Sodium in PDB 3ndh: Restriction Endonuclease in Complex with Substrate Dna

The structure of Restriction Endonuclease in Complex with Substrate Dna, PDB code: 3ndh was solved by M.Firczuk, M.Wojciechowski, H.Czapinska, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.51 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.310, 72.910, 88.760, 90.00, 101.99, 90.00
R / Rfree (%)	17.2 / 18.3

The structure of Restriction Endonuclease in Complex with Substrate Dna also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Restriction Endonuclease in Complex with Substrate Dna (pdb code 3ndh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Restriction Endonuclease in Complex with Substrate Dna, PDB code: 3ndh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Restriction Endonuclease in Complex with Substrate Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Restriction Endonuclease in Complex with Substrate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na217 b:12.7 occ:1.00 O A:ILE92 2.2 13.4 1.0 OP1 D:DC7 2.3 11.6 0.5 OP1 C:DC7 2.3 11.1 0.5 OD2 A:ASP82 2.4 13.1 1.0 O A:HOH232 2.4 15.8 1.0 O A:HOH228 2.4 15.5 1.0 O C:HOH17 2.5 13.2 1.0 CG A:ASP82 3.3 13.2 1.0 P D:DC7 3.3 9.6 0.5 C A:ILE92 3.4 12.4 1.0 OD1 A:ASP82 3.5 14.8 1.0 P C:DC7 3.5 14.0 0.5 OP2 D:DC7 3.6 10.3 0.5 O5' D:DC7 3.9 10.8 0.5 O5' C:DC7 3.9 12.9 0.5 N A:ILE92 3.9 12.0 1.0 C5' C:DC7 4.0 12.2 0.5 OP2 C:DC7 4.1 13.7 0.5 C5' D:DC7 4.2 9.7 0.5 CA A:ILE92 4.2 12.5 1.0 CG A:LYS93 4.2 17.5 1.0 NZ A:LYS93 4.4 19.5 1.0 N A:LYS93 4.4 12.3 1.0 O A:GLU80 4.5 16.0 1.0 O C:HOH16 4.5 14.6 1.0 OE1 A:GLU54 4.6 19.1 1.0 CB A:ILE92 4.6 12.2 1.0 OG A:SER91 4.6 16.1 1.0 CA A:LYS93 4.6 12.9 1.0 CB A:ASP82 4.6 13.4 1.0 O3' D:DG6 4.7 10.5 0.5 OP2 C:DG8 4.7 9.5 0.5 O3' C:DG6 4.7 12.3 0.5 OP1 D:DG8 4.8 13.6 0.5 CE A:LYS93 4.9 19.1 1.0 OP2 D:DG8 4.9 15.8 0.5 C A:SER91 5.0 12.2 1.0 OP1 C:DG8 5.0 9.4 0.5 O3' C:DC7 5.0 9.2 0.5

Sodium binding site 2 out of 2 in the Restriction Endonuclease in Complex with Substrate Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Restriction Endonuclease in Complex with Substrate Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na217 b:14.3 occ:1.00 OP1 C:DC7 2.2 11.5 0.5 O B:ILE92 2.2 14.6 1.0 OP1 D:DC7 2.4 12.1 0.5 O B:HOH251 2.4 17.8 1.0 O B:HOH261 2.4 15.0 1.0 OD2 B:ASP82 2.4 14.7 1.0 O B:HOH362 2.5 15.4 1.0 CG B:ASP82 3.3 15.9 1.0 P D:DC7 3.4 9.4 0.5 P C:DC7 3.4 13.3 0.5 C B:ILE92 3.4 13.9 1.0 OD1 B:ASP82 3.4 16.3 1.0 OP2 D:DC7 3.7 12.0 0.5 N B:ILE92 3.9 13.5 1.0 O5' C:DC7 3.9 12.6 0.5 OP2 C:DC7 4.0 11.9 0.5 O5' D:DC7 4.0 10.9 0.5 C5' C:DC7 4.0 10.8 0.5 CG B:LYS93 4.1 18.0 1.0 CA B:ILE92 4.2 13.6 1.0 C5' D:DC7 4.3 10.9 0.5 NZ B:LYS93 4.3 19.3 1.0 N B:LYS93 4.4 13.6 1.0 O B:GLU80 4.4 18.3 1.0 O D:HOH17 4.5 15.1 1.0 OE1 B:GLU54 4.5 17.2 1.0 CB B:ILE92 4.6 13.2 1.0 CA B:LYS93 4.6 13.7 1.0 O3' C:DG6 4.6 13.4 0.5 OG B:SER91 4.6 12.0 0.5 CB B:ASP82 4.7 14.9 1.0 OP2 D:DG8 4.7 10.4 0.5 O3' D:DG6 4.7 9.7 0.5 CE B:LYS93 4.9 19.5 1.0 OP1 D:DG8 4.9 12.3 0.5 C B:SER91 4.9 13.6 0.5 C B:SER91 4.9 14.3 0.5 OP2 C:DG8 5.0 14.9 0.5 O3' C:DC7 5.0 10.7 0.5 CB B:LYS93 5.0 15.3 1.0

M.Firczuk, M.Wojciechowski, H.Czapinska, M.Bochtler. Dna Intercalation Without Flipping in the Specific Thai-Dna Complex Nucleic Acids Res. V. 39 744 2011.
ISSN: ISSN 0305-1048
PubMed: 20861000
DOI: 10.1093/NAR/GKQ834