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Fluorine in PDB 5mfw: Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution

Protein crystallography data

The structure of Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution, PDB code: 5mfw was solved by A.P.Larsen, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.63 / 2.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.644, 68.644, 234.854, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 21.9

Other elements in 5mfw:

The structure of Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution (pdb code 5mfw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution, PDB code: 5mfw:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5mfw

Go back to Fluorine Binding Sites List in 5mfw
Fluorine binding site 1 out of 2 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:24.4
occ:0.69
F1 A:7M6901 0.0 24.4 0.7
C9 A:7M6901 1.3 18.4 0.7
C8 A:7M6901 2.3 21.0 0.7
O A:HOH1072 2.9 30.8 1.0
O A:HOH1122 3.1 20.7 1.0
CG2 A:THR535 3.2 21.7 0.6
C7 A:7M6901 3.3 15.8 0.7
N1 A:7M6901 3.4 18.4 0.7
CA A:MET534 3.6 16.0 1.0
O A:HOH1208 3.6 32.5 1.0
O A:PHE533 3.7 11.4 1.0
N A:THR535 3.7 13.5 1.0
C2 A:7M6901 3.7 16.3 0.7
N A:MET534 3.8 10.7 1.0
CG2 A:THR535 3.8 16.5 0.4
C A:PHE533 3.8 10.3 1.0
C A:MET534 3.8 17.5 1.0
OG B:SER761 4.2 27.1 1.0
OG1 A:THR535 4.3 24.7 0.4
C6 A:7M6901 4.4 18.2 0.7
CB A:THR535 4.4 21.9 0.6
CB A:THR535 4.4 21.5 0.4
O A:PRO532 4.5 11.9 1.0
CB B:SER761 4.6 15.9 1.0
CA A:THR535 4.6 16.0 0.6
C3 A:7M6901 4.6 17.1 0.7
CA A:THR535 4.6 16.0 0.4
O A:MET534 4.7 13.3 1.0
CA A:PHE533 4.8 7.6 1.0
CB A:MET534 5.0 10.6 1.0
CL1 B:7M6901 5.0 22.0 0.6
CG A:GLN786 5.0 25.2 1.0

Fluorine binding site 2 out of 2 in 5mfw

Go back to Fluorine Binding Sites List in 5mfw
Fluorine binding site 2 out of 2 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:17.0
occ:0.61
F1 B:7M6901 0.0 17.0 0.6
C9 B:7M6901 1.3 15.8 0.6
C8 B:7M6901 2.4 14.7 0.6
C7 B:7M6901 2.9 13.8 0.6
N1 B:7M6901 2.9 14.8 0.6
CG2 B:THR535 3.0 14.8 0.7
CG2 B:THR535 3.2 14.7 0.3
C2 B:7M6901 3.2 13.7 0.6
N B:MET534 3.3 7.3 1.0
CA B:MET534 3.3 9.5 1.0
C B:MET534 3.4 12.8 1.0
N B:THR535 3.4 12.9 1.0
C B:PHE533 3.6 7.0 1.0
O B:PHE533 3.8 8.0 1.0
O B:PRO532 3.9 7.4 1.0
O B:HOH1152 3.9 16.2 1.0
OG A:SER761 4.0 17.7 1.0
C6 B:7M6901 4.0 19.1 0.6
O B:MET534 4.0 12.1 1.0
CB B:THR535 4.2 17.5 0.3
C3 B:7M6901 4.2 20.0 0.6
C B:PRO532 4.2 9.1 1.0
CB B:THR535 4.2 17.6 0.7
CA B:THR535 4.3 14.2 0.3
CA B:THR535 4.3 14.1 0.7
CL1 A:7M6901 4.3 19.3 0.7
CA B:PHE533 4.3 6.2 1.0
CB B:PRO532 4.4 7.4 1.0
C1 B:7M6901 4.5 15.9 0.6
OG1 B:THR535 4.5 22.8 0.3
O B:HOH1215 4.5 24.3 1.0
N B:PHE533 4.5 10.6 1.0
CB A:SER761 4.8 14.2 1.0
CB B:MET534 4.8 12.8 1.0
CG B:PRO532 4.8 13.8 1.0
N2 B:7M6901 4.9 13.8 0.6

Reference:

A.P.Larsen, S.Fievre, K.Frydenvang, P.Francotte, B.Pirotte, J.S.Kastrup, C.Mulle. Identification and Structure-Function Study of Positive Allosteric Modulators of Kainate Receptors. Mol. Pharmacol. V. 91 576 2017.
ISSN: ESSN 1521-0111
PubMed: 28360094
DOI: 10.1124/MOL.116.107599
Page generated: Sun Dec 13 12:27:57 2020

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