Magnesium 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
Aluminium	(Al)	2 atoms
Sodium	(Na)	2 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg binding site number 1 of Dynamin 1 Gtpase Dimer, Short Axis Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1749 b:7.9 occ:1.00 F4 A:ALF1748 1.9 16.1 1.0 OG A:SER45 2.0 11.7 1.0 OG1 A:THR65 2.0 6.9 1.0 O A:HOH2063 2.1 7.6 1.0 O A:HOH2171 2.1 7.7 1.0 O1B A:GDP1747 2.1 9.7 1.0 CB A:THR65 3.1 4.4 1.0 CB A:SER45 3.1 9.3 1.0 PB A:GDP1747 3.2 7.8 1.0 O3B A:GDP1747 3.4 7.1 1.0 AL A:ALF1748 3.5 14.3 1.0 F1 A:ALF1748 3.7 15.2 1.0 N A:SER45 3.8 7.4 1.0 CA A:SER45 4.0 9.0 1.0 OD2 A:ASP136 4.0 13.2 1.0 N A:THR65 4.1 10.2 1.0 OD1 A:ASP136 4.1 11.4 1.0 CG2 A:THR65 4.1 2.6 1.0 O A:HOH2026 4.1 6.4 1.0 CA A:THR65 4.1 6.2 1.0 O2A A:GDP1747 4.2 6.8 1.0 O2B A:GDP1747 4.2 6.3 1.0 F2 A:ALF1748 4.3 15.3 1.0 O3A A:GDP1747 4.4 9.1 1.0 CG A:ASP136 4.4 12.1 1.0 O A:PRO58 4.5 11.4 1.0 PA A:GDP1747 4.6 8.3 1.0 O A:LEU137 4.6 10.8 1.0 O A:HOH2027 4.7 13.8 1.0 O1A A:GDP1747 4.8 8.8 1.0 C A:LYS44 4.9 8.2 1.0 CB A:LYS44 4.9 4.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg binding site number 2 of Dynamin 1 Gtpase Dimer, Short Axis Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1748 b:8.2 occ:1.00 OG D:SER45 2.0 4.2 1.0 F4 D:ALF1747 2.0 13.6 1.0 O1B D:GDP1746 2.0 8.5 1.0 OG1 D:THR65 2.1 10.7 1.0 O D:HOH2050 2.1 7.5 1.0 O D:HOH2150 2.1 9.8 1.0 CB D:SER45 3.0 5.0 1.0 PB D:GDP1746 3.1 7.9 1.0 CB D:THR65 3.2 3.3 1.0 O3B D:GDP1746 3.4 8.0 1.0 AL D:ALF1747 3.6 10.9 1.0 N D:SER45 3.7 9.4 1.0 F1 D:ALF1747 3.8 11.9 1.0 CA D:SER45 3.9 7.9 1.0 OD2 D:ASP136 3.9 10.1 1.0 OD1 D:ASP136 3.9 13.7 1.0 CG2 D:THR65 4.1 2.4 1.0 O D:HOH2015 4.1 7.2 1.0 O2A D:GDP1746 4.1 9.6 1.0 O2B D:GDP1746 4.2 5.6 1.0 N D:THR65 4.2 7.3 1.0 CA D:THR65 4.2 7.2 1.0 F2 D:ALF1747 4.3 12.6 1.0 CG D:ASP136 4.3 13.6 1.0 O3A D:GDP1746 4.3 7.3 1.0 O D:PRO58 4.4 14.5 1.0 PA D:GDP1746 4.6 8.2 1.0 O D:LEU137 4.6 12.0 1.0 O1A D:GDP1746 4.7 6.9 1.0 O D:HOH2020 4.7 8.2 1.0 CB D:LYS44 4.8 6.3 1.0 C D:LYS44 4.8 9.3 1.0 NZ D:LYS44 5.0 6.5 1.0 CE D:LYS44 5.0 8.2 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