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Sodium in PDB 1wyw: Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase

Protein crystallography data

The structure of Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase, PDB code: 1wyw was solved by D.Baba, N.Maita, J.G.Jee, Y.Uchimura, H.Saitoh, K.Sugasawa, F.Hanaoka, H.Tochio, H.Hiroaki, M.Shirakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.212, 70.420, 106.434, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.5

Other elements in 1wyw:

The structure of Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase (pdb code 1wyw). 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 Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase, PDB code: 1wyw:

Sodium binding site 1 out of 1 in 1wyw

Go back to Sodium Binding Sites List in 1wyw
Sodium binding site 1 out of 1 in the Crystal Structure of SUMO1-Conjugated Thymine Dna Glycosylase


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 SUMO1-Conjugated Thymine Dna Glycosylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:10.0
occ:1.00
N B:ASP73 3.0 16.4 1.0
CG B:ASP73 3.2 21.1 1.0
OD2 B:ASP73 3.4 20.8 1.0
O B:HOH228 3.5 15.2 1.0
CB B:ASP73 3.5 18.4 1.0
NZ B:LYS48 3.6 15.5 1.0
OD1 B:ASP73 3.6 22.3 1.0
CA B:ASP73 3.8 16.3 1.0
CA B:ALA72 3.9 15.6 1.0
C B:ALA72 3.9 15.1 1.0
CB B:ALA72 4.4 15.3 1.0
O B:ILE71 4.7 13.6 1.0
CE B:LYS48 5.0 15.2 1.0

Reference:

D.Baba, N.Maita, J.G.Jee, Y.Uchimura, H.Saitoh, K.Sugasawa, F.Hanaoka, H.Tochio, H.Hiroaki, M.Shirakawa. Crystal Structure of Thymine Dna Glycosylase Conjugated to Sumo-1. Nature V. 435 979 2005.
ISSN: ISSN 0028-0836
PubMed: 15959518
DOI: 10.1038/NATURE03634
Page generated: Tue Dec 15 05:41:26 2020

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