Sodium in PDB 3i2w: Crystal Structure of Efc/F-Bar Domain of Drosophila Syndapin/Pacsin

The structure of Crystal Structure of Efc/F-Bar Domain of Drosophila Syndapin/Pacsin, PDB code: 3i2w was solved by M.A.Edeling, D.J.Owen, L.M.Traub, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.07 / 2.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.595, 85.525, 192.860, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 25.8

The binding sites of Sodium atom in the Crystal Structure of Efc/F-Bar Domain of Drosophila Syndapin/Pacsin (pdb code 3i2w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Efc/F-Bar Domain of Drosophila Syndapin/Pacsin, PDB code: 3i2w:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Efc/F-Bar Domain of Drosophila Syndapin/Pacsin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Efc/F-Bar Domain of Drosophila Syndapin/Pacsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:26.6 occ:1.00 O A:GLU74 2.4 32.6 1.0 O A:GLY72 2.4 31.4 1.0 OE2 A:GLU79 2.7 35.3 1.0 O A:GLU70 2.8 39.2 1.0 O A:ILE69 2.9 33.1 1.0 CD A:GLU79 3.4 36.2 1.0 C A:GLU74 3.5 31.4 1.0 C A:GLY72 3.5 31.2 1.0 C A:GLU70 3.5 38.5 1.0 O A:HOH8 3.5 16.1 1.0 N A:GLU74 3.7 30.4 1.0 CA A:GLU70 3.9 37.7 1.0 C A:ILE69 3.9 32.5 1.0 C A:PRO73 4.0 29.5 1.0 OE1 A:GLU79 4.0 41.6 1.0 CA A:GLU74 4.1 30.6 1.0 N A:GLY72 4.2 35.4 1.0 O A:HOH348 4.2 49.9 1.0 CG A:GLU79 4.3 34.5 1.0 N A:GLU70 4.3 34.6 1.0 N A:PRO73 4.4 29.8 1.0 O A:HOH326 4.4 44.7 1.0 CA A:GLY72 4.4 32.0 1.0 N A:TYR75 4.5 32.2 1.0 O A:PRO73 4.5 31.4 1.0 CA A:PRO73 4.5 28.4 1.0 CA A:TYR75 4.6 33.8 1.0 C A:LYS71 4.6 36.7 1.0 N A:LYS71 4.6 38.5 1.0 CB A:GLU74 4.7 30.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Efc/F-Bar Domain of Drosophila Syndapin/Pacsin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Efc/F-Bar Domain of Drosophila Syndapin/Pacsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3 b:46.4 occ:1.00 O A:ASN273 3.4 35.0 1.0 CA A:ASN274 4.5 34.5 1.0 C A:ASN273 4.5 34.6 1.0 ND2 A:ASN274 4.6 39.2 1.0 O A:HOH330 4.7 34.8 1.0 O A:ALA275 4.7 37.0 1.0 OD2 A:ASP276 4.7 46.8 1.0 C A:ASN274 4.8 34.9 1.0 O A:ASN274 4.9 34.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Efc/F-Bar Domain of Drosophila Syndapin/Pacsin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Efc/F-Bar Domain of Drosophila Syndapin/Pacsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:33.5 occ:1.00 O B:GLU74 2.4 31.5 1.0 OE2 B:GLU79 2.5 35.2 1.0 O B:HOH322 2.6 48.7 1.0 O B:GLY72 2.7 32.2 1.0 O B:ILE69 2.8 35.1 1.0 O B:GLU70 2.8 42.4 1.0 CD B:GLU79 3.3 35.1 1.0 C B:GLU70 3.6 41.2 1.0 C B:GLU74 3.6 31.5 1.0 O B:HOH305 3.7 24.4 1.0 C B:GLY72 3.8 32.6 1.0 N B:GLU74 3.9 30.9 1.0 C B:ILE69 3.9 36.1 1.0 OE1 B:GLU79 4.0 40.3 1.0 CA B:GLU70 4.1 41.6 1.0 CG B:GLU79 4.1 30.4 1.0 C B:PRO73 4.3 30.2 1.0 CA B:GLU74 4.4 31.8 1.0 O B:HOH326 4.4 39.2 1.0 N B:GLY72 4.4 36.7 1.0 N B:GLU70 4.5 39.1 1.0 N B:PRO73 4.6 31.4 1.0 N B:LYS71 4.6 40.6 1.0 CA B:GLY72 4.6 33.8 1.0 N B:TYR75 4.7 30.7 1.0 CA B:PRO73 4.7 31.0 1.0 C B:LYS71 4.8 39.0 1.0 CA B:TYR75 4.8 30.4 1.0 O B:PRO73 4.9 29.4 1.0 CG2 B:ILE69 4.9 31.5 1.0 CB B:GLU74 5.0 31.2 1.0

M.A.Edeling, S.Sanker, T.Shima, P.K.Umasankar, S.Honing, H.Y.Kim, L.A.Davidson, S.C.Watkins, M.Tsang, D.J.Owen, L.M.Traub. Structural Requirements For Pacsin/Syndapin Operation During Zebrafish Embryonic Notochord Development. Plos One V. 4 E8150 2009.
ISSN: ESSN 1932-6203
PubMed: 19997509
DOI: 10.1371/JOURNAL.PONE.0008150