Sodium in PDB 6qm2: Nlaiv Restriction Endonuclease

All present enzymatic activity of Nlaiv Restriction Endonuclease:
3.1.21.4;

The structure of Nlaiv Restriction Endonuclease, PDB code: 6qm2 was solved by H.Czapinska, W.Siwek, R.H.Szczepanowski, J.M.Bujnicki, M.Bochtler, K.Skowronek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.72 / 2.80
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	110.380, 110.380, 209.006, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 22.1

The structure of Nlaiv Restriction Endonuclease also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Sodium atom in the Nlaiv Restriction Endonuclease (pdb code 6qm2). 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 Nlaiv Restriction Endonuclease, PDB code: 6qm2:

Sodium binding site 1 out of 1 in the Nlaiv Restriction Endonuclease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nlaiv Restriction Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:0.0 occ:1.00 O A:MET70 2.1 0.6 1.0 O A:ASN67 2.2 0.2 1.0 O A:PRO72 2.5 100.0 1.0 O A:HOH452 2.5 0.7 1.0 OG A:SER65 2.5 0.8 1.0 C A:MET70 3.3 0.2 1.0 C A:ASN67 3.4 0.2 1.0 CB A:SER65 3.4 0.2 1.0 O A:HOH453 3.4 94.7 1.0 O A:HOH492 3.5 95.2 1.0 C A:PRO72 3.6 0.5 1.0 C A:PRO71 3.8 0.1 1.0 N A:PRO72 4.0 0.7 1.0 CA A:PRO71 4.0 0.6 1.0 O A:PRO71 4.1 0.5 1.0 N A:PRO71 4.1 0.6 1.0 CB A:ASN67 4.2 0.1 1.0 CA A:ASN67 4.2 0.9 1.0 N A:MET70 4.2 0.8 1.0 CA A:MET70 4.3 0.3 1.0 CA A:PRO72 4.4 0.1 1.0 N A:THR68 4.4 0.9 1.0 N A:ASN67 4.4 0.5 1.0 CA A:THR68 4.5 0.9 1.0 CD A:PRO72 4.6 0.0 1.0 N A:ASP73 4.6 0.1 1.0 C A:THR68 4.6 0.5 1.0 CB A:MET70 4.7 0.1 1.0 OD1 A:ASP73 4.7 0.6 1.0 CG A:ASN67 4.8 0.8 1.0 CA A:SER65 4.8 0.3 1.0 O A:THR68 4.8 0.4 1.0 CA A:ASP73 4.8 0.6 1.0 O A:HOH454 4.8 96.4 1.0

H.Czapinska, W.Siwek, R.H.Szczepanowski, J.M.Bujnicki, M.Bochtler, K.J.Skowronek. Crystal Structure and Directed Evolution of Specificity of Nlaiv Restriction Endonuclease. J.Mol.Biol. V. 431 2082 2019.
ISSN: ESSN 1089-8638
PubMed: 30995450
DOI: 10.1016/J.JMB.2019.04.010