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Fluorine in PDB 3cem: Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423

Enzymatic activity of Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423

All present enzymatic activity of Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423:
2.4.1.1;

Protein crystallography data

The structure of Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423, PDB code: 3cem was solved by K.U.Wendt, M.K.Dreyer, O.Anderka, T.Klabunde, P.Loenze, E.Defossa, D.Schmoll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 2.47
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 124.383, 124.383, 123.429, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 21.5

Other elements in 3cem:

The structure of Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423 (pdb code 3cem). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423, PDB code: 3cem:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3cem

Go back to Fluorine Binding Sites List in 3cem
Fluorine binding site 1 out of 4 in the Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F833

b:25.7
occ:1.00
 F11 A:AVD833 0.0 25.7 1.0
C5 A:AVD833 1.3 24.1 1.0
C4 A:AVD833 2.3 22.4 1.0
C6 A:AVD833 2.3 23.3 1.0
CB A:LYS191 3.1 29.4 1.0
CH2 A:TRP67 3.5 23.0 1.0
CG A:LYS191 3.5 34.8 1.0
C3 A:AVD833 3.5 23.2 1.0
C1 A:AVD833 3.6 25.8 1.0
CB A:ASP227 3.7 18.4 1.0
CZ3 A:TRP67 3.8 24.5 1.0
CD A:ARG193 3.8 25.3 1.0
CZ2 A:TRP67 3.9 21.8 1.0
C2 A:AVD833 4.1 25.0 1.0
OD1 A:ASP227 4.2 24.8 1.0
CA A:LYS191 4.4 27.9 1.0
O A:LYS191 4.4 27.4 1.0
O A:ASP227 4.4 18.5 1.0
NH1 A:ARG193 4.4 27.0 1.0
NE A:ARG193 4.4 23.7 1.0
CG A:ASP227 4.5 21.6 1.0
CB B:VAL40 4.5 23.6 1.0
CG2 B:VAL40 4.5 22.1 1.0
CE3 A:TRP67 4.5 21.4 1.0
CE2 A:TRP67 4.6 19.8 1.0
F9 A:AVD833 4.7 28.2 1.0
C A:LYS191 4.7 26.4 1.0
CZ A:ARG193 4.7 25.2 1.0
CG1 B:VAL40 4.7 22.3 1.0
N A:LYS191 4.8 27.6 1.0
CA A:ASP227 4.8 18.9 1.0
C A:ASP227 4.8 19.0 1.0
CG A:ARG193 4.9 23.1 1.0
CD2 A:TRP67 4.9 22.1 1.0
CL12 A:AVD833 4.9 28.9 1.0

Fluorine binding site 2 out of 4 in 3cem

Go back to Fluorine Binding Sites List in 3cem
Fluorine binding site 2 out of 4 in the Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F833

b:28.2
occ:1.00
 F9 A:AVD833 0.0 28.2 1.0
C1 A:AVD833 1.3 25.8 1.0
C2 A:AVD833 2.3 25.0 1.0
C6 A:AVD833 2.4 23.3 1.0
N10 A:AVD833 2.7 26.1 1.0
O B:VAL40 2.8 23.5 1.0
CE B:LYS41 3.0 26.5 1.0
O B:LEU39 3.2 22.1 1.0
CD B:LYS41 3.2 27.0 1.0
CG B:LYS41 3.4 26.4 1.0
C13 A:AVD833 3.5 27.7 1.0
NH2 A:ARG193 3.5 22.5 1.0
C B:VAL40 3.5 23.8 1.0
C5 A:AVD833 3.6 24.1 1.0
C3 A:AVD833 3.6 23.2 1.0
O B:HOH948 3.7 28.8 1.0
CZ A:ARG193 3.8 25.2 1.0
C18 A:AVD833 4.0 25.6 1.0
NE A:ARG193 4.1 23.7 1.0
CB B:VAL40 4.1 23.6 1.0
C4 A:AVD833 4.1 22.4 1.0
N B:LYS41 4.2 24.1 1.0
O A:HOH909 4.2 29.5 1.0
CA B:LYS41 4.3 26.4 1.0
CA B:VAL40 4.3 22.8 1.0
NZ B:LYS41 4.3 28.0 1.0
NH1 A:ARG193 4.3 27.0 1.0
C B:LEU39 4.4 21.6 1.0
C14 A:AVD833 4.4 27.3 1.0
CB B:LYS41 4.4 26.8 1.0
CG1 B:VAL40 4.6 22.3 1.0
O A:HOH988 4.7 35.5 1.0
F11 A:AVD833 4.7 25.7 1.0
CL29 A:AVD833 4.8 31.0 1.0
N B:VAL40 4.9 21.0 1.0
CD A:ARG193 5.0 25.3 1.0

