Sodium in PDB 1zdn: Ubiquitin-Conjugating Enzyme E2S

All present enzymatic activity of Ubiquitin-Conjugating Enzyme E2S:
6.3.2.19;

The structure of Ubiquitin-Conjugating Enzyme E2S, PDB code: 1zdn was solved by J.R.Walker, G.V.Avvakumov, S.Xue, E.M.Newman, F.Mackenzie, M.Sundstrom, C.Arrowsmith, A.Edwards, A.Bochkarev, 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)	27.00 / 1.93
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	115.586, 115.586, 44.905, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 23.4

The binding sites of Sodium atom in the Ubiquitin-Conjugating Enzyme E2S (pdb code 1zdn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ubiquitin-Conjugating Enzyme E2S, PDB code: 1zdn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ubiquitin-Conjugating Enzyme E2S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ubiquitin-Conjugating Enzyme E2S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na157 b:21.6 occ:1.00 O A:PRO123 2.3 16.9 1.0 OD1 B:ASN124 2.3 11.8 1.0 OD1 A:ASN124 2.4 16.9 1.0 O B:PRO123 2.4 16.6 1.0 O A:HOH161 2.6 24.9 1.0 C A:PRO123 3.3 17.6 1.0 C B:PRO123 3.4 17.1 1.0 CG B:ASN124 3.4 18.1 1.0 O A:HIS122 3.4 15.7 1.0 CG A:ASN124 3.5 18.7 1.0 CA B:ASN124 3.7 18.3 1.0 CA A:ASN124 3.7 17.9 1.0 O B:HIS122 3.7 15.8 1.0 C A:HIS122 3.9 15.8 1.0 N B:ASN124 3.9 17.4 1.0 N A:ASN124 3.9 17.8 1.0 O A:HOH160 4.0 19.8 1.0 O B:HOH164 4.0 20.8 1.0 CB B:ASN124 4.1 17.9 1.0 C B:HIS122 4.1 15.2 1.0 CB A:ASN124 4.2 17.6 1.0 CB A:HIS122 4.2 15.3 1.0 CB B:HIS122 4.2 15.0 1.0 N A:PRO123 4.4 16.2 1.0 CA A:PRO123 4.4 16.6 1.0 ND2 B:ASN124 4.5 19.0 1.0 N B:PRO123 4.5 15.1 1.0 CA A:HIS122 4.5 15.9 1.0 CA B:PRO123 4.5 15.2 1.0 ND2 A:ASN124 4.6 16.4 1.0 CD A:PRO125 4.7 20.7 1.0 CD B:PRO125 4.7 23.3 1.0 CA B:HIS122 4.7 15.3 1.0 OE1 B:GLU126 4.8 24.0 1.0 OE1 A:GLU126 4.9 21.3 1.0 OE2 A:GLU126 4.9 27.1 1.0 C B:ASN124 5.0 20.4 1.0

Sodium binding site 2 out of 2 in the Ubiquitin-Conjugating Enzyme E2S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ubiquitin-Conjugating Enzyme E2S within 5.0Å range: probe atom residue distance (Å) B Occ B:Na157 b:40.0 occ:1.00 O B:ASP39 2.2 32.5 1.0 O B:ASP42 2.3 28.0 1.0 O B:HOH192 2.5 47.4 1.0 O B:ASN36 2.6 36.0 1.0 O B:HOH167 2.7 55.1 1.0 C B:ASP39 3.2 32.6 1.0 O B:HOH206 3.3 30.4 1.0 C B:ASP42 3.5 27.6 1.0 C B:ASN36 3.6 36.6 1.0 N B:ASN36 3.8 33.3 1.0 CB B:ASP42 4.0 30.7 1.0 N B:LEU40 4.0 30.4 1.0 N B:ASP39 4.0 36.0 1.0 CA B:ASN36 4.0 35.9 1.0 CA B:LEU40 4.0 28.6 1.0 CB B:ASN36 4.0 36.4 1.0 CA B:ASP39 4.1 34.3 1.0 CA B:ASP42 4.2 28.7 1.0 OH B:TYR17 4.2 20.6 1.0 N B:ASP42 4.3 28.1 1.0 CB B:ASP39 4.5 35.0 1.0 C B:LEU40 4.5 28.0 1.0 OD1 B:ASP42 4.5 41.5 1.0 CG B:ASP42 4.5 36.7 1.0 N B:LEU43 4.6 24.4 1.0 CA B:LEU43 4.8 22.0 1.0 O B:LEU40 4.8 26.1 1.0 N B:GLU37 4.8 38.0 1.0 CD2 B:LEU40 4.8 28.0 1.0 C B:PRO35 4.9 31.7 1.0 ND2 B:ASN36 5.0 41.8 1.0 N B:THR41 5.0 27.4 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.
PubMed: 22496338
DOI: 10.1074/MCP.O111.013706