Fluorine in PDB 4idq: Human Atlastin-1 1-446, N440T, GDPALF4-

The structure of Human Atlastin-1 1-446, N440T, GDPALF4-, PDB code: 4idq was solved by L.J.Byrnes, A.Singh, K.Szeto, N.M.Benvin, J.P.O'donnell, W.R.Zipfel, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.14 / 2.29
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.993, 267.084, 62.052, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.6

The structure of Human Atlastin-1 1-446, N440T, GDPALF4- also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Aluminium	(Al)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine atom in the Human Atlastin-1 1-446, N440T, GDPALF4- (pdb code 4idq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Human Atlastin-1 1-446, N440T, GDPALF4-, PDB code: 4idq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in the Human Atlastin-1 1-446, N440T, GDPALF4-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Atlastin-1 1-446, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:25.0 occ:1.00 F1 A:ALF502 0.0 25.0 1.0 AL A:ALF502 1.8 13.1 1.0 F3 A:ALF502 2.5 12.9 1.0 F4 A:ALF502 2.5 18.8 1.0 N A:GLU119 2.6 15.6 1.0 O3B A:GDP501 2.6 16.6 1.0 NH2 A:ARG77 2.7 16.1 1.0 O A:HOH605 2.8 14.2 1.0 N A:THR120 3.0 16.7 1.0 O A:HOH604 3.2 12.7 1.0 CA A:GLU119 3.2 16.6 1.0 CB A:GLU119 3.3 15.6 1.0 MG A:MG503 3.5 16.0 1.0 CZ A:ARG77 3.5 20.7 1.0 NE A:ARG77 3.5 24.3 1.0 F2 A:ALF502 3.6 18.6 1.0 C A:GLU119 3.6 16.8 1.0 C A:ARG118 3.6 15.4 1.0 PB A:GDP501 3.8 13.3 1.0 CA A:ARG118 3.9 15.1 1.0 OG1 A:THR120 3.9 14.7 1.0 O2B A:GDP501 4.0 14.9 1.0 CA A:THR120 4.1 18.9 1.0 CB A:THR120 4.2 14.8 1.0 O2A A:GDP501 4.4 17.0 1.0 CB A:ARG118 4.4 21.0 1.0 O A:THR120 4.4 21.2 1.0 CG A:GLU119 4.5 15.9 1.0 O3A A:GDP501 4.6 31.8 1.0 O A:GLU119 4.8 21.6 1.0 O A:ARG118 4.8 18.6 1.0 NH1 A:ARG77 4.8 18.0 1.0 C A:THR120 4.8 22.3 1.0 N A:ARG77 4.8 20.8 1.0 CD A:ARG77 4.9 24.3 1.0

Fluorine binding site 2 out of 16 in the Human Atlastin-1 1-446, N440T, GDPALF4-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Atlastin-1 1-446, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:18.6 occ:1.00 F2 A:ALF502 0.0 18.6 1.0 AL A:ALF502 1.8 13.1 1.0 F4 A:ALF502 2.5 18.8 1.0 NZ A:LYS80 2.5 12.6 1.0 F3 A:ALF502 2.6 12.9 1.0 O3B A:GDP501 2.7 16.6 1.0 O A:HOH605 2.7 14.2 1.0 N A:GLY149 2.9 17.9 1.0 CA A:GLY149 3.0 18.2 1.0 CA A:PHE76 3.2 18.5 1.0 CB A:PHE76 3.4 14.1 1.0 N A:ARG77 3.5 20.8 1.0 CE A:LYS80 3.5 12.2 1.0 O1B A:GDP501 3.5 14.1 1.0 PB A:GDP501 3.5 13.3 1.0 F1 A:ALF502 3.6 25.0 1.0 C A:PHE76 3.9 16.9 1.0 O A:HOH603 3.9 12.1 1.0 O2B A:GDP501 4.0 14.9 1.0 MG A:MG503 4.1 16.0 1.0 C A:GLN148 4.2 15.2 1.0 N A:PHE76 4.3 21.2 1.0 C A:GLY149 4.3 18.0 1.0 O A:HOH601 4.4 13.5 1.0 O A:ALA75 4.4 22.4 1.0 O A:THR147 4.5 20.5 1.0 CA A:ARG77 4.6 25.1 1.0 C A:ALA75 4.7 22.8 1.0 CG A:PHE76 4.7 18.2 1.0 CA A:GLN148 4.8 15.6 1.0 O A:GLY149 4.8 18.7 1.0 CD A:LYS80 4.9 16.6 1.0 O3A A:GDP501 5.0 31.8 1.0 O A:THR120 5.0 21.2 1.0

