Atomistry » Sodium » PDB 1z2u-1zud » 1zdn
Atomistry »
  Sodium »
    PDB 1z2u-1zud »
      1zdn »

Sodium in PDB 1zdn: Ubiquitin-Conjugating Enzyme E2S

Enzymatic activity of Ubiquitin-Conjugating Enzyme E2S

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

Protein crystallography data

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

Sodium Binding Sites:

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 1zdn

Go back to Sodium Binding Sites List in 1zdn
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 1zdn

Go back to Sodium Binding Sites List in 1zdn
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

Reference:

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
Page generated: Tue Dec 15 05:44:24 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy