Sodium in PDB 2jhj: 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus

All present enzymatic activity of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus:
3.2.2.21;

The structure of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus, PDB code: 2jhj was solved by I.Leiros, M.P.Nabong, K.Grosvik, J.Ringvoll, G.T.Haugland, L.Uldal, K.Reite, I.K.Olsbu, I.Knaevelsrud, E.Moe, O.A.Andersen, N.K.Birkeland, P.Ruoff, A.Klungland, S.Bjelland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 1.9
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.890, 48.850, 104.460, 90.00, 106.07, 90.00
R / Rfree (%)	18.1 / 23.9

The binding sites of Sodium atom in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus (pdb code 2jhj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus, PDB code: 2jhj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1296 b:15.3 occ:1.00 O A:THR213 2.3 12.0 1.0 O A:ILE218 2.3 9.0 1.0 O A:PHE215 2.5 11.4 1.0 O A:HOH2239 2.6 14.2 1.0 O A:HOH2238 3.3 15.9 1.0 C A:THR213 3.3 10.7 1.0 C A:ILE218 3.4 9.7 1.0 C A:PHE215 3.5 12.3 1.0 N A:ILE218 3.8 11.8 1.0 CA A:THR213 3.9 10.8 1.0 CA A:ILE218 4.1 10.0 1.0 N A:GLY217 4.1 14.5 1.0 CA A:LYS216 4.2 14.2 1.0 N A:LYS216 4.3 13.5 1.0 N A:PHE215 4.3 11.4 1.0 CB A:THR213 4.3 9.0 1.0 N A:GLY219 4.4 10.1 1.0 N A:SER214 4.4 11.3 1.0 C A:SER214 4.5 12.4 1.0 CA A:PHE215 4.5 11.8 1.0 CA A:GLY219 4.5 8.6 1.0 C A:LYS216 4.6 14.0 1.0 CB A:ILE218 4.6 9.8 1.0 CA A:SER214 4.7 11.6 1.0 C A:GLY217 4.8 13.5 1.0 O A:LEU212 4.9 8.4 1.0 O A:SER214 5.0 13.3 1.0

Sodium binding site 2 out of 4 in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1297 b:21.1 occ:1.00 O A:LEU24 2.2 17.2 1.0 O A:HOH2027 2.3 31.8 1.0 O A:ASP28 2.3 13.4 1.0 O A:LEU21 2.4 19.2 1.0 OG1 A:THR26 2.7 12.6 1.0 O A:PRO22 3.0 19.8 1.0 C A:PRO22 3.4 19.8 1.0 C A:LEU24 3.4 17.4 1.0 C A:LEU21 3.5 19.3 1.0 C A:ASP28 3.5 13.2 1.0 CA A:PRO22 3.5 19.5 1.0 N A:THR26 3.7 14.1 1.0 CB A:THR26 3.8 14.0 1.0 CG2 A:THR26 4.0 12.9 1.0 N A:LEU24 4.0 19.4 1.0 N A:PRO22 4.0 19.3 1.0 O A:HOH2148 4.1 27.9 1.0 N A:GLU23 4.2 20.3 1.0 CA A:LEU24 4.2 18.8 1.0 CA A:VAL29 4.3 13.8 1.0 N A:PRO25 4.3 16.4 1.0 CA A:PRO25 4.3 15.6 1.0 N A:VAL29 4.3 13.5 1.0 CA A:THR26 4.4 13.1 1.0 CA A:ASP28 4.4 13.2 1.0 C A:PRO25 4.5 15.1 1.0 CB A:ASP28 4.5 14.1 1.0 C A:GLU23 4.5 21.3 1.0 N A:ASP28 4.6 12.1 1.0 O A:HOH2028 4.7 37.0 1.0 CA A:LEU21 4.7 19.4 1.0 CB A:LEU24 4.8 19.0 1.0 CB A:LEU21 4.9 19.2 1.0 CA A:GLU23 4.9 20.9 1.0 CB A:PRO22 5.0 19.0 1.0

