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

The structure of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-5'-Monophosphate, PDB code: 8qjo 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)	41.64 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.178, 73.068, 81.607, 90, 105.32, 90
R / Rfree (%)	17.1 / 20.9

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

Chlorine	(Cl)	1 atom
Zinc	(Zn)	6 atoms

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

Sodium binding site 1 out of 1 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-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 Guanosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na415 b:38.5 occ:1.00 OD2 B:ASP214 2.4 37.2 1.0 OG B:SER209 2.7 30.8 1.0 O B:HOH562 2.7 37.0 1.0 O B:HOH648 3.2 34.9 1.0 CB B:SER209 3.3 33.6 1.0 CG B:ASP214 3.4 36.4 1.0 CB B:ASP214 3.5 35.3 1.0 CZ2 B:TRP218 3.6 23.0 1.0 CH2 B:TRP218 3.6 25.2 1.0 CA B:SER209 3.6 37.0 1.0 N B:ASN210 3.7 37.1 1.0 CD1 B:LEU264 3.8 24.6 1.0 C B:SER209 4.1 39.8 1.0 CB B:LEU264 4.2 22.1 1.0 C B:ASN210 4.2 36.2 1.0 N B:PRO211 4.3 38.4 1.0 O B:ASN210 4.3 35.3 1.0 CA B:LEU264 4.3 23.1 1.0 CA B:PRO211 4.4 40.6 1.0 CG B:LEU264 4.5 24.2 1.0 OD1 B:ASP214 4.5 37.7 1.0 CA B:ASN210 4.6 37.1 1.0 OE1 B:GLN263 4.6 30.5 1.0 N B:LEU264 4.7 22.8 1.0 CE2 B:TRP218 4.7 23.7 1.0 CZ3 B:TRP218 4.7 26.4 1.0 CD B:PRO211 4.8 37.2 1.0 O B:ASN260 4.9 23.1 1.0 CD2 B:LEU264 5.0 25.2 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