Sodium in PDB 4kyw: Restriction Endonuclease Dpni in Complex with Two Dna Molecules

All present enzymatic activity of Restriction Endonuclease Dpni in Complex with Two Dna Molecules:
3.1.21.4;

The structure of Restriction Endonuclease Dpni in Complex with Two Dna Molecules, PDB code: 4kyw was solved by K.Mierzejewska, W.Siwek, H.Czapinska, K.Skowronek, J.M.Bujnicki, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.23 / 2.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	95.700, 101.050, 114.850, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 21.9

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

Zinc	(Zn)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Restriction Endonuclease Dpni in Complex with Two Dna Molecules (pdb code 4kyw). 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 Restriction Endonuclease Dpni in Complex with Two Dna Molecules, PDB code: 4kyw:

Sodium binding site 1 out of 1 in the Restriction Endonuclease Dpni in Complex with Two Dna Molecules


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Restriction Endonuclease Dpni in Complex with Two Dna Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:28.9 occ:1.00 OP1 C:DT6 2.0 27.3 1.0 O A:HOH422 2.2 36.4 1.0 O A:HOH403 2.3 27.2 1.0 OD1 A:ASP53 2.3 31.6 1.0 O3' C:6MA5 2.3 27.6 1.0 O A:HOH443 2.6 43.6 1.0 P C:DT6 2.6 27.8 1.0 CG A:ASP53 3.4 30.9 1.0 C3' C:6MA5 3.5 26.8 1.0 CA A:CA302 3.6 30.6 1.0 O5' C:DT6 3.7 31.1 1.0 OP2 C:DT6 3.8 23.9 1.0 OD2 A:ASP53 3.8 30.7 1.0 C4' C:6MA5 3.9 26.1 1.0 O A:HOH406 4.1 30.3 1.0 O A:HOH434 4.2 43.0 1.0 OE1 A:GLU64 4.2 28.9 1.0 O A:ARG49 4.3 33.5 1.0 O A:HOH405 4.3 31.6 1.0 OE2 A:GLU25 4.3 37.0 1.0 OE2 A:GLU64 4.4 25.5 1.0 O A:HOH425 4.4 32.7 1.0 O C:HOH205 4.5 34.0 1.0 C5' C:DT6 4.5 31.5 1.0 C5' C:6MA5 4.6 26.6 1.0 O A:ALA52 4.6 30.1 1.0 CB A:ASP53 4.7 30.7 1.0 C2' C:6MA5 4.7 26.6 1.0 CD A:GLU64 4.7 29.2 1.0 CA A:ASP53 4.8 30.6 1.0 C A:ALA52 4.8 29.8 1.0 N A:ASP53 4.9 30.5 1.0 N A:ALA52 4.9 29.1 1.0 O A:HOH452 5.0 36.0 1.0

K.Mierzejewska, W.Siwek, H.Czapinska, M.Kaus-Drobek, M.Radlinska, K.Skowronek, J.M.Bujnicki, M.Dadlez, M.Bochtler. Structural Basis of the Methylation Specificity of R.Dpni. Nucleic Acids Res. V. 42 8745 2014.
ISSN: ISSN 0305-1048
PubMed: 24966351
DOI: 10.1093/NAR/GKU546