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Fluorine in PDB 3m3l: Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)

Protein crystallography data

The structure of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form), PDB code: 3m3l was solved by C.P.Ptak, A.H.Ahmed, R.E.Oswald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.29 / 1.85
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.127, 113.924, 164.806, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.2

Other elements in 3m3l:

The structure of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) also contains other interesting chemical elements:

Zinc (Zn) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) (pdb code 3m3l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form), PDB code: 3m3l:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3m3l

Go back to Fluorine Binding Sites List in 3m3l
Fluorine binding site 1 out of 6 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F800

b:27.8
occ:0.50
 F08 A:P99800 0.0 27.8 0.5
C07 A:P99800 1.4 24.5 0.5
C24 A:P99800 2.0 23.6 0.5
O17 A:P99800 2.2 26.7 0.5
C12 A:P99800 2.4 24.6 0.5
C06 A:P99800 2.5 23.5 0.5
C09 A:P99800 2.5 22.6 0.5
O D:LYS218 2.5 16.5 1.0
C D:LYS218 2.6 17.7 1.0
C13 A:P99800 2.6 25.6 0.5
N14 A:P99800 2.7 24.5 0.5
O05 A:P99800 2.9 25.0 0.5
S15 A:P99800 3.0 27.8 0.5
N D:GLY219 3.0 16.9 1.0
C25 A:P99800 3.1 22.7 0.5
C10 A:P99800 3.1 23.1 0.5
CA D:LYS218 3.2 18.9 1.0
F26 A:P99800 3.3 24.6 0.5
S11 A:P99800 3.4 28.0 0.5
CA D:GLY219 3.4 17.0 1.0
O03 A:P99800 3.7 27.0 0.5
O D:HOH292 3.7 24.4 1.0
C10 A:P99800 3.9 24.1 0.5
C04 A:P99800 3.9 24.9 0.5
C25 A:P99800 3.9 21.9 0.5
N D:LYS218 3.9 16.9 1.0
C18 A:P99800 4.0 23.4 0.5
C02 A:P99800 4.2 25.3 0.5
C19 A:P99800 4.3 21.4 0.5
O16 A:P99800 4.3 24.4 0.5
C24 A:P99800 4.5 23.2 0.5
CB D:LYS218 4.5 19.3 1.0
C06 A:P99800 4.5 23.9 0.5
C09 A:P99800 4.5 22.7 0.5
C D:SER217 4.6 22.2 1.0
CG D:PRO105 4.6 22.0 1.0
O D:SER217 4.7 23.8 1.0
CB D:PRO105 4.8 21.3 1.0
C D:GLY219 4.8 15.3 1.0
O A:HOH575 4.8 31.1 1.0

Fluorine binding site 2 out of 6 in 3m3l

Go back to Fluorine Binding Sites List in 3m3l
Fluorine binding site 2 out of 6 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F800

b:28.3
occ:0.50
 F08 A:P99800 0.0 28.3 0.5
C07 A:P99800 1.4 23.3 0.5
C12 A:P99800 1.8 20.8 0.5
C24 A:P99800 2.1 23.2 0.5
O17 A:P99800 2.3 18.1 0.5
C13 A:P99800 2.4 20.1 0.5
C06 A:P99800 2.5 23.9 0.5
C09 A:P99800 2.5 22.7 0.5
N14 A:P99800 2.6 17.4 0.5
C10 A:P99800 2.8 24.1 0.5
O A:LYS218 2.9 16.7 1.0
S11 A:P99800 2.9 25.4 0.5
C A:LYS218 2.9 16.6 1.0
O05 A:P99800 2.9 25.1 0.5
O03 A:P99800 3.0 25.9 0.5
S15 A:P99800 3.0 14.6 0.5
O A:HOH308 3.3 23.4 1.0
CA A:LYS218 3.3 18.4 1.0
C25 A:P99800 3.3 21.9 0.5
N A:GLY219 3.5 15.7 1.0
C04 A:P99800 3.6 25.4 0.5
C02 A:P99800 3.7 26.2 0.5
F26 A:P99800 3.7 20.1 0.5
N A:LYS218 3.9 17.9 1.0
C25 A:P99800 3.9 22.7 0.5
C10 A:P99800 3.9 23.1 0.5
CA A:GLY219 4.0 16.4 1.0
C18 A:P99800 4.2 14.7 0.5
O16 A:P99800 4.2 19.7 0.5
O A:SER217 4.3 20.7 1.0
C A:SER217 4.3 23.2 1.0
C09 A:P99800 4.3 22.6 0.5
C24 A:P99800 4.5 23.6 0.5
OG A:SER217 4.5 28.3 1.0
C19 A:P99800 4.6 15.7 0.5
CB A:LYS218 4.7 19.9 1.0
C06 A:P99800 4.7 23.5 0.5
CG A:PRO105 4.8 20.4 1.0
CB A:SER108 5.0 20.1 1.0

