Atomistry » Magnesium » PDB 2x13-2xbn » 2x2f
Atomistry »
  Magnesium »
    PDB 2x13-2xbn »
      2x2f »

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

Enzymatic activity of Dynamin 1 Gtpase Dimer, Short Axis Form

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

Protein crystallography data

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

Other elements in 2x2f:

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

Magnesium Binding Sites:

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 2x2f

Go back to Magnesium Binding Sites List in 2x2f
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 2x2f

Go back to Magnesium Binding Sites List in 2x2f
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

Reference:

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
Page generated: Mon Dec 14 07:45:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy