Zinc in PDB 8qjn: SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate

The structure of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate, PDB code: 8qjn 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)	43.39 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.47, 72.741, 82.752, 90, 102.68, 90
R / Rfree (%)	17.5 / 21.4

The binding sites of Zinc atom in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate (pdb code 8qjn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate, PDB code: 8qjn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:11.3 occ:1.00 NE2 A:HIS32 2.0 10.4 1.0 O A:HOH559 2.0 21.8 1.0 OD1 A:ASP145 2.1 8.9 1.0 N A:TRP27 2.2 9.3 1.0 O A:TRP27 2.2 10.2 1.0 O A:HOH527 2.5 43.2 1.0 C A:TRP27 3.0 9.7 1.0 CA A:TRP27 3.0 9.2 1.0 CE1 A:HIS32 3.0 10.9 1.0 CG A:ASP145 3.0 8.7 1.0 CD2 A:HIS32 3.0 9.6 1.0 ZN A:ZN402 3.4 12.0 1.0 OD2 A:ASP145 3.4 9.6 1.0 CB A:TRP27 3.7 8.4 1.0 OD2 A:ASP71 3.8 16.1 1.0 NE2 A:HIS141 3.9 9.7 1.0 CE1 A:HIS151 4.1 10.0 1.0 NE2 A:HIS151 4.1 8.8 1.0 ND1 A:HIS32 4.1 9.4 1.0 CG A:HIS32 4.2 9.6 1.0 CE1 A:HIS141 4.2 9.8 1.0 N A:GLY28 4.3 9.2 1.0 CB A:ASP145 4.4 8.3 1.0 CG A:TRP27 4.5 8.8 1.0 CD1 A:TRP27 4.6 8.7 1.0 ZN A:ZN403 4.6 13.7 1.0 OD1 A:ASP71 4.6 15.5 1.0 CG A:ASP71 4.6 15.2 1.0 OD1 A:ASP179 4.7 12.0 1.0 O A:HOH623 4.7 47.5 1.0 CA A:ASP145 4.7 8.0 1.0 O A:HOH721 4.8 25.2 1.0 O A:GLY28 4.9 10.9 1.0 CD2 A:HIS141 4.9 10.4 1.0 OD2 A:ASP179 4.9 12.7 1.0 ND1 A:HIS151 4.9 9.1 1.0 CG A:ASP179 5.0 11.2 1.0

Zinc binding site 2 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:12.0 occ:1.00 O A:HOH559 1.8 21.8 1.0 OD2 A:ASP145 2.0 9.6 1.0 ND1 A:HIS88 2.0 8.4 1.0 NE2 A:HIS141 2.1 9.7 1.0 OD1 A:ASP71 2.4 15.5 1.0 CE1 A:HIS88 2.8 9.2 1.0 CD2 A:HIS141 3.0 10.4 1.0 CG A:ASP145 3.1 8.7 1.0 CE1 A:HIS141 3.1 9.8 1.0 CG A:HIS88 3.2 9.1 1.0 CG A:ASP71 3.3 15.2 1.0 ZN A:ZN401 3.4 11.3 1.0 OD1 A:ASP145 3.5 8.9 1.0 OD2 A:ASP71 3.5 16.1 1.0 CB A:HIS88 3.7 9.4 1.0 NH1 A:ARG74 3.8 41.5 1.0 NE2 A:HIS32 4.0 10.4 1.0 O A:HOH527 4.0 43.2 1.0 NE2 A:HIS88 4.0 9.3 1.0 CG A:HIS141 4.2 9.7 1.0 ND1 A:HIS141 4.2 9.6 1.0 CD2 A:HIS88 4.2 10.0 1.0 CE1 A:HIS151 4.3 10.0 1.0 CB A:ASP145 4.4 8.3 1.0 CE1 A:HIS32 4.4 10.9 1.0 O A:HOH623 4.6 47.5 1.0 CB A:ASP71 4.7 14.2 1.0 CZ A:ARG74 4.7 46.7 1.0 CA A:HIS88 4.7 9.3 1.0 NH2 A:ARG74 4.8 47.1 1.0 O A:TRP27 4.9 10.2 1.0 O A:HOH721 4.9 25.2 1.0 ND1 A:HIS151 5.0 9.1 1.0 CD2 A:HIS32 5.0 9.6 1.0