Fluorine binding site 3 out of 6 in 3m3l

Go back to Fluorine Binding Sites List in 3m3l
Fluorine binding site 3 out of 6 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F800

b:20.1
occ:0.50
 F26 A:P99800 0.0 20.1 0.5
C25 A:P99800 1.3 21.9 0.5
C09 A:P99800 1.6 22.7 0.5
C10 A:P99800 2.1 23.1 0.5
S11 A:P99800 2.5 28.0 0.5
C24 A:P99800 2.5 23.2 0.5
C06 A:P99800 2.5 23.5 0.5
O A:MET107 2.9 16.6 1.0
O05 A:P99800 3.0 25.0 0.5
C07 A:P99800 3.0 23.3 0.5
C A:MET107 3.1 17.6 1.0
CA A:SER108 3.2 16.5 1.0
CB A:PRO105 3.2 18.0 1.0
N A:SER108 3.2 16.3 1.0
C04 A:P99800 3.3 24.9 0.5
CB A:SER108 3.5 20.1 1.0
CG A:PRO105 3.5 20.4 1.0
CA A:GLY219 3.6 16.4 1.0
C24 A:P99800 3.6 23.6 0.5
F08 A:P99800 3.7 28.3 0.5
C10 A:P99800 3.9 24.1 0.5
C07 A:P99800 3.9 24.5 0.5
O A:LYS218 3.9 16.7 1.0
N A:MET107 4.1 16.0 1.0
CA A:MET107 4.1 16.6 1.0
O17 A:P99800 4.2 18.1 0.5
C06 A:P99800 4.2 23.9 0.5
C12 A:P99800 4.2 24.6 0.5
N14 A:P99800 4.3 24.5 0.5
CA A:PRO105 4.4 15.4 1.0
N A:GLY219 4.4 15.7 1.0
C09 A:P99800 4.4 22.6 0.5
C25 A:P99800 4.5 22.7 0.5
C A:LYS218 4.5 16.6 1.0
C A:PRO105 4.5 17.1 1.0
C A:SER108 4.6 17.4 1.0
C A:GLY219 4.7 15.4 1.0
O A:PRO105 4.7 16.5 1.0
OG A:SER108 4.7 27.0 1.0
N A:TYR220 4.7 13.9 1.0
C02 A:P99800 4.8 25.3 0.5
O A:HOH308 4.8 23.4 1.0
C13 A:P99800 4.8 25.6 0.5
O A:HOH575 5.0 31.1 1.0

Fluorine binding site 4 out of 6 in 3m3l

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Fluorine binding site 4 out of 6 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F800

