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

The structure of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Uridine - 5'- Monophosphate, PDB code: 8qjp 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)	43.41 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.434, 72.8, 82.928, 90, 102.3, 90
R / Rfree (%)	13.4 / 16.7

The binding sites of Zinc atom in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Uridine - 5'- Monophosphate (pdb code 8qjp). 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 Uridine - 5'- Monophosphate, PDB code: 8qjp:
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 Uridine - 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 Uridine - 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:11.0 occ:1.00 O A:HOH588 1.9 12.7 1.0 NE2 A:HIS32 2.0 10.2 1.0 OD1 A:ASP145 2.1 10.6 1.0 N A:TRP27 2.1 10.0 1.0 O A:TRP27 2.2 12.2 1.0 C A:TRP27 3.0 10.6 1.0 CA A:TRP27 3.0 10.2 1.0 CE1 A:HIS32 3.0 8.7 1.0 CD2 A:HIS32 3.1 9.9 1.0 CG A:ASP145 3.1 9.8 1.0 ZN A:ZN402 3.3 11.2 1.0 OD2 A:ASP145 3.4 10.3 1.0 OD2 A:ASP71 3.6 14.6 1.0 CB A:TRP27 3.7 9.9 1.0 NE2 A:HIS141 3.9 10.1 1.0 CE1 A:HIS151 3.9 11.6 1.0 NE2 A:HIS151 4.1 11.5 1.0 ND1 A:HIS32 4.2 9.4 1.0 CE1 A:HIS141 4.2 10.0 1.0 CG A:HIS32 4.2 9.8 1.0 N A:GLY28 4.3 10.3 1.0 CB A:ASP145 4.4 10.1 1.0 CG A:TRP27 4.4 9.9 1.0 CD1 A:TRP27 4.5 10.2 1.0 CG A:ASP71 4.5 11.6 1.0 OD1 A:ASP71 4.6 12.4 1.0 ZN A:ZN403 4.6 12.0 1.0 OD1 A:ASP179 4.7 12.2 1.0 ND1 A:HIS151 4.7 10.3 1.0 CA A:ASP145 4.7 9.5 1.0 O A:HOH752 4.8 43.6 1.0 OD2 A:ASP179 4.9 13.3 1.0 CD2 A:HIS141 4.9 10.0 1.0 CG A:ASP179 4.9 10.7 1.0 O A:GLY28 4.9 10.7 1.0 CD2 A:HIS151 5.0 10.7 1.0

Zinc binding site 2 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Uridine - 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 Uridine - 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:11.2 occ:1.00 O A:HOH588 1.9 12.7 1.0 ND1 A:HIS88 2.0 10.4 1.0 NE2 A:HIS141 2.1 10.1 1.0 OD2 A:ASP145 2.1 10.3 1.0 OD1 A:ASP71 2.3 12.4 1.0 CE1 A:HIS88 2.8 11.7 1.0 CD2 A:HIS141 3.1 10.0 1.0 CG A:ASP145 3.1 9.8 1.0 CE1 A:HIS141 3.1 10.0 1.0 CG A:ASP71 3.2 11.6 1.0 CG A:HIS88 3.2 11.0 1.0 ZN A:ZN401 3.3 11.0 1.0 OD2 A:ASP71 3.3 14.6 1.0 OD1 A:ASP145 3.4 10.6 1.0 CB A:HIS88 3.7 9.8 1.0 NE2 A:HIS32 4.0 10.2 1.0 O2' A:U5P409 4.0 21.5 0.8 NE2 A:HIS88 4.1 11.6 1.0 O A:HOH655 4.1 30.2 1.0 ND1 A:HIS141 4.2 10.2 1.0 CG A:HIS141 4.2 10.2 1.0 CD2 A:HIS88 4.2 12.1 1.0 CE1 A:HIS151 4.2 11.6 1.0 CE1 A:HIS32 4.4 8.7 1.0 CB A:ASP145 4.4 10.1 1.0 CB A:ASP71 4.6 12.7 1.0 CA A:HIS88 4.8 9.9 1.0 ND1 A:HIS151 4.8 10.3 1.0 O A:TRP27 4.9 12.2 1.0 CD2 A:HIS32 4.9 9.9 1.0

Zinc binding site 3 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Uridine - 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 Uridine - 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:12.0 occ:1.00 OD2 A:ASP179 1.9 13.3 1.0 NE2 A:HIS151 2.0 11.5 1.0 NE2 A:HIS175 2.0 12.1 1.0 CG A:ASP179 2.7 10.7 1.0 OD1 A:ASP179 2.9 12.2 1.0 CE1 A:HIS151 3.0 11.6 1.0 CD2 A:HIS175 3.0 11.6 1.0 CE1 A:HIS175 3.0 12.6 1.0 CD2 A:HIS151 3.0 10.7 1.0 ND1 A:HIS151 4.1 10.3 1.0 O2 A:U5P409 4.1 20.8 0.8 CG A:HIS175 4.1 10.3 1.0 ND1 A:HIS175 4.1 11.3 1.0 CG A:HIS151 4.2 9.9 1.0 CB A:ASP179 4.2 10.6 1.0 N A:TRP27 4.2 10.0 1.0 O A:HOH588 4.3 12.7 1.0 ZN A:ZN401 4.6 11.0 1.0 NE2 A:GLN148 4.6 10.3 0.4 O2' A:U5P409 4.8 21.5 0.8 C1' A:U5P409 4.8 16.5 0.8 O A:TRP27 4.8 12.2 1.0 CA A:TRP27 4.9 10.2 1.0 C A:TRP27 4.9 10.6 1.0 C2 A:U5P409 5.0 17.6 0.8

Zinc binding site 4 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Uridine - 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 Uridine - 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:17.5 occ:1.00 O3 B:PO4404 1.8 37.6 0.5 O B:HOH505 2.0 19.8 0.5 NE2 B:HIS32 2.0 18.2 1.0 OD1 B:ASP145 2.1 16.3 1.0 N B:TRP27 2.1 16.8 1.0 O B:TRP27 2.2 17.5 1.0 C B:TRP27 3.0 17.7 1.0 CA B:TRP27 3.0 15.9 1.0 CE1 B:HIS32 3.0 16.5 1.0 CD2 B:HIS32 3.1 17.1 1.0 P B:PO4404 3.1 34.6 0.5 CG B:ASP145 3.1 16.0 1.0 O4 B:PO4404 3.3 30.9 0.5 ZN B:ZN402 3.4 19.5 1.0 OD2 B:ASP145 3.5 17.6 1.0 OD2 B:ASP71 3.7 24.4 1.0 CB B:TRP27 3.7 16.7 1.0 NE2 B:HIS141 4.0 17.8 1.0 O2 B:PO4404 4.0 39.6 0.5 O1 B:PO4404 4.1 41.5 0.5 ND1 B:HIS32 4.1 16.6 1.0 CE1 B:HIS141 4.2 17.2 1.0 CG B:HIS32 4.2 16.3 1.0 CE1 B:HIS151 4.2 17.8 1.0 N B:GLY28 4.3 16.4 1.0 NE2 B:HIS151 4.3 16.2 1.0 CB B:ASP145 4.4 14.5 1.0 CG B:TRP27 4.5 15.5 1.0 OD1 B:ASP179 4.5 16.3 1.0 CD1 B:TRP27 4.5 15.6 1.0 ZN B:ZN403 4.6 18.7 0.6 CG B:ASP71 4.6 20.7 1.0 OD1 B:ASP71 4.6 23.3 1.0 CA B:ASP145 4.7 15.4 1.0 CD2 B:HIS141 4.9 18.4 1.0 O B:GLY28 4.9 16.8 1.0 CG B:ASP179 5.0 16.8 1.0

