Fluorine in PDB 1n6k: Crystal Structure of Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride

The structure of Crystal Structure of Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride, PDB code: 1n6k was solved by G.Zhu, J.Liu, S.Terzyan, P.Zhai, G.Li, X.C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.840, 64.040, 65.880, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20

The structure of Crystal Structure of Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Aluminium	(Al)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride (pdb code 1n6k). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride, PDB code: 1n6k:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride


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 Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:12.6 occ:1.00 F1 A:AF3202 0.0 12.6 1.0 AL A:AF3202 1.9 11.3 1.0 NZ A:LYS33 2.6 8.0 1.0 N A:GLY78 2.7 9.8 1.0 F2 A:AF3202 2.8 11.4 1.0 O A:HOH303 2.9 18.2 1.0 O2B A:GDP200 2.9 10.6 1.0 OG A:SER29 3.0 17.1 1.0 CB A:SER29 3.0 13.4 1.0 CE A:LYS33 3.3 10.8 1.0 CA A:GLY78 3.5 10.5 1.0 CA A:SER29 3.6 10.8 1.0 PB A:GDP200 3.6 9.9 1.0 C A:ALA77 3.7 10.2 1.0 O1B A:GDP200 3.7 8.7 1.0 O A:HOH301 3.8 10.0 1.0 CA A:ALA77 3.8 11.5 1.0 F3 A:AF3202 3.9 23.5 1.0 O A:THR76 4.0 11.5 1.0 O3B A:GDP200 4.0 9.6 1.0 MG A:MG201 4.0 10.1 1.0 N A:SER29 4.2 10.3 1.0 OE1 A:GLN79 4.3 16.9 1.0 O A:GLU28 4.5 11.0 1.0 C A:GLY78 4.5 12.3 1.0 O A:GLY27 4.6 10.8 1.0 N A:GLN79 4.6 15.5 1.0 C A:GLU28 4.7 10.6 1.0 CB A:ALA77 4.8 9.6 1.0 CA A:PRO30 4.8 12.6 0.4 CD A:LYS33 4.8 10.1 1.0 C A:THR76 4.8 11.9 1.0 N A:ALA77 4.8 11.2 1.0 O A:ALA77 4.9 11.1 1.0 C A:SER29 4.9 13.4 1.0 CA A:PRO30 4.9 11.5 0.6

Fluorine binding site 2 out of 3 in the Crystal Structure of Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride


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 Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:11.4 occ:1.00 F2 A:AF3202 0.0 11.4 1.0 AL A:AF3202 1.8 11.3 1.0 MG A:MG201 2.0 10.1 1.0 O A:HOH303 2.6 18.2 1.0 F1 A:AF3202 2.8 12.6 1.0 O2B A:GDP200 2.8 10.6 1.0 OG1 A:THR52 2.8 9.0 1.0 N A:THR52 2.9 12.9 1.0 O A:HOH302 2.9 10.7 1.0 F3 A:AF3202 3.0 23.5 1.0 CB A:THR52 3.0 10.4 1.0 O A:HOH301 3.0 10.0 1.0 O3B A:GDP200 3.1 9.6 1.0 PB A:GDP200 3.5 9.9 1.0 CA A:THR52 3.5 10.4 1.0 C A:SER51 3.9 17.7 1.0 OG A:SER34 4.1 10.2 1.0 CA A:SER51 4.1 20.9 1.0 O A:THR52 4.2 14.0 1.0 OG A:SER51 4.2 25.6 0.4 OG A:SER29 4.2 17.1 1.0 C A:THR52 4.3 11.6 1.0 CA A:ALA77 4.4 11.5 1.0 CG2 A:THR52 4.4 13.6 1.0 O1B A:GDP200 4.5 8.7 1.0 O1A A:GDP200 4.7 10.9 1.0 O3A A:GDP200 4.7 8.8 1.0 O A:THR76 4.7 11.5 1.0 CB A:SER51 4.7 21.6 0.6 O A:HOH304 4.7 17.6 1.0 CB A:SER51 4.8 22.0 0.4 NZ A:LYS33 4.8 8.0 1.0 N A:GLY78 4.8 9.8 1.0 O A:GLU50 4.9 20.9 1.0 CB A:ALA77 4.9 9.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human RAB5A A30P Mutant Complex with Gdp and Aluminum Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:23.5 occ:1.00 F3 A:AF3202 0.0 23.5 1.0 AL A:AF3202 2.1 11.3 1.0 OG A:SER51 2.6 25.6 0.4 OG A:SER29 2.7 17.1 1.0 O2B A:GDP200 2.8 10.6 1.0 OG A:SER51 2.8 31.2 0.6 O A:HOH303 2.9 18.2 1.0 F2 A:AF3202 3.0 11.4 1.0 O A:HOH304 3.1 17.6 1.0 CB A:SER51 3.2 21.6 0.6 CB A:SER51 3.2 22.0 0.4 CA A:SER51 3.4 20.9 1.0 O A:HOH305 3.4 28.6 1.0 CB A:PRO30 3.8 15.4 0.4 F1 A:AF3202 3.9 12.6 1.0 N A:THR52 4.0 12.9 1.0 CB A:SER29 4.1 13.4 1.0 CB A:PRO30 4.1 14.2 0.6 O A:HOH302 4.2 10.7 1.0 C A:SER51 4.2 17.7 1.0 PB A:GDP200 4.2 9.9 1.0 CA A:PRO30 4.5 12.6 0.4 N A:SER51 4.5 22.7 1.0 MG A:MG201 4.6 10.1 1.0 O1A A:GDP200 4.6 10.9 1.0 NE2 A:GLN79 4.6 20.4 1.0 CA A:PRO30 4.6 11.5 0.6 O3B A:GDP200 4.7 9.6 1.0 O3A A:GDP200 4.7 8.8 1.0 OE1 A:GLN79 4.9 16.9 1.0 CA A:SER29 4.9 10.8 1.0 CG A:PRO30 4.9 14.2 0.4 N A:PRO30 5.0 13.2 0.4 CD A:GLN79 5.0 18.2 1.0

G.Zhu, J.Liu, S.Terzyan, P.Zhai, G.Li, X.C.Zhang. High Resolution Crystal Structures of Human RAB5A and Five Mutants with Substitutions in the Catalytically Important Phosphate-Binding Loop J.Biol.Chem. V. 278 2452 2003.
ISSN: ISSN 0021-9258
PubMed: 12433916
DOI: 10.1074/JBC.M211042200