Sodium in PDB 2v79: Crystal Structure of the N-Terminal Domain of Dnad From Bacillus Subtilis

The structure of Crystal Structure of the N-Terminal Domain of Dnad From Bacillus Subtilis, PDB code: 2v79 was solved by S.Schneider, W.Zhang, P.Soultanas, M.Paoli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.666, 78.666, 124.558, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21

The structure of Crystal Structure of the N-Terminal Domain of Dnad From Bacillus Subtilis also contains other interesting chemical elements:

Chlorine

(Cl)

11 atoms

The binding sites of Sodium atom in the Crystal Structure of the N-Terminal Domain of Dnad From Bacillus Subtilis (pdb code 2v79). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the N-Terminal Domain of Dnad From Bacillus Subtilis, PDB code: 2v79:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the N-Terminal Domain of Dnad From Bacillus Subtilis


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 the N-Terminal Domain of Dnad From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1116 b:32.2 occ:1.00 O A:ILE63 2.3 32.2 1.0 OE1 A:GLN58 2.4 35.7 1.0 O A:MET61 2.4 32.3 1.0 O A:HOH2080 2.4 34.7 1.0 O A:GLN58 2.5 31.0 1.0 O A:HOH2077 2.8 29.6 1.0 CD A:GLN58 3.4 35.7 1.0 C A:MET61 3.4 32.5 1.0 C A:GLN58 3.5 30.4 1.0 C A:ILE63 3.5 33.0 1.0 CB A:GLN58 3.9 29.7 1.0 N A:MET61 3.9 31.6 1.0 CA A:MET61 4.1 31.2 1.0 CA A:GLN58 4.2 29.0 1.0 N A:ILE63 4.2 33.2 1.0 C A:SER62 4.2 35.0 1.0 CG A:GLN58 4.2 32.2 1.0 NE2 A:GLN58 4.3 38.0 1.0 NZ B:LYS26 4.3 50.5 1.0 N A:SER64 4.3 34.0 1.0 CB A:MET61 4.3 29.0 1.0 CA A:SER64 4.4 35.3 1.0 N A:GLU59 4.4 31.7 1.0 O A:SER62 4.4 36.9 1.0 N A:SER62 4.4 33.6 1.0 CA A:ILE63 4.4 33.0 1.0 CA A:GLU59 4.6 36.1 1.0 N A:GLY60 4.6 32.5 1.0 CA A:SER62 4.7 36.0 1.0 O A:HOH2075 4.8 52.7 1.0 C A:GLU59 4.9 35.7 1.0 C A:SER64 5.0 34.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the N-Terminal Domain of Dnad From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the N-Terminal Domain of Dnad From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1117 b:39.9 occ:1.00 O A:HOH2026 2.3 28.2 1.0 OE1 A:GLU46 2.7 35.2 1.0 OG1 A:THR16 2.9 22.8 1.0 O A:HOH2063 3.3 25.8 1.0 CD A:GLU46 3.4 35.9 1.0 O A:THR14 3.4 23.1 1.0 OE2 A:GLU46 3.5 39.7 1.0 CG2 A:THR16 3.8 22.4 1.0 N A:THR16 3.8 22.0 1.0 CB A:THR16 3.8 21.9 1.0 NZ A:LYS42 4.0 25.6 1.0 O B:HOH2029 4.2 30.7 1.0 C A:SER15 4.4 22.7 1.0 CA A:THR16 4.4 21.7 1.0 CA A:SER15 4.4 23.9 1.0 C A:THR14 4.5 23.1 1.0 CG A:GLU46 4.6 31.6 1.0 O A:HOH2025 4.6 41.6 1.0 N A:SER15 5.0 23.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the N-Terminal Domain of Dnad From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the N-Terminal Domain of Dnad From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1118 b:30.0 occ:1.00 O B:ILE63 2.3 30.4 1.0 OE1 B:GLN58 2.3 27.5 1.0 O B:GLN58 2.3 27.0 1.0 O B:HOH2085 2.4 29.8 1.0 O B:MET61 2.6 28.1 1.0 O A:HOH2039 2.8 23.1 1.0 CD B:GLN58 3.3 28.9 1.0 C B:GLN58 3.3 27.5 1.0 C B:ILE63 3.5 31.2 1.0 C B:MET61 3.6 27.8 1.0 CB B:GLN58 3.8 27.6 1.0 O B:HOH2079 3.9 40.7 1.0 N B:MET61 4.0 28.1 1.0 CA B:GLN58 4.0 26.8 1.0 N B:ILE63 4.1 31.5 1.0 CG B:GLN58 4.1 28.4 1.0 NZ A:LYS26 4.2 48.6 1.0 CA B:MET61 4.2 27.4 1.0 NE2 B:GLN58 4.2 31.3 1.0 N B:GLU59 4.2 28.6 1.0 N B:SER64 4.3 33.0 1.0 CB B:MET61 4.4 26.7 1.0 C B:SER62 4.4 31.4 1.0 CA B:SER64 4.4 34.5 1.0 CA B:ILE63 4.4 31.4 1.0 N B:GLY60 4.5 32.1 1.0 CA B:GLU59 4.5 31.9 1.0 N B:SER62 4.5 28.2 1.0 O B:HOH2081 4.7 37.5 1.0 CA B:SER62 4.8 30.6 1.0 O B:SER62 4.8 33.6 1.0 C B:GLU59 4.8 31.7 1.0 C B:SER64 5.0 32.8 1.0

S.Schneider, W.Zhang, P.Soultanas, M.Paoli. Structure of the N-Terminal Oligomerization Domain of Dnad Reveals A Unique Tetramerization Motif and Provides Insights Into Scaffold Formation. J.Mol.Biol. V. 376 1237 2008.
ISSN: ISSN 0022-2836
PubMed: 18206906
DOI: 10.1016/J.JMB.2007.12.045