Sodium in PDB 8qjm: SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-5'-Monophosphate

The structure of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-5'-Monophosphate, PDB code: 8qjm was solved by K.Adamkova, T.Koval, P.Kolenko, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.66 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.139, 72.805, 81.238, 90, 105.07, 90
R / Rfree (%)	17.3 / 19.8

The structure of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-5'-Monophosphate also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Sodium atom in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-5'-Monophosphate (pdb code 8qjm). 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 SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-5'-Monophosphate, PDB code: 8qjm:

Sodium binding site 1 out of 1 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na313 b:47.3 occ:1.00 O A:GLN198 2.4 7.3 1.0 O A:HOH878 2.4 27.6 1.0 O A:HOH685 3.1 20.0 1.0 C A:GLN198 3.5 6.9 1.0 O A:HOH688 3.6 27.4 1.0 O2 A:SO4312 3.6 53.0 1.0 CA A:GLN198 4.3 6.3 1.0 O A:HOH912 4.3 13.4 0.5 O3 A:SO4312 4.3 48.6 1.0 CB A:GLN198 4.4 6.5 1.0 N A:SER199 4.4 7.5 1.0 NH1 A:ARG255 4.5 7.5 1.0 S A:SO4312 4.6 52.7 1.0 NH2 A:ARG255 4.6 7.0 1.0 CA A:SER199 4.6 8.3 1.0 O A:GLN200 4.7 9.5 1.0 CZ A:ARG255 4.8 6.8 1.0 NH2 A:ARG42 5.0 12.8 1.0 C A:SER199 5.0 8.9 1.0

K.Adamkova, M.Trundova, T.Koval, B.Hustakova, J.Duskova, T.Skalova, P.Kolenko, J.Dohnalek. Substrate Preference, Rna Binding and Active Site Versatility of the Stenotrophomonas Maltophilia Nuclease SMNUC1, Explained By A Structural Study The Febs Journal 2024.
DOI: 10.1111/FEBS.17265