Sodium in PDB 2x2e: Dynamin Gtpase Dimer, Long Axis Form

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

The structure of Dynamin Gtpase Dimer, Long Axis Form, PDB code: 2x2e 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 (°)	43.610, 81.020, 181.540, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23

The structure of Dynamin Gtpase Dimer, Long 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 Gtpase Dimer, Long Axis Form (pdb code 2x2e). 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 Gtpase Dimer, Long Axis Form, PDB code: 2x2e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dynamin Gtpase Dimer, Long 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 Gtpase Dimer, Long Axis Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1747 b:8.6 occ:1.00 O A:GLY60 2.2 7.5 1.0 OG A:SER41 2.2 4.7 1.0 O A:GLY62 2.3 10.6 1.0 F3 A:ALF1745 2.5 15.6 1.0 F1 A:ALF1745 2.7 15.4 1.0 O3B A:GDP1744 3.0 4.0 1.0 AL A:ALF1745 3.3 15.0 1.0 CB A:SER41 3.4 4.5 1.0 C A:GLY60 3.4 7.6 1.0 C A:GLY62 3.5 10.1 1.0 CA A:SER41 3.6 6.3 1.0 C A:SER61 3.7 10.6 1.0 N A:SER41 3.9 5.0 1.0 N A:GLY62 3.9 10.8 1.0 CA A:SER61 3.9 8.7 1.0 CG2 A:VAL64 4.0 4.5 1.0 O2A A:GDP1744 4.0 5.9 1.0 N A:VAL64 4.0 5.3 1.0 N A:SER61 4.1 6.8 1.0 O A:SER61 4.2 12.4 1.0 PB A:GDP1744 4.3 4.0 1.0 CB A:VAL64 4.3 4.2 1.0 OD2 D:ASP180 4.3 13.5 1.0 C5' A:GDP1744 4.3 5.6 1.0 CA A:ILE63 4.4 8.6 1.0 CA A:GLY62 4.4 10.5 1.0 N A:ILE63 4.5 8.3 1.0 CG A:GLN40 4.5 2.7 1.0 O3A A:GDP1744 4.5 4.7 1.0 C A:ILE63 4.6 9.2 1.0 F2 A:ALF1745 4.6 15.0 1.0 O A:HOH2331 4.6 5.6 1.0 CA A:GLY60 4.6 9.1 1.0 F4 A:ALF1745 4.7 15.3 1.0 O A:HOH2071 4.7 15.1 1.0 N A:GLY60 4.7 10.2 1.0 PA A:GDP1744 4.7 5.5 1.0 CA A:VAL64 4.8 3.7 1.0 C A:GLN40 5.0 3.9 1.0 O2B A:GDP1744 5.0 4.0 1.0 C A:SER41 5.0 7.5 1.0

Sodium binding site 2 out of 2 in the Dynamin Gtpase Dimer, Long 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 Gtpase Dimer, Long Axis Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1747 b:9.2 occ:1.00 O D:GLY60 2.2 7.8 1.0 O D:GLY62 2.2 6.2 1.0 OG D:SER41 2.3 7.2 1.0 F3 D:ALF1745 2.5 13.1 1.0 F1 D:ALF1745 2.7 12.8 1.0 O3B D:GDP1744 2.9 6.7 1.0 AL D:ALF1745 3.3 12.2 1.0 CB D:SER41 3.4 3.0 1.0 C D:GLY60 3.4 8.5 1.0 C D:GLY62 3.5 6.5 1.0 CA D:SER41 3.7 3.3 1.0 C D:SER61 3.8 8.5 1.0 CG2 D:VAL64 3.8 5.7 1.0 N D:GLY62 3.8 8.3 1.0 CA D:SER61 3.9 8.2 1.0 N D:SER41 3.9 4.2 1.0 O2A D:GDP1744 4.0 7.1 1.0 N D:VAL64 4.0 7.0 1.0 N D:SER61 4.1 7.2 1.0 O D:SER61 4.2 8.6 1.0 CB D:VAL64 4.2 5.3 1.0 PB D:GDP1744 4.3 6.5 1.0 OD1 A:ASP180 4.3 15.9 1.0 CA D:ILE63 4.4 6.1 1.0 CA D:GLY62 4.4 8.6 1.0 C5' D:GDP1744 4.4 6.5 1.0 N D:ILE63 4.4 6.0 1.0 CG D:GLN40 4.5 5.7 1.0 O3A D:GDP1744 4.5 6.2 1.0 O D:HOH2287 4.5 4.4 1.0 C D:ILE63 4.5 6.5 1.0 F2 D:ALF1745 4.6 12.0 1.0 CA D:GLY60 4.6 7.0 1.0 F4 D:ALF1745 4.7 12.8 1.0 O D:HOH2051 4.7 12.3 1.0 N D:GLY60 4.7 5.5 1.0 PA D:GDP1744 4.7 6.7 1.0 CA D:VAL64 4.8 5.9 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