Sodium in PDB 2x2f: Dynamin 1 Gtpase Dimer, Short Axis Form

All present enzymatic activity of Dynamin 1 Gtpase Dimer, Short Axis Form:
3.6.5.5;

The structure of Dynamin 1 Gtpase Dimer, Short Axis Form, PDB code: 2x2f was solved by J.S.Chappie, S.Acharya, M.Leonard, S.L.Schmid, F.Dyda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.444, 81.274, 175.697, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.4

The structure of Dynamin 1 Gtpase Dimer, Short Axis Form also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Magnesium	(Mg)	2 atoms
Aluminium	(Al)	2 atoms

The binding sites of Sodium atom in the Dynamin 1 Gtpase Dimer, Short Axis Form (pdb code 2x2f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dynamin 1 Gtpase Dimer, Short Axis Form, PDB code: 2x2f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dynamin 1 Gtpase Dimer, Short Axis Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dynamin 1 Gtpase Dimer, Short Axis Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1750 b:14.6 occ:1.00 O A:GLY62 2.2 16.2 1.0 O A:GLY60 2.2 12.8 1.0 OG A:SER41 2.4 8.7 1.0 F3 A:ALF1748 2.6 15.9 1.0 F1 A:ALF1748 2.7 15.2 1.0 O3B A:GDP1747 3.1 7.1 1.0 AL A:ALF1748 3.4 14.3 1.0 C A:GLY60 3.4 12.3 1.0 C A:GLY62 3.4 16.0 1.0 CB A:SER41 3.6 9.0 1.0 C A:SER61 3.6 17.8 1.0 N A:GLY62 3.7 16.4 1.0 CA A:SER41 3.7 7.3 1.0 CA A:SER61 3.7 16.6 1.0 CG2 A:VAL64 3.8 9.9 1.0 N A:VAL64 4.0 11.8 1.0 N A:SER41 4.0 7.4 1.0 N A:SER61 4.0 13.6 1.0 O A:SER61 4.1 18.1 1.0 O2A A:GDP1747 4.1 6.8 1.0 CB A:VAL64 4.2 10.1 1.0 CA A:GLY62 4.3 15.3 1.0 OD2 D:ASP180 4.3 18.8 1.0 N A:ILE63 4.3 15.4 1.0 CA A:ILE63 4.4 14.2 1.0 C5' A:GDP1747 4.4 8.3 1.0 PB A:GDP1747 4.4 7.8 1.0 CG A:GLN40 4.5 6.4 1.0 C A:ILE63 4.5 15.0 1.0 O3A A:GDP1747 4.6 9.1 1.0 CA A:GLY60 4.6 11.0 1.0 O A:HOH2171 4.6 7.7 1.0 N A:GLY60 4.7 9.9 1.0 F4 A:ALF1748 4.7 16.1 1.0 F2 A:ALF1748 4.7 15.3 1.0 CA A:VAL64 4.7 10.5 1.0 O A:HOH2027 4.8 13.8 1.0 PA A:GDP1747 4.8 8.3 1.0

Sodium binding site 2 out of 2 in the Dynamin 1 Gtpase Dimer, Short Axis Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dynamin 1 Gtpase Dimer, Short Axis Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1749 b:17.5 occ:1.00 O D:GLY60 2.2 13.6 1.0 O D:GLY62 2.2 10.6 1.0 OG D:SER41 2.3 10.6 1.0 F1 D:ALF1747 2.6 11.9 1.0 F3 D:ALF1747 2.7 14.3 1.0 O3B D:GDP1746 3.0 8.0 1.0 AL D:ALF1747 3.3 10.9 1.0 C D:GLY60 3.4 14.3 1.0 C D:GLY62 3.5 12.5 1.0 CB D:SER41 3.5 9.7 1.0 C D:SER61 3.7 18.5 1.0 CA D:SER41 3.7 6.7 1.0 N D:GLY62 3.8 17.8 1.0 O2A D:GDP1746 3.9 9.6 1.0 CA D:SER61 3.9 18.3 1.0 N D:SER41 4.0 6.9 1.0 CG2 D:VAL64 4.0 4.4 1.0 N D:VAL64 4.0 8.2 1.0 N D:SER61 4.1 15.0 1.0 O D:SER61 4.1 17.2 1.0 CB D:VAL64 4.2 5.4 1.0 PB D:GDP1746 4.3 7.9 1.0 OD2 A:ASP180 4.3 21.8 1.0 C5' D:GDP1746 4.3 7.8 1.0 CA D:ILE63 4.3 9.8 1.0 CA D:GLY62 4.3 16.3 1.0 N D:ILE63 4.4 11.3 1.0 O3A D:GDP1746 4.5 7.3 1.0 CG D:GLN40 4.5 3.1 1.0 CA D:GLY60 4.5 11.7 1.0 C D:ILE63 4.5 10.1 1.0 N D:GLY60 4.6 11.0 1.0 O D:HOH2150 4.6 9.8 1.0 F4 D:ALF1747 4.6 13.6 1.0 PA D:GDP1746 4.7 8.2 1.0 F2 D:ALF1747 4.7 12.6 1.0 O D:HOH2020 4.8 8.2 1.0 CA D:VAL64 4.8 6.2 1.0

J.S.Chappie, S.Acharya, M.Leonard, S.L.Schmid, F.Dyda. G Domain Dimerization Controls Dynamin'S Assembly-Stimulated Gtpase Activity. Nature V. 465 435 2010.
ISSN: ISSN 0028-0836
PubMed: 20428113
DOI: 10.1038/NATURE09032