CA A:GLU770 4.7 37.2 1.0
C A:ALA771 4.8 38.0 1.0
C22 A:03Q1 4.9 37.4 1.0
CD1 A:LEU796 4.9 31.1 1.0
N A:MET774 5.0 36.7 1.0

Fluorine binding site 3 out of 6 in 3pp0

Go back to Fluorine Binding Sites List in 3pp0
Fluorine binding site 3 out of 6 in the Crystal Structure of the Kinase Domain of Human HER2 (ERBB2).


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 Kinase Domain of Human HER2 (ERBB2). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:47.6
occ:1.00
 F30 A:03Q1 0.0 47.6 1.0
C27 A:03Q1 1.4 41.5 1.0
F28 A:03Q1 2.2 45.2 1.0
F29 A:03Q1 2.3 55.0 1.0
C25 A:03Q1 2.3 43.3 1.0
C24 A:03Q1 3.0 36.6 1.0
C26 A:03Q1 3.3 35.0 1.0
CB A:GLU770 3.4 35.2 1.0
CD2 A:PHE864 3.4 37.9 1.0
CB A:PHE864 3.4 36.2 1.0
O A:GLU770 3.4 40.7 1.0
CG A:MET774 3.5 44.7 1.0
CB A:MET774 3.6 37.7 1.0
CG A:PHE864 3.6 35.9 1.0
C A:GLU770 3.7 39.0 1.0
CE A:MET774 3.8 58.8 1.0
CA A:GLU770 4.0 37.2 1.0
CG A:GLU770 4.2 36.4 1.0
C23 A:03Q1 4.3 41.1 1.0
CE2 A:PHE864 4.3 41.8 1.0
OE2 A:GLU770 4.4 47.2 1.0
N A:ALA771 4.5 38.7 1.0
C21 A:03Q1 4.5 35.4 1.0
CD1 A:PHE864 4.6 36.1 1.0
SD A:MET774 4.6 50.2 1.0
O A:ASP863 4.6 38.7 1.0
CD A:GLU770 4.8 43.3 1.0
CA A:PHE864 4.9 38.8 1.0
C22 A:03Q1 4.9 37.4 1.0
CA A:MET774 4.9 37.5 1.0
CA A:ALA771 5.0 38.9 1.0

Fluorine binding site 4 out of 6 in 3pp0

Go back to Fluorine Binding Sites List in 3pp0
Fluorine binding site 4 out of 6 in the Crystal Structure of the Kinase Domain of Human HER2 (ERBB2).


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 the Kinase Domain of Human HER2 (ERBB2). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:46.4
occ:1.00
 F28 B:03Q2 0.0 46.4 1.0
C27 B:03Q2 1.4 40.6 1.0
F30 B:03Q2 2.2 49.6 1.0
F29 B:03Q2 2.3 51.6 1.0
C25 B:03Q2 2.4 33.6 1.0
C26 B:03Q2 2.7 29.9 1.0
OE1 B:GLU770 2.9 53.2 1.0
CB B:GLU770 3.2 39.0 1.0
C24 B:03Q2 3.7 28.7 1.0
O B:HOH81 3.8 41.3 1.0
CD1 B:LEU796 3.8 36.6 1.0
CD B:GLU770 3.8 52.0 1.0
CG B:GLU770 4.0 45.6 1.0
C21 B:03Q2 4.1 33.3 1.0
CB B:PHE864 4.1 33.2 1.0
C B:GLU770 4.2 38.8 1.0
CA B:GLU770 4.4 40.1 1.0
O B:GLU770 4.4 37.4 1.0
N B:ALA771 4.4 37.3 1.0
CD2 B:PHE864 4.6 32.1 1.0
CG B:PHE864 4.7 31.1 1.0
O B:ASP863 4.7 40.3 1.0
O B:ILE767 4.8 39.6 1.0
C23 B:03Q2 4.8 29.8 1.0
O20 B:03Q2 4.9 29.3 1.0
CA B:ALA771 4.9 38.8 1.0
C22 B:03Q2 5.0 30.3 1.0

Fluorine binding site 5 out of 6 in 3pp0

Go back to Fluorine Binding Sites List in 3pp0
Fluorine binding site 5 out of 6 in the Crystal Structure of the Kinase Domain of Human HER2 (ERBB2).


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Kinase Domain of Human HER2 (ERBB2). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:51.6
occ:1.00
 F29 B:03Q2 0.0 51.6 1.0
C27 B:03Q2 1.4 40.6 1.0
F30 B:03Q2 2.2 49.6 1.0
F28 B:03Q2 2.3 46.4 1.0
C25 B:03Q2 2.4 33.6 1.0
C24 B:03Q2 3.0 28.7 1.0
C26 B:03Q2 3.3 29.9 1.0
CD1 B:LEU785 3.4 29.3 1.0
CD2 B:LEU785 3.5 34.8 1.0
CA B:ALA771 3.6 38.8 1.0
O B:GLU770 3.7 37.4 1.0
CG B:LEU785 3.7 36.6 1.0
CB B:LEU785 3.8 35.2 1.0
N B:ALA771 3.8 37.3 1.0
C B:GLU770 3.8 38.8 1.0
CB B:ALA771 4.2 37.8 1.0
CD1 B:LEU796 4.3 36.6 1.0
CB B:MET774 4.3 39.0 1.0
CB B:GLU770 4.3 39.0 1.0
C23 B:03Q2 4.3 29.8 1.0
C21 B:03Q2 4.5 33.3 1.0
CD2 B:LEU796 4.6 25.6 1.0
CA B:GLU770 4.8 40.1 1.0
C B:ALA771 4.8 36.4 1.0
C22 B:03Q2 4.9 30.3 1.0
CG B:LEU796 4.9 28.8 1.0
CA B:LEU785 4.9 35.1 1.0
OE1 B:GLU770 5.0 53.2 1.0

Fluorine binding site 6 out of 6 in 3pp0

Go back to Fluorine Binding Sites List in 3pp0
Fluorine binding site 6 out of 6 in the Crystal Structure of the Kinase Domain of Human HER2 (ERBB2).


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Kinase Domain of Human HER2 (ERBB2). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:49.6
occ:1.00
 F30 B:03Q2 0.0 49.6 1.0
C27 B:03Q2 1.4 40.6 1.0
F28 B:03Q2 2.2 46.4 1.0
F29 B:03Q2 2.2 51.6 1.0
C25 B:03Q2 2.4 33.6 1.0
C24 B:03Q2 2.9 28.7 1.0
O B:GLU770 3.0 37.4 1.0
CE B:MET774 3.1 47.8 1.0
CB B:MET774 3.3 39.0 1.0
C B:GLU770 3.5 38.8 1.0
CB B:GLU770 3.5 39.0 1.0
C26 B:03Q2 3.5 29.9 1.0
CG B:MET774 3.8 41.5 1.0
CD2 B:PHE864 3.8 32.1 1.0
CA B:GLU770 4.0 40.1 1.0
N B:ALA771 4.1 37.3 1.0
CG B:PHE864 4.1 31.1 1.0
C23 B:03Q2 4.2 29.8 1.0
CB B:PHE864 4.3 33.2 1.0
SD B:MET774 4.3 43.1 1.0
CE2 B:PHE864 4.4 26.1 1.0
OE1 B:GLU770 4.5 53.2 1.0
CA B:ALA771 4.5 38.8 1.0
CG B:GLU770 4.5 45.6 1.0
CA B:MET774 4.6 40.6 1.0
C21 B:03Q2 4.7 33.3 1.0
N B:MET774 4.7 37.7 1.0
C22 B:03Q2 4.9 30.3 1.0
CD1 B:PHE864 4.9 34.4 1.0

Reference:

K.Aertgeerts, R.Skene, J.Yano, B.C.Sang, H.Zou, G.Snell, A.Jennings, K.Iwamoto, N.Habuka, A.Hirokawa, T.Ishikawa, T.Tanaka, H.Miki, Y.Ohta, S.Sogabe. Structural Analysis of the Mechanism of Inhibition and Allosteric Activation of the Kinase Domain of HER2 Protein. J.Biol.Chem. V. 286 18756 2011.
ISSN: ISSN 0021-9258
PubMed: 21454582
DOI: 10.1074/JBC.M110.206193
Page generated: Sun Dec 13 11:53:20 2020

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