Sodium binding site 3 out of 4 in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1296 b:17.8 occ:1.00 O B:THR213 2.3 12.7 1.0 O B:ILE218 2.3 10.6 1.0 O B:HOH2231 2.4 13.8 1.0 O B:PHE215 2.4 13.9 1.0 C B:THR213 3.3 12.4 1.0 O B:HOH2230 3.3 14.9 1.0 C B:ILE218 3.4 11.5 1.0 C B:PHE215 3.5 13.8 1.0 CA B:THR213 3.8 12.2 1.0 N B:ILE218 3.8 14.0 1.0 N B:GLY217 4.1 15.5 1.0 CA B:ILE218 4.1 12.1 1.0 N B:PHE215 4.2 13.6 1.0 N B:LYS216 4.2 15.3 1.0 CA B:LYS216 4.2 15.3 1.0 CB B:THR213 4.3 12.6 1.0 N B:GLY219 4.3 10.2 1.0 N B:SER214 4.4 14.1 1.0 CA B:PHE215 4.4 13.8 1.0 C B:SER214 4.4 15.2 1.0 CA B:GLY219 4.5 10.6 1.0 CB B:ILE218 4.6 12.3 1.0 C B:LYS216 4.6 15.6 1.0 C B:GLY217 4.8 14.6 1.0 CA B:SER214 4.8 14.7 1.0 O B:LEU212 4.9 10.6 1.0 O B:SER214 4.9 15.9 1.0

Sodium binding site 4 out of 4 in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1297 b:26.4 occ:1.00 O B:HOH2029 2.3 32.9 1.0 O B:LEU24 2.3 21.6 1.0 O B:ASP28 2.3 16.6 1.0 O B:LEU21 2.5 24.1 1.0 OG1 B:THR26 2.7 18.6 1.0 O B:PRO22 2.9 24.4 1.0 C B:PRO22 3.3 24.2 1.0 C B:ASP28 3.4 16.0 1.0 C B:LEU24 3.5 22.3 1.0 CA B:PRO22 3.5 23.8 1.0 C B:LEU21 3.5 23.2 1.0 CB B:THR26 3.8 18.3 1.0 N B:THR26 3.9 18.6 1.0 CG2 B:THR26 3.9 19.6 1.0 O B:HOH2143 3.9 37.6 1.0 N B:LEU24 4.0 23.9 1.0 N B:PRO22 4.0 23.4 1.0 N B:GLU23 4.1 24.6 1.0 CA B:VAL29 4.2 17.4 1.0 N B:VAL29 4.2 16.9 1.0 CA B:LEU24 4.3 23.0 1.0 CA B:ASP28 4.3 16.3 1.0 N B:PRO25 4.4 21.4 1.0 CB B:ASP28 4.4 16.5 1.0 CA B:PRO25 4.5 20.9 1.0 C B:GLU23 4.5 25.0 1.0 CA B:THR26 4.5 18.0 1.0 N B:ASP28 4.5 15.4 1.0 C B:PRO25 4.6 20.2 1.0 O B:HOH2028 4.6 33.6 1.0 CA B:GLU23 4.8 25.8 1.0 CA B:LEU21 4.8 23.3 1.0 CB B:LEU24 4.8 23.2 1.0 N B:VAL30 4.9 18.2 1.0 CB B:LEU21 4.9 23.3 1.0 CB B:PRO22 5.0 23.3 1.0

I.Leiros, M.P.Nabong, K.Grosvik, J.Ringvoll, G.T.Haugland, L.Uldal, K.Reite, I.K.Olsbu, I.Knaevelsrud, E.Moe, O.A.Andersen, N.K.Birkeland, P.Ruoff, A.Klungland, S.Bjelland. Structural Basis For Enzymatic Excision of N1- Methyladenine and N3-Methylcytosine From Dna Embo J. V. 26 2206 2007.
ISSN: ISSN 0261-4189
PubMed: 17396151
DOI: 10.1038/SJ.EMBOJ.7601662