Magnesium in PDB 3t34: Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State

The structure of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State, PDB code: 3t34 was solved by L.M.Yan, Y.Y.Ma, Y.N.Sun, Z.Y.Lou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.31 / 2.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.471, 86.407, 88.485, 90.00, 90.55, 90.00
R / Rfree (%)	23.7 / 28.4

The structure of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State 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 Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State (pdb code 3t34). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State, PDB code: 3t34:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:40.0 occ:1.00 O1B A:GDP1000 2.1 39.7 1.0 F4 A:ALF1001 2.2 35.8 1.0 OG1 A:THR68 2.3 39.8 1.0 O A:HOH1006 2.3 38.2 1.0 OG A:SER48 2.3 33.5 1.0 O A:HOH1007 2.4 36.6 1.0 CB A:THR68 3.0 38.0 1.0 CB A:SER48 3.2 33.8 1.0 PB A:GDP1000 3.3 34.5 1.0 O3B A:GDP1000 3.4 33.5 1.0 AL A:ALF1001 3.6 41.2 1.0 N A:SER48 3.8 39.4 1.0 F1 A:ALF1001 3.9 53.8 1.0 CG2 A:THR68 4.0 37.4 1.0 CA A:SER48 4.0 36.8 1.0 OD1 A:ASP142 4.0 42.3 1.0 N A:THR68 4.1 41.4 1.0 O A:HOH1021 4.1 35.9 1.0 OD2 A:ASP142 4.1 37.8 1.0 CA A:THR68 4.1 36.8 1.0 O2A A:GDP1000 4.2 34.9 1.0 F2 A:ALF1001 4.2 32.6 1.0 O2B A:GDP1000 4.2 36.9 1.0 O A:LEU143 4.4 32.1 1.0 O A:PRO61 4.5 35.2 1.0 CG A:ASP142 4.5 44.5 1.0 O3A A:GDP1000 4.5 39.2 1.0 O A:HOH1004 4.6 39.4 1.0 CB A:LYS47 4.7 32.5 1.0 PA A:GDP1000 4.8 40.2 1.0 C A:LYS47 4.8 41.6 1.0 CE A:LYS47 4.8 37.9 1.0 NZ A:LYS47 4.9 32.3 1.0

Magnesium binding site 2 out of 2 in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:50.6 occ:1.00 O B:HOH1006 2.2 58.1 1.0 O1B B:GDP1000 2.2 46.3 1.0 O B:HOH1007 2.3 45.9 1.0 F4 B:ALF1001 2.4 46.9 1.0 OG B:SER48 2.6 47.1 1.0 OG1 B:THR68 2.8 49.6 1.0 CB B:THR68 3.2 45.4 1.0 OD1 B:ASP142 3.3 55.0 1.0 O B:LEU143 3.4 52.2 1.0 N B:SER48 3.5 40.6 1.0 PB B:GDP1000 3.5 38.6 1.0 CB B:SER48 3.6 39.3 1.0 AL B:ALF1001 3.8 46.4 1.0 O3B B:GDP1000 3.8 37.6 1.0 CG2 B:THR68 3.9 43.6 1.0 OD2 B:ASP142 3.9 44.7 1.0 CB B:LYS47 4.0 32.1 1.0 CG B:ASP142 4.0 48.6 1.0 O2B B:GDP1000 4.0 39.7 1.0 CA B:SER48 4.0 40.6 1.0 F2 B:ALF1001 4.1 49.8 1.0 CE B:LYS47 4.1 48.4 1.0 C B:LEU143 4.4 51.3 1.0 F1 B:ALF1001 4.4 47.1 1.0 C B:LYS47 4.4 44.3 1.0 NZ B:LYS47 4.5 37.6 1.0 CA B:THR68 4.5 47.7 1.0 CA B:LYS47 4.6 38.9 1.0 N B:THR68 4.7 41.0 1.0 O3A B:GDP1000 4.8 37.1 1.0 O2A B:GDP1000 4.8 43.4 1.0 N B:LEU143 4.8 45.7 1.0 N B:LYS47 4.9 42.2 1.0 O B:HOH1004 4.9 40.3 1.0

L.M.Yan, Y.Y.Ma, Y.N.Sun, J.Gao, X.Chen, J.Liu, C.Wang, Z.Rao, Z.Y.Lou. Structural Basis For Mechanochemical Role of Arabidopsis Thaliana Dynamin-Related Protein in Membrane Fission J Mol Cell Biol V. 3 378 2011.
ISSN: ISSN 1674-2788
PubMed: 22107825
DOI: 10.1093/JMCB/MJR032