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Fluorine in PDB 9dxs: Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine (pdb code 9dxs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine, PDB code: 9dxs:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 9dxs

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Fluorine binding site 1 out of 4 in the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:27.9
occ:1.00
FAC A:2J91001 0.0 27.9 1.0
CAK A:2J91001 1.4 27.9 1.0
CAD A:2J91001 2.4 27.9 1.0
CAF A:2J91001 2.4 27.9 1.0
CA D:GLY763 3.3 115.7 1.0
O D:LYS762 3.3 114.9 1.0
CG2 D:THR535 3.5 116.2 1.0
CB D:PRO532 3.6 116.7 1.0
CAE A:2J91001 3.6 27.9 1.0
CAM A:2J91001 3.7 27.9 1.0
C D:LYS762 3.8 114.9 1.0
N D:GLY763 3.8 115.7 1.0
CG D:PRO532 3.9 116.7 1.0
CA D:THR535 3.9 116.2 1.0
O D:MET534 4.0 123.6 1.0
CB D:THR535 4.1 116.2 1.0
CAL A:2J91001 4.1 27.9 1.0
C D:MET534 4.5 123.6 1.0
N D:THR535 4.5 116.2 1.0
C D:GLY763 4.6 115.7 1.0
CA D:LYS762 4.9 114.9 1.0

Fluorine binding site 2 out of 4 in 9dxs

Go back to Fluorine Binding Sites List in 9dxs
Fluorine binding site 2 out of 4 in the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:29.7
occ:1.00
FAC B:2J91001 0.0 29.7 1.0
CAK B:2J91001 1.4 29.7 1.0
CAD B:2J91001 2.4 29.7 1.0
CAF B:2J91001 2.4 29.7 1.0
O C:LYS762 3.2 112.0 1.0
CA C:GLY763 3.3 108.4 1.0
CB C:PRO532 3.5 98.8 1.0
CAE B:2J91001 3.6 29.7 1.0
CAM B:2J91001 3.7 29.7 1.0
CG C:PRO532 3.7 98.8 1.0
C C:LYS762 3.7 112.0 1.0
O C:MET534 3.8 102.4 1.0
N C:GLY763 3.8 108.4 1.0
CG2 C:THR535 3.9 105.2 1.0
CA C:THR535 4.1 105.2 1.0
CAL B:2J91001 4.1 29.7 1.0
CB C:THR535 4.3 105.2 1.0
C C:MET534 4.6 102.4 1.0
C C:GLY763 4.6 108.4 1.0
N C:THR535 4.7 105.2 1.0
CAD B:2J91004 4.9 68.5 1.0
CA C:LYS762 4.9 112.0 1.0
CD C:PRO532 5.0 98.8 1.0

Fluorine binding site 3 out of 4 in 9dxs

Go back to Fluorine Binding Sites List in 9dxs
Fluorine binding site 3 out of 4 in the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1004

b:68.5
occ:1.00
FAC B:2J91004 0.0 68.5 1.0
CAK B:2J91004 1.4 68.5 1.0
CAD B:2J91004 2.4 68.5 1.0
CAF B:2J91004 2.4 68.5 1.0
O B:LYS762 3.3 114.1 1.0
CA B:GLY763 3.3 115.2 1.0
CG2 B:THR535 3.4 115.7 1.0
CAE B:2J91004 3.6 68.5 1.0
CAM B:2J91004 3.7 68.5 1.0
CB B:PRO532 3.7 116.0 1.0
C B:LYS762 3.7 114.1 1.0
CA B:THR535 3.8 115.7 1.0
N B:GLY763 3.8 115.2 1.0
O B:MET534 3.9 123.2 1.0
CB B:THR535 3.9 115.7 1.0
CG B:PRO532 4.0 116.0 1.0
CAL B:2J91004 4.1 68.5 1.0
N B:THR535 4.4 115.7 1.0
C B:MET534 4.4 123.2 1.0
C B:GLY763 4.7 115.2 1.0
CA B:LYS762 4.9 114.1 1.0
C B:THR535 4.9 115.7 1.0
N B:LEU536 5.0 115.9 1.0
CAD B:2J91001 5.0 29.7 1.0

Fluorine binding site 4 out of 4 in 9dxs

Go back to Fluorine Binding Sites List in 9dxs
Fluorine binding site 4 out of 4 in the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with Positive Allosteric Modulator Bpam-344 and Channel Blocker Spermine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1002

b:27.7
occ:1.00
FAC D:2J91002 0.0 27.7 1.0
CAK D:2J91002 1.4 27.7 1.0
CAF D:2J91002 2.4 27.7 1.0
CAD D:2J91002 2.4 27.7 1.0
O A:LYS762 3.1 112.4 1.0
CA A:GLY763 3.3 108.4 1.0
CB A:PRO532 3.5 98.3 1.0
CAE D:2J91002 3.6 27.7 1.0
CAM D:2J91002 3.7 27.7 1.0
O A:MET534 3.7 103.5 1.0
C A:LYS762 3.7 112.4 1.0
CG A:PRO532 3.7 98.3 1.0
N A:GLY763 3.8 108.4 1.0
CG2 A:THR535 3.8 104.8 1.0
CA A:THR535 4.0 104.8 1.0
CAL D:2J91002 4.1 27.7 1.0
CB A:THR535 4.2 104.8 1.0
C A:MET534 4.4 103.5 1.0
C A:GLY763 4.5 108.4 1.0
N A:THR535 4.6 104.8 1.0
CAD A:2J91001 4.8 27.9 1.0
CA A:LYS762 4.9 112.4 1.0
N A:TYR764 5.0 104.2 1.0

Reference:

S.P.Gangwar, M.V.Yelshanskaya, M.Aktolun, L.Y.Yen, T.P.Newton, K.Stromgaard, M.G.Kurnikova, A.I.Sobolevsky. Trapping of Spermine, Kukoamine A, and Polyamine Toxin Blockers in GLUK2 Kainate Receptor Channels. Nat Commun V. 15 10257 2024.
ISSN: ESSN 2041-1723
PubMed: 39592599
DOI: 10.1038/S41467-024-54538-X
Page generated: Wed Jul 16 10:50:20 2025

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