Sodium in PDB 2jhn: 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: 2jhn 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 / 1.8
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.494, 49.968, 105.798, 90.00, 107.43, 90.00
R / Rfree (%)	18.5 / 22.3

The structure of 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus also contains other interesting chemical elements:

Mercury

(Hg)

4 atoms

The binding sites of Sodium atom in the 3-Methyladenine Dna-Glycosylase From Archaeoglobus Fulgidus (pdb code 2jhn). 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: 2jhn:
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:Na1298 b:18.8 occ:1.00 O A:THR213 2.3 15.0 1.0 O A:ILE218 2.4 14.0 1.0 O A:PHE215 2.4 16.8 1.0 O A:HOH2167 2.4 17.0 1.0 O A:HOH2165 2.5 19.2 1.0 C A:THR213 3.3 14.2 1.0 O A:HOH2163 3.4 26.5 1.0 C A:ILE218 3.5 13.7 1.0 C A:PHE215 3.5 18.1 1.0 CA A:THR213 3.8 13.8 1.0 N A:ILE218 3.9 15.2 1.0 N A:GLY217 4.0 18.1 1.0 CA A:LYS216 4.1 20.4 1.0 CA A:ILE218 4.2 14.2 1.0 N A:LYS216 4.2 18.9 1.0 N A:PHE215 4.2 16.6 1.0 CB A:THR213 4.3 12.4 1.0 N A:SER214 4.4 14.5 1.0 N A:GLY219 4.4 12.8 1.0 CA A:PHE215 4.5 17.0 1.0 C A:SER214 4.5 17.2 1.0 C A:LYS216 4.5 19.6 1.0 CB A:ILE218 4.6 14.1 1.0 CA A:GLY219 4.7 12.4 1.0 CA A:SER214 4.8 16.3 1.0 C A:GLY217 4.9 16.4 1.0 O A:LEU212 4.9 12.6 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:Na1299 b:22.3 occ:1.00 O A:HOH2028 2.1 27.5 1.0 O A:LEU24 2.2 21.4 1.0 O A:ASP28 2.3 13.6 1.0 O A:LEU21 2.6 25.8 1.0 OG1 A:THR26 2.8 20.8 1.0 O A:PRO22 3.2 24.4 1.0 C A:LEU24 3.4 22.4 1.0 C A:ASP28 3.4 13.2 1.0 C A:PRO22 3.5 24.4 1.0 C A:LEU21 3.5 25.7 1.0 CA A:PRO22 3.7 24.5 1.0 N A:THR26 3.8 18.5 1.0 O A:HOH2023 3.8 41.3 1.0 CB A:THR26 3.8 18.9 1.0 CG2 A:THR26 3.8 18.3 1.0 N A:LEU24 4.0 23.7 1.0 N A:PRO22 4.0 25.4 1.0 CA A:LEU24 4.3 22.9 1.0 N A:VAL29 4.3 14.1 1.0 CA A:VAL29 4.3 15.8 1.0 N A:GLU23 4.4 24.1 1.0 CA A:ASP28 4.4 14.3 1.0 N A:PRO25 4.4 21.6 1.0 O A:HOH2027 4.4 29.4 1.0 CA A:THR26 4.4 17.9 1.0 CA A:PRO25 4.5 20.6 1.0 CB A:ASP28 4.5 13.9 1.0 C A:PRO25 4.6 19.7 1.0 N A:ASP28 4.6 13.3 1.0 C A:GLU23 4.6 24.3 1.0 CB A:LEU24 4.7 23.4 1.0 CA A:LEU21 4.7 26.0 1.0 CB A:LEU21 5.0 26.0 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:Na1298 b:9.9 occ:1.00 O B:THR213 2.3 7.8 1.0 O B:ILE218 2.4 6.8 1.0 O B:PHE215 2.4 9.0 1.0 O B:HOH2225 2.5 12.4 1.0 O B:HOH2226 3.3 16.4 1.0 C B:THR213 3.3 8.5 1.0 C B:ILE218 3.4 5.9 1.0 C B:PHE215 3.4 9.5 1.0 N B:ILE218 3.8 6.4 1.0 CA B:THR213 3.8 8.1 1.0 CA B:ILE218 4.1 5.9 1.0 N B:GLY217 4.1 8.7 1.0 CA B:LYS216 4.1 10.4 1.0 N B:LYS216 4.2 10.2 1.0 N B:PHE215 4.2 8.7 1.0 CB B:THR213 4.3 6.6 1.0 N B:SER214 4.4 7.7 1.0 N B:GLY219 4.4 5.5 1.0 CA B:PHE215 4.4 8.7 1.0 C B:SER214 4.4 10.2 1.0 CB B:ILE218 4.5 5.4 1.0 C B:LYS216 4.5 9.7 1.0 CA B:GLY219 4.7 5.5 1.0 CA B:SER214 4.8 8.9 1.0 C B:GLY217 4.8 8.1 1.0 O B:LEU212 4.9 5.3 1.0 O B:HOH2229 4.9 38.4 1.0 O B:SER214 4.9 12.0 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:Na1299 b:20.1 occ:1.00 O B:HOH2032 2.1 26.0 1.0 O B:ASP28 2.3 11.5 1.0 O B:LEU24 2.3 17.1 1.0 O B:LEU21 2.6 19.0 1.0 OG1 B:THR26 2.8 17.0 1.0 O B:PRO22 3.0 21.7 1.0 C B:PRO22 3.4 20.9 1.0 C B:ASP28 3.4 12.4 1.0 C B:LEU24 3.5 18.0 1.0 C B:LEU21 3.6 19.9 1.0 CA B:PRO22 3.6 20.2 1.0 O B:HOH2028 3.7 32.0 1.0 N B:THR26 3.8 13.6 1.0 CG2 B:THR26 3.8 14.1 1.0 CB B:THR26 3.8 13.5 1.0 N B:LEU24 4.0 19.9 1.0 N B:PRO22 4.1 19.9 1.0 CA B:VAL29 4.2 13.5 1.0 N B:VAL29 4.2 13.1 1.0 N B:GLU23 4.3 21.2 1.0 CA B:LEU24 4.3 18.7 1.0 CA B:ASP28 4.4 11.8 1.0 N B:PRO25 4.4 17.5 1.0 CA B:THR26 4.4 13.9 1.0 CA B:PRO25 4.5 16.3 1.0 CB B:ASP28 4.5 11.7 1.0 C B:PRO25 4.5 15.5 1.0 C B:GLU23 4.6 21.4 1.0 O B:HOH2031 4.6 32.2 1.0 N B:ASP28 4.7 10.8 1.0 CB B:LEU24 4.8 18.9 1.0 CA B:LEU21 4.8 19.9 1.0 N B:VAL30 4.9 13.5 1.0 CA B:GLU23 5.0 21.9 1.0 CB B:LEU21 5.0 20.2 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