Fluorine binding site 3 out of 16 in the Human Atlastin-1 1-446, N440T, GDPALF4-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Atlastin-1 1-446, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:12.9 occ:1.00 F3 A:ALF502 0.0 12.9 1.0 AL A:ALF502 1.8 13.1 1.0 F1 A:ALF502 2.5 25.0 1.0 O3B A:GDP501 2.5 16.6 1.0 F2 A:ALF502 2.6 18.6 1.0 N A:ARG77 2.7 20.8 1.0 NE A:ARG77 2.8 24.3 1.0 O A:HOH605 2.8 14.2 1.0 CB A:PHE76 3.2 14.1 1.0 CA A:ARG77 3.5 25.1 1.0 CD2 A:PHE76 3.5 20.5 1.0 C A:PHE76 3.5 16.9 1.0 F4 A:ALF502 3.6 18.8 1.0 CA A:PHE76 3.6 18.5 1.0 CA A:ARG118 3.6 15.1 1.0 NH2 A:ARG77 3.6 16.1 1.0 CZ A:ARG77 3.7 20.7 1.0 CG A:ARG77 3.7 32.5 1.0 CD A:ARG77 3.7 24.3 1.0 CG A:PHE76 3.8 18.2 1.0 CB A:ARG118 3.9 21.0 1.0 N A:GLU119 4.0 15.6 1.0 O A:HOH603 4.0 12.1 1.0 PB A:GDP501 4.0 13.3 1.0 CB A:ARG77 4.1 30.3 1.0 C A:ARG118 4.4 15.4 1.0 O1B A:GDP501 4.6 14.1 1.0 N A:ARG118 4.6 19.1 1.0 O A:PHE76 4.7 15.3 1.0 NZ A:LYS80 4.7 12.6 1.0 CE2 A:PHE76 4.8 16.5 1.0 O3A A:GDP501 4.8 31.8 1.0 C A:ARG77 4.8 21.2 1.0 O2B A:GDP501 4.8 14.9 1.0 N A:GLY149 4.9 17.9 1.0 NH1 A:ARG77 4.9 18.0 1.0 CA A:GLY149 5.0 18.2 1.0

Fluorine binding site 4 out of 16 in the Human Atlastin-1 1-446, N440T, GDPALF4-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Atlastin-1 1-446, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:18.8 occ:1.00 F4 A:ALF502 0.0 18.8 1.0 AL A:ALF502 1.8 13.1 1.0 MG A:MG503 1.9 16.0 1.0 F2 A:ALF502 2.5 18.6 1.0 F1 A:ALF502 2.5 25.0 1.0 O A:HOH605 2.6 14.2 1.0 O3B A:GDP501 2.8 16.6 1.0 OG1 A:THR120 2.8 14.7 1.0 O A:HOH601 2.8 13.5 1.0 O2B A:GDP501 2.9 14.9 1.0 CB A:THR120 2.9 14.8 1.0 O A:HOH604 3.2 12.7 1.0 PB A:GDP501 3.3 13.3 1.0 N A:THR120 3.5 16.7 1.0 F3 A:ALF502 3.6 12.9 1.0 CA A:THR120 3.7 18.9 1.0 O A:THR147 3.8 20.5 1.0 O A:THR120 3.9 21.2 1.0 NZ A:LYS80 4.0 12.6 1.0 N A:GLY149 4.0 17.9 1.0 O1B A:GDP501 4.1 14.1 1.0 CG2 A:THR120 4.1 14.9 1.0 OG A:SER81 4.1 17.3 1.0 C A:THR120 4.3 22.3 1.0 CE A:LYS80 4.4 12.2 1.0 CA A:GLN148 4.6 15.6 1.0 C A:GLU119 4.7 16.8 1.0 N A:GLU119 4.7 15.6 1.0 O3A A:GDP501 4.7 31.8 1.0 NH2 A:ARG77 4.8 16.1 1.0 C A:GLN148 4.8 15.2 1.0 C A:THR147 4.8 22.9 1.0 CA A:GLY149 4.8 18.2 1.0 O A:HOH603 4.9 12.1 1.0