Zinc binding site 3 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:13.7 occ:1.00 NE2 A:HIS175 2.0 11.9 1.0 OD2 A:ASP179 2.1 12.7 1.0 NE2 A:HIS151 2.1 8.8 1.0 O A:HOH721 2.2 25.2 1.0 O A:HOH527 2.5 43.2 1.0 CG A:ASP179 2.7 11.2 1.0 OD1 A:ASP179 2.7 12.0 1.0 CD2 A:HIS175 3.0 11.6 1.0 CE1 A:HIS151 3.0 10.0 1.0 CE1 A:HIS175 3.1 12.2 1.0 CD2 A:HIS151 3.1 9.6 1.0 ND1 A:HIS151 4.1 9.1 1.0 CG A:HIS175 4.1 11.3 1.0 O A:HOH623 4.1 47.5 1.0 CB A:ASP179 4.2 10.4 1.0 ND1 A:HIS175 4.2 10.6 1.0 N A:TRP27 4.2 9.3 1.0 CG A:HIS151 4.2 9.8 1.0 O A:HOH734 4.3 21.7 0.5 O A:HOH559 4.4 21.8 1.0 NE2 A:GLN148 4.5 9.9 0.6 O A:HOH689 4.5 38.1 1.0 ZN A:ZN401 4.6 11.3 1.0 O A:TRP27 4.8 10.2 1.0 O A:HOH756 4.9 40.1 1.0 CA A:TRP27 4.9 9.2 1.0 C A:TRP27 5.0 9.7 1.0 CG A:GLN148 5.0 8.3 0.4

Zinc binding site 4 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:15.1 occ:1.00 O3 B:PO4404 2.0 39.9 1.0 OD1 B:ASP145 2.0 10.8 1.0 NE2 B:HIS32 2.0 12.2 1.0 N B:TRP27 2.1 12.2 1.0 O B:TRP27 2.2 14.4 1.0 O4 B:PO4404 2.7 33.6 1.0 P B:PO4404 2.9 46.5 1.0 C B:TRP27 3.0 12.8 1.0 CD2 B:HIS32 3.0 12.0 1.0 CA B:TRP27 3.0 12.9 1.0 CG B:ASP145 3.1 9.8 1.0 CE1 B:HIS32 3.1 13.5 1.0 OD2 B:ASP145 3.4 10.0 1.0 ZN B:ZN402 3.4 18.8 1.0 CB B:TRP27 3.7 12.6 1.0 OD2 B:ASP71 3.8 23.8 1.0 O2 B:PO4404 3.9 41.9 1.0 NE2 B:HIS141 4.0 11.8 1.0 O1 B:PO4404 4.0 46.0 1.0 CE1 B:HIS141 4.1 13.9 1.0 CG B:HIS32 4.2 12.1 1.0 ND1 B:HIS32 4.2 11.6 1.0 CE1 B:HIS151 4.2 11.1 1.0 NE2 B:HIS151 4.2 12.7 1.0 N B:GLY28 4.2 12.8 1.0 CB B:ASP145 4.4 9.7 1.0 CG B:TRP27 4.5 11.4 1.0 OD1 B:ASP179 4.5 10.9 1.0 ZN B:ZN403 4.5 23.9 1.0 CD1 B:TRP27 4.6 11.4 1.0 OD1 B:ASP71 4.6 20.4 1.0 CG B:ASP71 4.7 24.1 1.0 CA B:ASP145 4.7 10.3 1.0 O B:GLY28 4.9 14.8 1.0 CG B:ASP179 5.0 12.8 1.0 CD2 B:HIS141 5.0 14.1 1.0

