Sodium in PDB 3w6p: Crystal Structure of Human DLP1 in Complex with Gdp.ALF4

All present enzymatic activity of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4:
3.6.5.5;

The structure of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4, PDB code: 3w6p was solved by H.Kishida, S.Sugio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.410, 109.130, 128.730, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.4

The structure of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Magnesium	(Mg)	2 atoms
Aluminium	(Al)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 (pdb code 3w6p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4, PDB code: 3w6p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na804 b:8.0 occ:1.00 O A:GLY54 2.3 10.3 1.0 O A:GLY56 2.3 9.3 1.0 F3 A:ALF802 2.4 11.9 1.0 OG A:SER35 2.4 5.7 1.0 F1 A:ALF802 2.8 14.7 1.0 O3B A:GDP801 2.8 5.0 1.0 AL A:ALF802 3.3 8.2 1.0 C A:GLY54 3.5 11.0 1.0 C A:GLY56 3.5 9.9 1.0 CB A:SER35 3.6 6.2 1.0 CA A:SER35 3.7 6.0 1.0 N A:VAL58 3.9 8.0 1.0 N A:SER35 4.0 5.2 1.0 C A:THR55 4.0 12.1 1.0 O1A A:GDP801 4.0 7.3 1.0 CA A:THR55 4.0 13.1 1.0 CG2 A:VAL58 4.1 7.6 1.0 O3A A:GDP801 4.1 5.8 1.0 PB A:GDP801 4.1 6.3 1.0 N A:GLY56 4.1 11.5 1.0 CB A:VAL58 4.2 7.9 1.0 N A:THR55 4.2 12.6 1.0 C5' A:GDP801 4.3 7.0 1.0 CA A:ILE57 4.3 9.1 1.0 N A:ILE57 4.4 9.4 1.0 OD2 B:ASP190 4.4 9.2 1.0 O A:THR55 4.4 12.3 1.0 F2 A:ALF802 4.5 9.4 1.0 C A:ILE57 4.5 9.1 1.0 CA A:GLY56 4.5 10.7 1.0 N A:GLY54 4.6 10.0 1.0 CA A:GLY54 4.6 11.2 1.0 O A:HOH1101 4.6 8.2 1.0 CG A:GLN34 4.6 7.1 1.0 PA A:GDP801 4.6 6.5 1.0 CA A:VAL58 4.7 7.7 1.0 F4 A:ALF802 4.7 11.9 1.0 O A:HOH1103 4.7 6.8 1.0 O2B A:GDP801 4.9 6.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na804 b:10.5 occ:1.00 O B:GLY56 2.3 11.9 1.0 O B:GLY54 2.3 13.2 1.0 F3 B:ALF802 2.4 14.0 1.0 OG B:SER35 2.4 7.7 1.0 F1 B:ALF802 2.8 16.6 1.0 O3B B:GDP801 2.9 6.1 1.0 AL B:ALF802 3.3 9.3 1.0 C B:GLY54 3.5 13.0 1.0 C B:GLY56 3.5 12.4 1.0 CB B:SER35 3.6 7.1 1.0 CA B:SER35 3.7 6.8 1.0 N B:SER35 3.9 6.1 1.0 N B:VAL58 3.9 8.8 1.0 CG2 B:VAL58 4.0 8.3 1.0 C B:THR55 4.0 14.3 1.0 CA B:THR55 4.0 15.2 1.0 O1A B:GDP801 4.0 7.0 1.0 O3A B:GDP801 4.1 5.0 1.0 PB B:GDP801 4.2 5.8 1.0 N B:GLY56 4.2 14.3 1.0 CB B:VAL58 4.2 8.6 1.0 N B:THR55 4.2 14.3 1.0 CA B:ILE57 4.3 10.6 1.0 OD2 A:ASP190 4.3 9.8 1.0 C5' B:GDP801 4.3 6.5 1.0 N B:ILE57 4.3 11.5 1.0 O B:THR55 4.4 15.5 1.0 C B:ILE57 4.4 10.3 1.0 F2 B:ALF802 4.5 10.6 1.0 CG B:GLN34 4.5 8.6 1.0 CA B:GLY56 4.5 13.3 1.0 CA B:GLY54 4.6 12.5 1.0 N B:GLY54 4.6 12.1 1.0 O B:HOH1135 4.7 5.0 1.0 PA B:GDP801 4.7 6.1 1.0 O B:HOH1134 4.7 7.9 1.0 CA B:VAL58 4.7 8.3 1.0 F4 B:ALF802 4.7 13.1 1.0 C B:GLN34 4.9 5.7 1.0

H.Kishida, S.Sugio. Crystal Structure of Gtpase Domain Fused with Minimal Stalks From Human Dynamin-1-Like Protein (DLP1) in Complex with Several Nucleotide Analogues Curr Top Pept Protein Res. V. 14 67 2013.
ISSN: ISSN 0972-4524