Fluorine binding site 5 out of 16 in the Human Atlastin-1 1-446, N440T, GDPALF4-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Atlastin-1 1-446, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:10.6 occ:1.00 F1 B:ALF502 0.0 10.6 1.0 AL B:ALF502 1.8 13.4 1.0 F4 B:ALF502 2.5 16.6 1.0 N B:GLU119 2.5 21.1 1.0 F3 B:ALF502 2.6 14.5 1.0 O B:HOH604 2.6 14.8 1.0 O1B B:GDP501 2.7 19.3 1.0 N B:THR120 2.8 17.3 1.0 NH2 B:ARG77 3.0 16.8 1.0 CA B:GLU119 3.1 22.6 1.0 CB B:GLU119 3.2 22.4 1.0 O B:HOH603 3.2 7.2 1.0 C B:GLU119 3.4 17.7 1.0 MG B:MG503 3.5 24.6 1.0 F2 B:ALF502 3.6 26.7 1.0 C B:ARG118 3.6 17.5 1.0 NE B:ARG77 3.8 16.9 1.0 CZ B:ARG77 3.8 17.2 1.0 OG1 B:THR120 3.8 28.4 1.0 CA B:ARG118 3.9 17.0 1.0 CA B:THR120 3.9 17.3 1.0 CB B:THR120 4.0 16.9 1.0 PB B:GDP501 4.0 13.2 1.0 O2B B:GDP501 4.1 12.3 1.0 O B:THR120 4.2 20.0 1.0 CG B:GLU119 4.4 26.4 1.0 CB B:ARG118 4.5 18.5 1.0 O1A B:GDP501 4.5 19.4 1.0 C B:THR120 4.6 21.9 1.0 O B:GLU119 4.6 26.6 1.0 O B:ARG118 4.7 18.1 1.0 O3A B:GDP501 4.8 20.5 1.0 N B:ARG77 4.9 17.4 1.0

Fluorine binding site 6 out of 16 in the Human Atlastin-1 1-446, N440T, GDPALF4-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Atlastin-1 1-446, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:26.7 occ:1.00 F2 B:ALF502 0.0 26.7 1.0 AL B:ALF502 1.8 13.4 1.0 F3 B:ALF502 2.5 14.5 1.0 F4 B:ALF502 2.6 16.6 1.0 NZ B:LYS80 2.6 13.5 1.0 O1B B:GDP501 2.7 19.3 1.0 O B:HOH604 2.9 14.8 1.0 CA B:PHE76 3.1 21.8 1.0 N B:GLY149 3.1 19.2 1.0 CA B:GLY149 3.1 14.9 1.0 N B:ARG77 3.3 17.4 1.0 CB B:PHE76 3.3 20.7 1.0 O3B B:GDP501 3.4 16.3 1.0 PB B:GDP501 3.5 13.2 1.0 F1 B:ALF502 3.6 10.6 1.0 CE B:LYS80 3.7 13.1 1.0 C B:PHE76 3.7 17.4 1.0 O2B B:GDP501 3.9 12.3 1.0 O B:HOH602 4.0 19.7 1.0 N B:PHE76 4.2 24.2 1.0 O B:ALA75 4.3 18.4 1.0 C B:GLN148 4.3 16.3 1.0 C B:GLY149 4.4 14.8 1.0 MG B:MG503 4.4 24.6 1.0 CA B:ARG77 4.5 19.7 1.0 O B:HOH601 4.5 12.0 1.0 O B:THR147 4.6 16.7 1.0 CG B:PHE76 4.6 23.0 1.0 C B:ALA75 4.6 20.0 1.0 O B:GLY149 4.8 15.2 1.0 O B:PHE76 4.9 15.6 1.0 CA B:GLN148 4.9 16.7 1.0 O3A B:GDP501 4.9 20.5 1.0 N B:LYS78 5.0 15.3 1.0 CD2 B:PHE76 5.0 23.4 1.0

