Magnesium in PDB 3zyc: Dynamin 1 Gtpase Ged Fusion Dimer Complexed with Gmppcp

The structure of Dynamin 1 Gtpase Ged Fusion Dimer Complexed with Gmppcp, PDB code: 3zyc was solved by J.S.Chappie, J.A.Mears, S.Fang, M.Leonard, S.L.Schmid, R.A.Milligan, J.E.Hinshaw, F.Dyda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.151, 82.635, 95.014, 90.00, 96.68, 90.00
R / Rfree (%)	22.5 / 26.9

The binding sites of Magnesium atom in the Dynamin 1 Gtpase Ged Fusion Dimer Complexed with Gmppcp (pdb code 3zyc). 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 Ged Fusion Dimer Complexed with Gmppcp, PDB code: 3zyc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dynamin 1 Gtpase Ged Fusion Dimer Complexed with Gmppcp


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 Ged Fusion Dimer Complexed with Gmppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1750 b:5.0 occ:1.00 O2G A:GCP1749 2.0 13.2 1.0 O A:HOH1752 2.1 3.5 1.0 O A:HOH1751 2.1 4.7 1.0 OG1 A:THR65 2.1 8.7 1.0 O1B A:GCP1749 2.2 8.9 1.0 OG A:SER45 2.2 7.7 1.0 CB A:THR65 3.1 6.2 1.0 PB A:GCP1749 3.1 6.3 1.0 PG A:GCP1749 3.2 10.9 1.0 C3B A:GCP1749 3.3 8.5 1.0 CB A:SER45 3.3 1.7 1.0 N A:SER45 3.8 5.6 1.0 O2B A:GCP1749 3.9 5.6 1.0 OD2 A:ASP136 4.0 8.2 1.0 O1G A:GCP1749 4.0 7.5 1.0 N A:THR65 4.1 14.5 1.0 CG2 A:THR65 4.1 1.7 1.0 O2A A:GCP1749 4.1 13.0 1.0 OD1 A:ASP136 4.1 8.9 1.0 CA A:SER45 4.1 1.5 1.0 O3G A:GCP1749 4.2 9.8 1.0 CA A:THR65 4.2 13.8 1.0 O A:HOH2047 4.3 27.5 1.0 O A:LEU137 4.4 8.1 1.0 O3A A:GCP1749 4.5 6.1 1.0 CG A:ASP136 4.5 9.7 1.0 O A:PRO58 4.6 8.7 1.0 CB A:LYS44 4.6 3.8 1.0 CE A:LYS44 4.7 3.5 1.0 PA A:GCP1749 4.7 9.4 1.0 C A:LYS44 4.9 7.0 1.0 CB A:VAL64 5.0 5.2 1.0 NZ A:LYS44 5.0 1.5 1.0

Magnesium binding site 2 out of 2 in the Dynamin 1 Gtpase Ged Fusion Dimer Complexed with Gmppcp


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 Ged Fusion Dimer Complexed with Gmppcp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1750 b:9.5 occ:1.00 OG D:SER45 2.0 5.7 1.0 O D:HOH1752 2.1 10.5 1.0 OG1 D:THR65 2.1 8.1 1.0 O D:HOH1751 2.1 8.0 1.0 O1B D:GCP1749 2.2 10.4 1.0 O2G D:GCP1749 2.2 14.2 1.0 CB D:SER45 3.1 2.8 1.0 CB D:THR65 3.2 13.8 1.0 PB D:GCP1749 3.2 8.4 1.0 PG D:GCP1749 3.4 11.1 1.0 C3B D:GCP1749 3.4 9.8 1.0 N D:SER45 3.8 5.8 1.0 O D:HOH2033 3.9 18.1 1.0 O2A D:GCP1749 3.9 12.4 1.0 CA D:SER45 4.0 6.1 1.0 OD1 D:ASP136 4.1 11.8 1.0 CG2 D:THR65 4.1 6.0 1.0 O2B D:GCP1749 4.1 4.7 1.0 N D:THR65 4.1 11.3 1.0 OD2 D:ASP136 4.2 14.4 1.0 CA D:THR65 4.3 17.7 1.0 O3G D:GCP1749 4.3 11.3 1.0 O1G D:GCP1749 4.4 7.8 1.0 O D:PRO58 4.4 10.8 1.0 O D:LEU137 4.5 14.3 1.0 O3A D:GCP1749 4.5 8.2 1.0 CG D:ASP136 4.5 14.5 1.0 PA D:GCP1749 4.6 12.2 1.0 CE D:LYS44 4.7 1.5 1.0 CB D:LYS44 4.9 1.5 1.0 CB D:VAL64 4.9 7.9 1.0 C D:LYS44 5.0 7.6 1.0

J.S.Chappie, J.A.Mears, S.Fang, M.Leonard, S.L.Schmid, R.A.Milligan, J.E.Hinshaw, F.Dyda. A Pseudoatomic Model of the Dynamin Polymer Identifies A Hydrolysis-Dependent Powerstroke. Cell(Cambridge,Mass.) V. 147 209 2011.
ISSN: ISSN 0092-8674
PubMed: 21962517
DOI: 10.1016/J.CELL.2011.09.003