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Fluorine in PDB 4equ: Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7

Enzymatic activity of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7

All present enzymatic activity of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7:
2.7.11.1;

Protein crystallography data

The structure of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7, PDB code: 4equ was solved by E.A.Merritt, E.T.Larson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.810, 49.040, 133.760, 90.00, 101.42, 90.00
R / Rfree (%) 22.3 / 24.6

Other elements in 4equ:

The structure of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 also contains other interesting chemical elements:

Calcium (Ca) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 (pdb code 4equ). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7, PDB code: 4equ:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4equ

Go back to Fluorine Binding Sites List in 4equ
Fluorine binding site 1 out of 6 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:56.0
occ:1.00
 FAF A:G6I401 0.0 56.0 1.0
CBP A:G6I401 1.3 61.2 1.0
FAE A:G6I401 2.1 64.7 1.0
FAD A:G6I401 2.2 61.1 1.0
CBJ A:G6I401 2.3 58.0 1.0
CAU A:G6I401 2.8 54.5 1.0
CAL A:G6I401 3.5 58.4 1.0
CD2 A:HIS155 3.6 43.1 1.0
O A:LEU173 3.6 41.3 1.0
C A:ALA174 3.8 45.1 1.0
NE2 A:HIS155 3.8 44.6 1.0
O A:ALA174 3.9 42.4 1.0
CA A:ALA174 3.9 44.7 1.0
C A:LEU173 3.9 43.1 1.0
N A:ALA174 4.0 42.4 1.0
CBI A:G6I401 4.1 53.6 1.0
N A:ASP175 4.2 48.8 1.0
CG A:LEU173 4.3 47.1 1.0
CB A:LEU173 4.6 43.5 1.0
CB A:ASP175 4.6 51.2 1.0
CG2 A:ILE93 4.6 44.0 1.0
CAH A:G6I401 4.6 57.9 1.0
CD2 A:LEU173 4.7 45.2 1.0
CG A:HIS155 4.8 43.8 1.0
CAK A:G6I401 4.9 59.4 1.0
CA A:LEU173 4.9 41.6 1.0
CG2 A:VAL94 4.9 45.2 1.0
CD1 A:LEU148 4.9 46.5 1.0

Fluorine binding site 2 out of 6 in 4equ

Go back to Fluorine Binding Sites List in 4equ
Fluorine binding site 2 out of 6 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:61.1
occ:1.00
 FAD A:G6I401 0.0 61.1 1.0
CBP A:G6I401 1.3 61.2 1.0
FAF A:G6I401 2.2 56.0 1.0
FAE A:G6I401 2.2 64.7 1.0
CBJ A:G6I401 2.3 58.0 1.0
CAU A:G6I401 3.1 54.5 1.0
CAL A:G6I401 3.2 58.4 1.0
CG2 A:ILE93 3.5 44.0 1.0
SG A:CYS88 4.2 67.7 1.0
CBI A:G6I401 4.4 53.6 1.0
CB A:CYS88 4.4 64.7 1.0
CAH A:G6I401 4.4 57.9 1.0
CD2 A:LEU148 4.5 50.0 1.0
CD2 A:LEU85 4.5 61.1 1.0
O A:LEU173 4.5 41.3 1.0
CG2 A:ILE84 4.6 66.7 1.0
CG2 A:VAL94 4.7 45.2 1.0
CB A:ILE93 4.8 44.4 1.0
CG1 A:ILE93 4.9 44.3 1.0
CAK A:G6I401 4.9 59.4 1.0
CD1 A:LEU148 5.0 46.5 1.0
CD1 A:ILE93 5.0 46.2 1.0

Fluorine binding site 3 out of 6 in 4equ

Go back to Fluorine Binding Sites List in 4equ
Fluorine binding site 3 out of 6 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:64.7
occ:1.00
 FAE A:G6I401 0.0 64.7 1.0
CBP A:G6I401 1.3 61.2 1.0
FAF A:G6I401 2.1 56.0 1.0
FAD A:G6I401 2.2 61.1 1.0
CBJ A:G6I401 2.4 58.0 1.0
CAL A:G6I401 2.8 58.4 1.0
CAU A:G6I401 3.6 54.5 1.0
CB A:LYS181 3.7 94.5 1.0
CD2 A:HIS155 3.8 43.1 1.0
CAH A:G6I401 4.1 57.9 1.0
CD1 A:LEU148 4.3 46.5 1.0
NE2 A:HIS155 4.4 44.6 1.0
CD2 A:LEU148 4.5 50.0 1.0
CG2 A:ILE84 4.5 66.7 1.0
CG A:HIS155 4.6 43.8 1.0
CBI A:G6I401 4.8 53.6 1.0
CG2 A:ILE153 4.9 53.8 1.0
CAK A:G6I401 5.0 59.4 1.0
CB A:HIS155 5.0 43.1 1.0