Fluorine binding site 7 out of 16 in the Human Atlastin-1 1-446, N440T, GDPALF4-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Human Atlastin-1 1-446, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:14.5 occ:1.00 F3 B:ALF502 0.0 14.5 1.0 AL B:ALF502 1.8 13.4 1.0 F2 B:ALF502 2.5 26.7 1.0 F1 B:ALF502 2.6 10.6 1.0 O1B B:GDP501 2.7 19.3 1.0 N B:ARG77 2.8 17.4 1.0 NE B:ARG77 2.9 16.9 1.0 O B:HOH604 3.0 14.8 1.0 CB B:PHE76 3.3 20.7 1.0 CD2 B:PHE76 3.5 23.4 1.0 CA B:ARG118 3.5 17.0 1.0 F4 B:ALF502 3.6 16.6 1.0 CA B:ARG77 3.6 19.7 1.0 C B:PHE76 3.6 17.4 1.0 CA B:PHE76 3.7 21.8 1.0 CG B:ARG77 3.8 26.9 1.0 CD B:ARG77 3.8 23.3 1.0 CZ B:ARG77 3.8 17.2 1.0 NH2 B:ARG77 3.8 16.8 1.0 N B:GLU119 3.8 21.1 1.0 CG B:PHE76 3.9 23.0 1.0 CB B:ARG118 3.9 18.5 1.0 O B:HOH602 3.9 19.7 1.0 PB B:GDP501 4.1 13.2 1.0 CB B:ARG77 4.2 25.9 1.0 C B:ARG118 4.2 17.5 1.0 N B:ARG118 4.5 22.6 1.0 O3B B:GDP501 4.6 16.3 1.0 CE2 B:PHE76 4.7 17.5 1.0 O B:PHE76 4.8 15.6 1.0 NZ B:LYS80 4.9 13.5 1.0 O2B B:GDP501 4.9 12.3 1.0 N B:GLY149 4.9 19.2 1.0 C B:ARG77 5.0 22.1 1.0 O3A B:GDP501 5.0 20.5 1.0

Fluorine binding site 8 out of 16 in the Human Atlastin-1 1-446, N440T, GDPALF4-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Human Atlastin-1 1-446, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:16.6 occ:1.00 F4 B:ALF502 0.0 16.6 1.0 AL B:ALF502 1.8 13.4 1.0 MG B:MG503 2.1 24.6 1.0 F1 B:ALF502 2.5 10.6 1.0 O B:HOH604 2.5 14.8 1.0 F2 B:ALF502 2.6 26.7 1.0 O1B B:GDP501 2.7 19.3 1.0 O B:HOH601 2.7 12.0 1.0 OG1 B:THR120 2.9 28.4 1.0 O2B B:GDP501 2.9 12.3 1.0 CB B:THR120 2.9 16.9 1.0 O B:HOH603 3.3 7.2 1.0 PB B:GDP501 3.4 13.2 1.0 N B:THR120 3.5 17.3 1.0 F3 B:ALF502 3.6 14.5 1.0 O B:THR147 3.7 16.7 1.0 CA B:THR120 3.7 17.3 1.0 O B:THR120 4.0 20.0 1.0 NZ B:LYS80 4.0 13.5 1.0 CG2 B:THR120 4.1 17.1 1.0 O3B B:GDP501 4.1 16.3 1.0 N B:GLY149 4.1 19.2 1.0 OG B:SER81 4.2 14.9 1.0 C B:THR120 4.3 21.9 1.0 CE B:LYS80 4.4 13.1 1.0 CA B:GLN148 4.6 16.7 1.0 C B:GLU119 4.7 17.7 1.0 C B:THR147 4.7 22.2 1.0 N B:GLU119 4.7 21.1 1.0 O3A B:GDP501 4.8 20.5 1.0 C B:GLN148 4.8 16.3 1.0 CA B:GLY149 4.9 14.9 1.0 NH2 B:ARG77 4.9 16.8 1.0