Fluorine binding site 3 out of 4 in 3cem

Go back to Fluorine Binding Sites List in 3cem
Fluorine binding site 3 out of 4 in the Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F833

b:24.9
occ:1.00
 F11 B:AVD833 0.0 24.9 1.0
C5 B:AVD833 1.3 23.9 1.0
C4 B:AVD833 2.3 21.9 1.0
C6 B:AVD833 2.3 25.4 1.0
CB B:LYS191 3.2 24.5 1.0
CH2 B:TRP67 3.3 23.3 1.0
CB B:ASP227 3.4 22.9 1.0
C3 B:AVD833 3.6 20.7 1.0
C1 B:AVD833 3.6 26.1 1.0
CZ3 B:TRP67 3.6 23.2 1.0
CD B:ARG193 3.7 22.2 1.0
CZ2 B:TRP67 3.8 22.9 1.0
OD1 B:ASP227 4.0 24.1 1.0
C2 B:AVD833 4.1 21.9 1.0
O B:ASP227 4.2 22.6 1.0
CG B:LYS191 4.2 28.6 1.0
CG B:ASP227 4.2 24.3 1.0
O B:LYS191 4.3 20.6 1.0
CA B:LYS191 4.3 23.5 1.0
NE B:ARG193 4.4 19.4 1.0
CG2 A:VAL40 4.5 20.0 1.0
CD B:LYS191 4.5 30.6 1.0
NH1 B:ARG193 4.5 17.9 1.0
CE3 B:TRP67 4.5 21.6 1.0
CA B:ASP227 4.5 23.0 1.0
N B:LYS191 4.6 24.8 1.0
CE2 B:TRP67 4.6 20.3 1.0
C B:ASP227 4.6 23.1 1.0
CB A:VAL40 4.6 22.3 1.0
C B:LYS191 4.7 22.1 1.0
F9 B:AVD833 4.7 26.2 1.0
CZ B:ARG193 4.8 22.0 1.0
CG B:ARG193 4.9 20.4 1.0
CG1 A:VAL40 4.9 22.2 1.0
CD2 B:TRP67 4.9 21.9 1.0
O B:HOH870 4.9 27.1 1.0
N B:ASP227 5.0 23.6 1.0
CL12 B:AVD833 5.0 28.0 1.0

Fluorine binding site 4 out of 4 in 3cem

Go back to Fluorine Binding Sites List in 3cem
Fluorine binding site 4 out of 4 in the Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Glycogen Phosphorylase (Tense State) in Complex with the Allosteric Inhibitor AVE9423 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F833

b:26.2
occ:1.00
 F9 B:AVD833 0.0 26.2 1.0
C1 B:AVD833 1.4 26.1 1.0
C2 B:AVD833 2.4 21.9 1.0
C6 B:AVD833 2.4 25.4 1.0
N10 B:AVD833 2.7 26.8 1.0
CE A:LYS41 2.8 29.1 1.0
O A:VAL40 3.1 22.6 1.0
CD A:LYS41 3.3 32.0 1.0
O A:LEU39 3.4 20.7 1.0
NH2 B:ARG193 3.4 18.6 1.0
CG A:LYS41 3.4 26.7 1.0
C13 B:AVD833 3.5 28.2 1.0
CZ B:ARG193 3.6 22.0 1.0
C3 B:AVD833 3.6 20.7 1.0
C5 B:AVD833 3.7 23.9 1.0
NE B:ARG193 3.7 19.4 1.0
C A:VAL40 3.8 22.6 1.0
C18 B:AVD833 4.0 28.9 1.0
CB A:VAL40 4.1 22.3 1.0
NZ A:LYS41 4.1 30.3 1.0
C4 B:AVD833 4.2 21.9 1.0
NH1 B:ARG193 4.3 17.9 1.0
CA A:VAL40 4.5 21.7 1.0
N A:LYS41 4.5 23.1 1.0
C A:LEU39 4.5 20.7 1.0
C14 B:AVD833 4.5 29.6 1.0
CB A:LYS41 4.6 24.7 1.0
CA A:LYS41 4.6 25.3 1.0
CD B:ARG193 4.7 22.2 1.0
F11 B:AVD833 4.7 24.9 1.0
O B:HOH926 4.8 19.5 1.0
CG1 A:VAL40 4.9 22.2 1.0
N A:VAL40 5.0 21.8 1.0

Reference:

O.Anderka, P.Loenze, T.Klabunde, M.K.Dreyer, E.Defossa, K.U.Wendt, D.Schmoll. Thermodynamic Characterization of Allosteric Glycogen Phosphorylase Inhibitors. Biochemistry V. 47 4683 2008.
ISSN: ISSN 0006-2960
PubMed: 18373353
DOI: 10.1021/BI702397D
Page generated: Sun Dec 13 11:43:53 2020

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