Zinc binding site 5 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Uridine - 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 Uridine - 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:19.5 occ:1.00 O B:HOH505 1.9 19.8 0.5 ND1 B:HIS88 2.0 18.3 1.0 OD2 B:ASP145 2.1 17.6 1.0 NE2 B:HIS141 2.1 17.8 1.0 O3 B:PO4404 2.2 37.6 0.5 OD1 B:ASP71 2.3 23.3 1.0 O2 B:PO4404 2.7 39.6 0.5 CE1 B:HIS88 2.8 17.2 1.0 P B:PO4404 3.0 34.6 0.5 CG B:ASP145 3.1 16.0 1.0 CD2 B:HIS141 3.1 18.4 1.0 CE1 B:HIS141 3.1 17.2 1.0 CG B:ASP71 3.2 20.7 1.0 CG B:HIS88 3.2 17.6 1.0 ZN B:ZN401 3.4 17.5 1.0 OD1 B:ASP145 3.4 16.3 1.0 OD2 B:ASP71 3.4 24.4 1.0 CB B:HIS88 3.7 16.4 1.0 O1 B:PO4404 3.8 41.5 0.5 O B:HOH654 3.9 37.1 1.0 NE2 B:HIS88 4.1 21.2 1.0 NE2 B:HIS32 4.1 18.2 1.0 CD2 B:HIS88 4.2 20.3 1.0 ND1 B:HIS141 4.3 18.4 1.0 CG B:HIS141 4.3 17.4 1.0 O4 B:PO4404 4.3 30.9 0.5 CB B:ASP145 4.4 14.5 1.0 CE1 B:HIS151 4.4 17.8 1.0 CE1 B:HIS32 4.5 16.5 1.0 CB B:ASP71 4.6 20.8 1.0 CA B:HIS88 4.8 17.0 1.0 O2' B:U5P406 4.9 27.1 1.0 O B:TRP27 5.0 17.5 1.0 O3' B:U5P406 5.0 38.1 1.0

Zinc binding site 6 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Uridine - 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 Uridine - 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:18.7 occ:0.60 O4 B:PO4404 1.9 30.9 0.5 NE2 B:HIS175 2.1 18.4 1.0 NE2 B:HIS151 2.1 16.2 1.0 OD2 B:ASP179 2.2 23.7 1.0 OD1 B:ASP179 2.4 16.3 1.0 CG B:ASP179 2.6 16.8 1.0 CE1 B:HIS151 2.9 17.8 1.0 CD2 B:HIS175 3.0 18.4 1.0 CE1 B:HIS175 3.1 17.8 1.0 CD2 B:HIS151 3.2 15.8 1.0 P B:PO4404 3.2 34.6 0.5 O2 B:PO4404 3.7 39.6 0.5 O3' B:U5P406 3.9 38.1 1.0 ND1 B:HIS151 4.0 16.7 1.0 C1' B:U5P406 4.0 26.5 1.0 O4' B:U5P406 4.1 26.3 1.0 CB B:ASP179 4.1 16.1 1.0 N B:TRP27 4.1 16.8 1.0 O1 B:PO4404 4.2 41.5 0.5 ND1 B:HIS175 4.2 17.6 1.0 CG B:HIS175 4.2 15.6 1.0 O3 B:PO4404 4.2 37.6 0.5 CG B:HIS151 4.2 14.4 1.0 C4' B:U5P406 4.3 29.6 1.0 NE2 B:GLN148 4.3 14.7 1.0 O B:HOH505 4.4 19.8 0.5 O2 B:U5P406 4.5 27.3 1.0 ZN B:ZN401 4.6 17.5 1.0 C3' B:U5P406 4.6 34.9 1.0 O2' B:U5P406 4.6 27.1 1.0 C2' B:U5P406 4.7 28.5 1.0 CA B:TRP27 4.9 15.9 1.0 O B:TRP27 4.9 17.5 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