Fluorine binding site 9 out of 16 in the Human Atlastin-1 1-446, N440T, GDPALF4-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Human Atlastin-1 1-446, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:12.6 occ:1.00 F1 C:ALF502 0.0 12.6 1.0 AL C:ALF502 1.8 13.5 1.0 F4 C:ALF502 2.5 19.6 1.0 N C:GLU119 2.5 20.6 1.0 F3 C:ALF502 2.5 17.0 1.0 O C:HOH604 2.7 11.1 1.0 O1B C:GDP501 2.7 16.3 1.0 N C:THR120 2.8 17.0 1.0 NH2 C:ARG77 3.1 17.2 1.0 CA C:GLU119 3.1 16.9 1.0 CB C:GLU119 3.2 15.7 1.0 O C:HOH603 3.2 8.1 1.0 C C:GLU119 3.4 14.9 1.0 F2 C:ALF502 3.6 24.9 1.0 MG C:MG503 3.6 18.2 1.0 C C:ARG118 3.6 22.5 1.0 CA C:ARG118 3.9 18.4 1.0 NE C:ARG77 3.9 18.2 1.0 CZ C:ARG77 3.9 19.0 1.0 CA C:THR120 3.9 17.7 1.0 OG1 C:THR120 3.9 22.2 1.0 CB C:THR120 4.0 13.8 1.0 PB C:GDP501 4.0 12.9 1.0 O2B C:GDP501 4.1 12.4 1.0 O C:THR120 4.2 20.2 1.0 CB C:ARG118 4.3 20.3 1.0 CG C:GLU119 4.4 19.3 1.0 O C:GLU119 4.5 20.5 1.0 C C:THR120 4.6 21.6 1.0 O1A C:GDP501 4.6 17.7 1.0 O C:ARG118 4.7 15.7 1.0 O3A C:GDP501 4.8 18.4 1.0 O C:HOH602 4.9 18.7 1.0

Fluorine binding site 10 out of 16 in the Human Atlastin-1 1-446, N440T, GDPALF4-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Human Atlastin-1 1-446, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:24.9 occ:1.00 F2 C:ALF502 0.0 24.9 1.0 AL C:ALF502 1.8 13.5 1.0 F3 C:ALF502 2.5 17.0 1.0 F4 C:ALF502 2.6 19.6 1.0 NZ C:LYS80 2.7 14.6 1.0 O1B C:GDP501 2.7 16.3 1.0 O C:HOH604 2.8 11.1 1.0 N C:GLY149 3.0 12.8 1.0 CA C:GLY149 3.1 12.5 1.0 CA C:PHE76 3.2 21.3 1.0 N C:ARG77 3.4 15.6 1.0 CB C:PHE76 3.4 16.0 1.0 O3B C:GDP501 3.5 15.2 1.0 PB C:GDP501 3.5 12.9 1.0 F1 C:ALF502 3.6 12.6 1.0 CE C:LYS80 3.6 12.6 1.0 C C:PHE76 3.8 20.0 1.0 O C:HOH602 3.9 18.7 1.0 O2B C:GDP501 4.0 12.4 1.0 C C:GLN148 4.2 15.5 1.0 N C:PHE76 4.3 27.5 1.0 MG C:MG503 4.3 18.2 1.0 C C:GLY149 4.3 12.7 1.0 O C:ALA75 4.4 15.8 1.0 O C:HOH601 4.4 8.0 1.0 O C:THR147 4.5 14.1 1.0 CA C:ARG77 4.6 16.1 1.0 C C:ALA75 4.7 14.4 1.0 CG C:PHE76 4.7 17.2 1.0 O C:GLY149 4.8 13.1 1.0 CA C:GLN148 4.8 13.9 1.0 O3A C:GDP501 4.9 18.4 1.0 O C:THR120 5.0 20.2 1.0

L.J.Byrnes, A.Singh, K.Szeto, N.M.Benvin, J.P.O'donnell, W.R.Zipfel, H.Sondermann. Structural Basis For Conformational Switching and Gtp Loading of the Large G Protein Atlastin. Embo J. V. 32 369 2013.
ISSN: ISSN 0261-4189
PubMed: 23334294
DOI: 10.1038/EMBOJ.2012.353