Fluorine binding site 4 out of 6 in 4equ

Go back to Fluorine Binding Sites List in 4equ
Fluorine binding site 4 out of 6 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:44.1
occ:1.00
 FAF B:G6I401 0.0 44.1 1.0
CBP B:G6I401 1.3 48.0 1.0
FAE B:G6I401 2.1 49.3 1.0
FAD B:G6I401 2.2 52.1 1.0
CBJ B:G6I401 2.3 48.4 1.0
CAU B:G6I401 2.8 42.5 1.0
O B:LEU173 3.5 29.7 1.0
CAL B:G6I401 3.6 48.4 1.0
CD2 B:HIS155 3.7 31.8 1.0
C B:ALA174 3.8 31.5 1.0
CA B:ALA174 3.8 31.6 1.0
C B:LEU173 3.9 31.0 1.0
O B:ALA174 3.9 29.3 1.0
NE2 B:HIS155 4.0 31.3 1.0
N B:ALA174 4.0 30.2 1.0
CBI B:G6I401 4.1 45.5 1.0
N B:ASP175 4.2 33.2 1.0
CG B:LEU173 4.3 38.8 1.0
CG2 B:ILE93 4.4 29.8 1.0
CB B:LEU173 4.5 33.2 1.0
CD2 B:LEU173 4.6 36.9 1.0
CAH B:G6I401 4.7 47.3 1.0
CB B:ASP175 4.7 37.5 1.0
CD1 B:LEU148 4.7 36.1 1.0
CA B:LEU173 4.9 33.0 1.0
CAK B:G6I401 4.9 47.6 1.0
CG2 B:VAL94 5.0 30.6 1.0
OAC B:G6I401 5.0 37.9 1.0
CG B:HIS155 5.0 32.9 1.0

Fluorine binding site 5 out of 6 in 4equ

Go back to Fluorine Binding Sites List in 4equ
Fluorine binding site 5 out of 6 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:52.1
occ:1.00
 FAD B:G6I401 0.0 52.1 1.0
CBP B:G6I401 1.3 48.0 1.0
FAF B:G6I401 2.2 44.1 1.0
FAE B:G6I401 2.2 49.3 1.0
CBJ B:G6I401 2.3 48.4 1.0
CAU B:G6I401 3.1 42.5 1.0
CAL B:G6I401 3.2 48.4 1.0
CG2 B:ILE93 3.5 29.8 1.0
SG B:CYS88 4.1 54.3 1.0
CBI B:G6I401 4.4 45.5 1.0
CD2 B:LEU85 4.4 46.0 1.0
CB B:CYS88 4.4 50.5 1.0
CAH B:G6I401 4.4 47.3 1.0
CD2 B:LEU148 4.5 36.8 1.0
CG2 B:ILE84 4.6 47.8 1.0
O B:LEU173 4.6 29.7 1.0
CD1 B:LEU148 4.7 36.1 1.0
CB B:ILE93 4.8 30.4 1.0
CAK B:G6I401 4.9 47.6 1.0
CG2 B:VAL94 4.9 30.6 1.0
CG1 B:ILE93 4.9 31.3 1.0

Fluorine binding site 6 out of 6 in 4equ

Go back to Fluorine Binding Sites List in 4equ
Fluorine binding site 6 out of 6 in the Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Stk-10 (Lok) Kinase Domain in Dfg-Out Conformation with Inhibitor Dsa-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:49.3
occ:1.00
 FAE B:G6I401 0.0 49.3 1.0
CBP B:G6I401 1.3 48.0 1.0
FAF B:G6I401 2.1 44.1 1.0
FAD B:G6I401 2.2 52.1 1.0
CBJ B:G6I401 2.4 48.4 1.0
CAL B:G6I401 2.8 48.4 1.0
CAU B:G6I401 3.6 42.5 1.0
CD2 B:HIS155 3.7 31.8 1.0
CD1 B:LEU148 3.9 36.1 1.0
CB B:LYS181 3.9 86.1 1.0
CAH B:G6I401 4.2 47.3 1.0
NE2 B:HIS155 4.4 31.3 1.0
CG B:HIS155 4.5 32.9 1.0
CD2 B:LEU148 4.5 36.8 1.0
CG2 B:ILE84 4.7 47.8 1.0
CBI B:G6I401 4.8 45.5 1.0
CG B:LEU148 4.9 37.1 1.0
CB B:HIS155 4.9 34.3 1.0
CAK B:G6I401 5.0 47.6 1.0
CG2 B:ILE153 5.0 46.0 1.0

Reference:

P.Ranjitkar, B.G.Perera, D.L.Swaney, S.B.Hari, E.T.Larson, R.Krishnamurty, E.A.Merritt, J.Villen, D.J.Maly. Affinity-Based Probes Based on Type II Kinase Inhibitors. J.Am.Chem.Soc. V. 134 19017 2012.
ISSN: ISSN 0002-7863
PubMed: 23088519
DOI: 10.1021/JA306035V
Page generated: Sun Dec 13 12:02:08 2020

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