Sodium in PDB 2z5d: Human Ubiquitin-Conjugating Enzyme E2 H

All present enzymatic activity of Human Ubiquitin-Conjugating Enzyme E2 H:
6.3.2.19;

The structure of Human Ubiquitin-Conjugating Enzyme E2 H, PDB code: 2z5d was solved by A.Bochkarev, H.Cui, J.R.Walker, E.M.Newman, F.Mackenzie, K.P.Battaile, M.Sundstrom, C.Arrowsmith, A.Edwards, S.Dhe-Paganon, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.80 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.959, 85.861, 102.558, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.3

The binding sites of Sodium atom in the Human Ubiquitin-Conjugating Enzyme E2 H (pdb code 2z5d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Ubiquitin-Conjugating Enzyme E2 H, PDB code: 2z5d:

Sodium binding site 1 out of 1 in the Human Ubiquitin-Conjugating Enzyme E2 H


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Ubiquitin-Conjugating Enzyme E2 H within 5.0Å range: probe atom residue distance (Å) B Occ B:Na180 b:22.7 occ:1.00 O B:ILE38 2.2 15.5 1.0 O B:HIS42 2.4 18.5 1.0 O B:SER40 2.4 18.9 1.0 O B:HOH216 2.4 24.8 1.0 O B:HOH214 2.5 21.3 1.0 C B:ILE38 3.2 15.5 1.0 O B:LEU37 3.3 15.2 1.0 C B:HIS42 3.4 17.9 1.0 C B:SER40 3.5 19.2 1.0 CA B:ILE38 3.8 15.5 1.0 N B:SER40 3.9 18.5 1.0 N B:HIS42 4.0 18.1 1.0 C B:GLU39 4.1 18.8 1.0 C B:LYS41 4.2 19.1 1.0 N B:GLU39 4.2 16.4 1.0 OG B:SER40 4.2 18.4 1.0 CA B:SER40 4.3 18.9 1.0 CA B:HIS42 4.3 18.0 1.0 N B:GLU43 4.3 17.9 1.0 C B:LEU37 4.3 15.3 1.0 CA B:GLU43 4.4 18.6 1.0 N B:LYS41 4.5 20.0 1.0 O B:LYS41 4.5 19.2 1.0 O B:GLU39 4.5 19.9 1.0 CA B:GLU39 4.5 18.4 1.0 N B:VAL44 4.6 16.8 1.0 CG2 B:VAL44 4.6 14.3 1.0 N B:ILE38 4.6 15.2 1.0 CA B:LYS41 4.7 20.5 1.0 CG2 B:ILE38 4.9 15.7 1.0 CB B:SER40 4.9 18.6 1.0 C B:GLU43 5.0 17.4 1.0

Y.Sheng, J.H.Hong, R.Doherty, T.Srikumar, J.Shloush, G.V.Avvakumov, J.R.Walker, S.Xue, D.Neculai, J.W.Wan, S.K.Kim, C.H.Arrowsmith, B.Raught, S.Dhe-Paganon. A Human Ubiquitin Conjugating Enzyme (E2)-Hect E3 Ligase Structure-Function Screen. Mol.Cell Proteomics V. 11 329 2012.
ISSN: ISSN 1535-9476
PubMed: 22496338
DOI: 10.1074/MCP.O111.013706