Fluorine in PDB 8g18: Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108

Protein crystallography data

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108, PDB code: 8g18 was solved by M.C.Regan, H.Furukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.37 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 269.172, 60.076, 145.572, 90, 117.02, 90
R / Rfree (%) 17.4 / 24.6

Other elements in 8g18:

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108 (pdb code 8g18). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108, PDB code: 8g18:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8g18

Go back to Fluorine Binding Sites List in 8g18
Fluorine binding site 1 out of 4 in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:41.9
occ:1.00
F29 B:YGW503 0.0 41.9 1.0
C04 B:YGW503 1.4 38.0 1.0
C05 B:YGW503 2.3 37.3 1.0
C03 B:YGW503 2.4 38.6 1.0
F30 B:YGW503 2.7 50.4 1.0
CB B:PRO78 3.3 23.8 1.0
CG B:PRO78 3.5 23.7 1.0
CA A:THR110 3.5 19.9 1.0
OG1 A:THR110 3.5 20.3 1.0
C06 B:YGW503 3.6 37.5 1.0
C02 B:YGW503 3.6 37.6 1.0
CB A:THR110 3.8 20.6 1.0
CG2 A:THR110 3.9 22.0 1.0
N A:THR110 4.0 19.2 1.0
C01 B:YGW503 4.1 37.4 1.0
C A:TYR109 4.3 19.2 1.0
O A:TYR109 4.4 18.0 1.0
CA B:PRO78 4.5 24.5 1.0
C A:THR110 4.6 19.6 1.0
CG1 B:ILE111 4.7 17.4 1.0
O A:THR110 4.7 17.8 1.0
N07 B:YGW503 4.7 41.3 1.0
CB A:PHE113 4.9 23.2 1.0
CB A:TYR109 4.9 17.9 1.0
CD B:PRO78 5.0 24.0 1.0

Fluorine binding site 2 out of 4 in 8g18

Go back to Fluorine Binding Sites List in 8g18
Fluorine binding site 2 out of 4 in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:50.4
occ:1.00
F30 B:YGW503 0.0 50.4 1.0
C03 B:YGW503 1.3 38.6 1.0
C02 B:YGW503 2.3 37.6 1.0
C04 B:YGW503 2.3 38.0 1.0
F29 B:YGW503 2.7 41.9 1.0
CD2 B:PHE114 3.5 19.3 1.0
C01 B:YGW503 3.5 37.4 1.0
C05 B:YGW503 3.6 37.3 1.0
CE2 B:PHE114 3.6 19.5 1.0
CD1 B:ILE82 3.7 33.6 1.0
C06 B:YGW503 4.0 37.5 1.0
CG B:PHE114 4.2 19.5 1.0
CB A:ALA75 4.2 23.0 1.0
CZ B:PHE114 4.4 20.5 1.0
OG1 A:THR110 4.5 20.3 1.0
CG2 B:ILE111 4.6 17.2 1.0
CG1 B:ILE82 4.7 31.8 1.0
CB B:PHE114 4.8 19.8 1.0
CB B:PRO78 4.8 23.8 1.0
CD1 B:PHE114 4.9 19.8 1.0
CG1 B:ILE111 4.9 17.4 1.0
CE1 B:PHE114 4.9 19.9 1.0
CA B:ILE111 5.0 18.0 1.0

Fluorine binding site 3 out of 4 in 8g18

Go back to Fluorine Binding Sites List in 8g18
Fluorine binding site 3 out of 4 in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F503

b:76.9
occ:1.00
F29 D:YGW503 0.0 76.9 1.0
C04 D:YGW503 1.4 72.0 1.0
C05 D:YGW503 2.3 69.0 1.0
C03 D:YGW503 2.4 73.4 1.0
F30 D:YGW503 2.8 91.5 1.0
CB D:PRO78 3.0 52.2 1.0
CG D:PRO78 3.2 49.6 1.0
CA C:THR110 3.4 40.9 1.0
OG1 C:THR110 3.5 46.2 1.0
CG2 C:THR110 3.6 49.3 1.0
C06 D:YGW503 3.6 66.8 1.0
CB C:THR110 3.7 47.7 1.0
C02 D:YGW503 3.7 69.2 1.0
N C:THR110 4.1 36.1 1.0
C01 D:YGW503 4.1 68.3 1.0
O C:TYR109 4.3 34.2 1.0
C C:TYR109 4.3 33.1 1.0
CA D:PRO78 4.4 52.4 1.0
C C:THR110 4.4 41.2 1.0
O C:THR110 4.4 37.2 1.0
CB C:PHE113 4.5 37.1 1.0
CD D:PRO78 4.7 48.6 1.0
N07 D:YGW503 4.8 67.8 1.0
CG C:PHE113 4.8 37.9 1.0
CG1 D:ILE111 5.0 41.1 1.0
CB C:TYR109 5.0 32.2 1.0

Fluorine binding site 4 out of 4 in 8g18

Go back to Fluorine Binding Sites List in 8g18
Fluorine binding site 4 out of 4 in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F503

b:91.5
occ:1.00
F30 D:YGW503 0.0 91.5 1.0
C03 D:YGW503 1.3 73.4 1.0
C02 D:YGW503 2.3 69.2 1.0
C04 D:YGW503 2.4 72.0 1.0
F29 D:YGW503 2.8 76.9 1.0
C01 D:YGW503 3.6 68.3 1.0
C05 D:YGW503 3.6 69.0 1.0
CD1 D:ILE82 3.6 48.2 1.0
C06 D:YGW503 4.1 66.8 1.0
CD2 D:PHE114 4.1 42.8 1.0
CB D:PRO78 4.1 52.2 1.0
CE2 D:PHE114 4.2 38.2 1.0
CG2 D:ILE111 4.3 37.9 1.0
OG1 C:THR110 4.3 46.2 1.0
CB C:ALA75 4.4 44.4 1.0
CG1 D:ILE82 4.6 49.4 1.0
CG1 D:ILE111 4.6 41.1 1.0
CG D:PHE114 4.8 39.7 1.0
CZ D:PHE114 4.9 40.4 1.0
CB D:ILE111 4.9 39.0 1.0
CA D:PRO78 5.0 52.4 1.0

Reference:

L.D.Harris, M.C.Regan, S.J.Myers, K.A.Nocilla, N.S.Akins, Y.A.Tahirovic, L.J.Wilson, R.Dingledine, H.Furukawa, S.F.Traynelis, D.C.Liotta. Novel GLUN2B-Selective Nmda Receptor Negative Allosteric Modulator Possesses Intrinsic Analgesic Properties and Enhances Analgesia of Morphine in A Rodent Tail Flick Pain Model. Acs Chem Neurosci 2023.
ISSN: ESSN 1948-7193
PubMed: 36779874
DOI: 10.1021/ACSCHEMNEURO.2C00779
Page generated: Wed Apr 5 02:31:46 2023

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