Zinc binding site 5 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:18.8 occ:1.00 OD2 B:ASP145 2.0 10.0 1.0 NE2 B:HIS141 2.1 11.8 1.0 ND1 B:HIS88 2.1 16.7 1.0 O3 B:PO4404 2.2 39.9 1.0 OD1 B:ASP71 2.4 20.4 1.0 O2 B:PO4404 2.6 41.9 1.0 CE1 B:HIS88 2.9 17.1 1.0 P B:PO4404 3.0 46.5 1.0 CG B:ASP145 3.0 9.8 1.0 CD2 B:HIS141 3.1 14.1 1.0 CE1 B:HIS141 3.1 13.9 1.0 CG B:HIS88 3.3 16.9 1.0 CG B:ASP71 3.4 24.1 1.0 OD1 B:ASP145 3.4 10.8 1.0 ZN B:ZN401 3.4 15.1 1.0 OD2 B:ASP71 3.6 23.8 1.0 CB B:HIS88 3.7 16.6 1.0 NH2 B:ARG74 3.8 45.5 1.0 O4 B:PO4404 4.0 33.6 1.0 O1 B:PO4404 4.1 46.0 1.0 NE2 B:HIS88 4.1 17.7 1.0 NE2 B:HIS32 4.1 12.2 1.0 ND1 B:HIS141 4.2 13.6 1.0 CG B:HIS141 4.2 14.2 1.0 CD2 B:HIS88 4.3 17.9 1.0 CB B:ASP145 4.3 9.7 1.0 CE1 B:HIS151 4.4 11.1 1.0 CE1 B:HIS32 4.5 13.5 1.0 CZ B:ARG74 4.7 49.1 1.0 CA B:HIS88 4.7 16.2 1.0 CB B:ASP71 4.8 23.4 1.0 NH1 B:ARG74 4.8 49.7 1.0 O2' B:AMP406 4.8 37.2 1.0 O B:TRP27 5.0 14.4 1.0

Zinc binding site 6 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Adenosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:23.9 occ:1.00 NE2 B:HIS175 2.1 15.1 1.0 O4 B:PO4404 2.1 33.6 1.0 O3' B:AMP406 2.2 32.5 1.0 NE2 B:HIS151 2.2 12.7 1.0 OD2 B:ASP179 2.2 12.8 1.0 OD1 B:ASP179 2.5 10.9 1.0 CG B:ASP179 2.7 12.8 1.0 CD2 B:HIS175 3.0 14.6 1.0 CE1 B:HIS151 3.0 11.1 1.0 CE1 B:HIS175 3.1 14.6 1.0 CD2 B:HIS151 3.2 11.2 1.0 P B:PO4404 3.4 46.5 1.0 C3' B:AMP406 3.5 44.2 1.0 O2 B:PO4404 3.8 41.9 1.0 C4' B:AMP406 3.8 44.2 1.0 O4' B:AMP406 3.9 43.8 1.0 C1' B:AMP406 3.9 39.6 1.0 O1 B:PO4404 4.0 46.0 1.0 CB B:ASP179 4.2 12.2 1.0 CG B:HIS175 4.2 13.9 1.0 ND1 B:HIS151 4.2 11.2 1.0 N B:TRP27 4.2 12.2 1.0 ND1 B:HIS175 4.2 13.1 1.0 C2' B:AMP406 4.2 40.2 1.0 CG B:HIS151 4.3 10.7 1.0 O2' B:AMP406 4.3 37.2 1.0 NE2 B:GLN148 4.4 10.8 1.0 ZN B:ZN401 4.5 15.1 1.0 O3 B:PO4404 4.6 39.9 1.0 O B:TRP27 4.8 14.4 1.0 CA B:TRP27 5.0 12.9 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