b:24.6
occ:0.50
 F26 A:P99800 0.0 24.6 0.5
C25 A:P99800 1.4 22.7 0.5
C09 A:P99800 1.4 22.6 0.5
C10 A:P99800 2.3 24.1 0.5
C24 A:P99800 2.5 23.6 0.5
C06 A:P99800 2.5 23.9 0.5
O D:MET107 2.7 17.1 1.0
C07 A:P99800 2.7 24.5 0.5
S11 A:P99800 2.8 25.4 0.5
O05 A:P99800 2.9 25.1 0.5
CA D:SER108 3.0 20.2 1.0
C D:MET107 3.0 20.7 1.0
N D:SER108 3.1 17.4 1.0
CA D:GLY219 3.3 17.0 1.0
F08 A:P99800 3.3 27.8 0.5
O D:LYS218 3.3 16.5 1.0
CB D:SER108 3.4 22.4 1.0
CB D:PRO105 3.4 21.3 1.0
C04 A:P99800 3.6 25.4 0.5
C24 A:P99800 3.8 23.2 0.5
CG D:PRO105 3.9 22.0 1.0
C10 A:P99800 3.9 23.1 0.5
C07 A:P99800 3.9 23.3 0.5
O17 A:P99800 4.0 26.7 0.5
C06 A:P99800 4.1 23.5 0.5
C D:LYS218 4.1 17.7 1.0
N D:GLY219 4.1 16.9 1.0
CA D:MET107 4.1 18.8 1.0
N D:MET107 4.2 17.1 1.0
C D:SER108 4.3 19.9 1.0
C D:GLY219 4.4 15.3 1.0
C25 A:P99800 4.5 21.9 0.5
C09 A:P99800 4.5 22.7 0.5
N D:TYR220 4.5 14.5 1.0
C12 A:P99800 4.6 20.8 0.5
OG D:SER108 4.6 28.0 1.0
O D:HOH292 4.6 24.4 1.0
N14 A:P99800 4.7 17.4 0.5
CA D:PRO105 4.7 17.3 1.0
N D:LEU109 4.8 17.6 1.0
C D:PRO105 4.8 18.9 1.0

Fluorine binding site 5 out of 6 in 3m3l

Go back to Fluorine Binding Sites List in 3m3l
Fluorine binding site 5 out of 6 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F801

b:27.8
occ:0.50
 F08 G:P99801 0.0 27.8 0.5
C07 G:P99801 1.4 24.5 0.5
C06 G:P99801 2.5 23.5 0.5
C09 G:P99801 2.5 22.6 0.5
O05 G:P99801 2.9 25.0 0.5
O03 G:P99801 3.7 27.0 0.5
C10 G:P99801 3.9 24.1 0.5
C04 G:P99801 3.9 24.9 0.5
C25 G:P99801 3.9 21.9 0.5
C02 G:P99801 4.2 25.3 0.5
C24 G:P99801 4.5 23.2 0.5
ND2 G:ASN242 4.6 24.8 1.0

Fluorine binding site 6 out of 6 in 3m3l

Go back to Fluorine Binding Sites List in 3m3l
Fluorine binding site 6 out of 6 in the Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Pepa Bound to the Ligand Binding Domain of GLUA2 (Flop Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F801

b:20.1
occ:0.50
 F26 G:P99801 0.0 20.1 0.5
C25 G:P99801 1.4 21.9 0.5
C24 G:P99801 2.5 23.2 0.5
C06 G:P99801 2.5 23.5 0.5
CA G:SER108 2.8 18.6 1.0
CB G:SER108 2.9 21.4 1.0
N G:SER108 2.9 17.1 1.0
O05 G:P99801 3.0 25.0 0.5
O G:MET107 3.2 17.9 1.0
C G:MET107 3.2 19.6 1.0
C04 G:P99801 3.3 24.9 0.5
O G:LYS218 3.8 15.5 1.0
OG G:SER108 3.8 27.2 1.0
C10 G:P99801 3.9 24.1 0.5
C07 G:P99801 3.9 24.5 0.5
O G:HOH353 4.1 25.6 1.0
O17 G:P99801 4.2 18.1 0.5
CA G:GLY219 4.2 14.8 1.0
CB G:PRO105 4.2 16.3 1.0
CA G:MET107 4.2 18.7 1.0
C G:SER108 4.3 21.4 1.0
C09 G:P99801 4.4 22.6 0.5
N G:MET107 4.5 15.3 1.0
CG G:PRO105 4.5 17.6 1.0
C G:LYS218 4.6 16.5 1.0
C02 G:P99801 4.8 25.3 0.5
N G:LEU109 4.8 18.1 1.0
N G:GLY219 4.8 13.3 1.0
O G:HOH413 4.9 23.6 1.0

Reference:

A.H.Ahmed, C.P.Ptak, R.E.Oswald. Molecular Mechanism of Flop Selectivity and Subsite Recognition For An Ampa Receptor Allosteric Modulator: Structures of GLUA2 and GLUA3 in Complexes with Pepa. Biochemistry V. 49 2843 2010.
ISSN: ISSN 0006-2960
PubMed: 20199107
DOI: 10.1021/BI1000678
Page generated: Wed Jul 31 20:39:43 2024

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