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

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State, PDB code: 3t34:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na1003 b:45.0 occ:1.00 F3 A:ALF1001 2.4 46.9 1.0 O A:GLY63 2.5 39.2 1.0 O A:GLY65 2.6 44.9 1.0 OG A:SER44 2.7 33.0 1.0 O3B A:GDP1000 2.8 33.5 1.0 F1 A:ALF1001 2.9 53.8 1.0 AL A:ALF1001 3.1 41.2 1.0 C A:GLY63 3.4 35.5 1.0 CG1 A:VAL67 3.5 46.5 1.0 C A:GLY65 3.7 48.2 1.0 N A:SER64 3.8 57.1 1.0 O2A A:GDP1000 3.8 34.9 1.0 N A:VAL67 3.8 39.5 1.0 CB A:SER44 3.9 36.4 1.0 C A:SER64 3.9 47.3 1.0 CA A:SER44 3.9 35.6 1.0 O A:SER64 3.9 47.3 1.0 C5' A:GDP1000 3.9 34.7 1.0 PB A:GDP1000 4.0 34.5 1.0 O3A A:GDP1000 4.2 39.2 1.0 F2 A:ALF1001 4.2 32.6 1.0 N A:SER44 4.2 39.1 1.0 N A:GLY65 4.2 44.4 1.0 CA A:SER64 4.2 43.3 1.0 O A:HOH1007 4.2 36.6 1.0 F4 A:ALF1001 4.5 35.8 1.0 CB A:VAL67 4.5 48.6 1.0 CA A:ILE66 4.5 44.1 1.0 CA A:GLY63 4.5 42.0 1.0 C A:ILE66 4.5 46.3 1.0 PA A:GDP1000 4.5 40.2 1.0 N A:GLY63 4.6 42.3 1.0 N A:ILE66 4.6 42.9 1.0 CA A:GLY65 4.6 52.3 1.0 CA A:VAL67 4.7 39.4 1.0 O5' A:GDP1000 4.8 42.8 1.0 O1B A:GDP1000 4.8 39.7 1.0 O A:HOH1004 4.9 39.4 1.0 CG2 A:VAL67 4.9 44.8 1.0 CG A:GLN43 5.0 43.0 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1003 b:42.5 occ:1.00 O B:GLY65 2.5 44.0 1.0 O B:GLY63 2.5 50.4 1.0 OG B:SER44 2.6 38.9 1.0 F1 B:ALF1001 2.6 47.1 1.0 F3 B:ALF1001 2.8 60.0 1.0 O3B B:GDP1000 2.9 37.6 1.0 C B:GLY63 3.1 47.5 1.0 N B:SER64 3.2 54.7 1.0 AL B:ALF1001 3.5 46.4 1.0 C B:GLY65 3.6 47.9 1.0 CG2 B:VAL67 3.6 56.7 1.0 CB B:SER44 3.7 46.2 1.0 CA B:SER44 3.8 37.9 1.0 O2A B:GDP1000 3.8 43.4 1.0 N B:GLY65 3.8 55.6 1.0 N B:VAL67 3.9 42.9 1.0 C B:SER64 3.9 57.7 1.0 C5' B:GDP1000 4.0 39.4 1.0 CA B:SER64 4.0 49.9 1.0 CG1 B:VAL67 4.1 46.3 1.0 N B:SER44 4.2 33.7 1.0 PB B:GDP1000 4.3 38.6 1.0 CB B:VAL67 4.3 53.6 1.0 CA B:GLY65 4.4 55.6 1.0 CA B:GLY63 4.5 54.0 1.0 N B:ILE66 4.5 41.3 1.0 C B:ILE66 4.5 49.6 1.0 O B:SER64 4.5 56.4 1.0 CG B:GLN43 4.6 44.9 1.0 CA B:ILE66 4.6 50.3 1.0 O B:HOH1004 4.6 40.3 1.0 PA B:GDP1000 4.6 40.4 1.0 O3A B:GDP1000 4.6 37.1 1.0 N B:GLY63 4.6 50.9 1.0 CA B:VAL67 4.7 46.7 1.0 O5' B:GDP1000 4.8 39.9 1.0 F4 B:ALF1001 4.8 46.9 1.0 F2 B:ALF1001 4.9 49.8 1.0 C4' B:GDP1000 5.0 39.5 1.0 O B:HOH1007 5.0 45.9 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