Zinc in PDB 8qjl: SMNUC1 Nuclease From Stenotrophomonas Maltophilia

The structure of SMNUC1 Nuclease From Stenotrophomonas Maltophilia, PDB code: 8qjl 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)	41.22 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.47, 72.97, 49.95, 90, 90, 90
R / Rfree (%)	11.9 / 16.1

The binding sites of Zinc atom in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia (pdb code 8qjl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia, PDB code: 8qjl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:8.8 occ:1.00 O A:HOH544 1.9 8.9 1.0 NE2 A:HIS32 2.0 7.8 1.0 OD1 A:ASP145 2.1 8.2 1.0 N A:TRP27 2.1 8.4 1.0 O A:TRP27 2.3 8.6 1.0 C A:TRP27 3.0 7.7 1.0 CA A:TRP27 3.0 7.2 1.0 CE1 A:HIS32 3.0 7.6 1.0 CD2 A:HIS32 3.0 7.5 1.0 CG A:ASP145 3.1 8.0 1.0 O A:HOH662 3.2 13.4 1.0 ZN A:ZN402 3.3 9.5 1.0 OD2 A:ASP145 3.4 7.8 1.0 CB A:TRP27 3.6 7.8 1.0 OD2 A:ASP71 3.7 11.0 1.0 NE2 A:HIS141 3.9 8.0 1.0 CE1 A:HIS141 4.0 8.3 1.0 ND1 A:HIS32 4.1 7.2 1.0 CG A:HIS32 4.2 7.3 1.0 CE1 A:HIS151 4.2 9.7 1.0 N A:GLY28 4.3 9.2 1.0 CG A:TRP27 4.3 8.9 1.0 NE2 A:HIS151 4.4 8.8 1.0 CD1 A:TRP27 4.4 10.0 1.0 CB A:ASP145 4.4 7.8 1.0 O A:HOH748 4.5 22.9 1.0 OD1 A:ASP179 4.6 9.6 1.0 CG A:ASP71 4.6 9.7 1.0 OD1 A:ASP71 4.7 9.9 1.0 CA A:ASP145 4.7 7.5 1.0 CD2 A:HIS141 4.8 8.1 1.0 ZN A:ZN403 4.8 11.9 0.9 O A:GLY28 4.9 9.5 1.0 O A:HOH804 5.0 20.4 1.0

Zinc binding site 2 out of 3 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:9.5 occ:1.00 O A:HOH544 2.0 8.9 1.0 ND1 A:HIS88 2.0 10.0 1.0 OD2 A:ASP145 2.1 7.8 1.0 NE2 A:HIS141 2.1 8.0 1.0 OD1 A:ASP71 2.5 9.9 1.0 O A:HOH748 2.5 22.9 1.0 CE1 A:HIS88 2.9 9.5 1.0 CG A:ASP145 3.1 8.0 1.0 CD2 A:HIS141 3.1 8.1 1.0 CG A:HIS88 3.2 10.4 1.0 CE1 A:HIS141 3.2 8.3 1.0 CG A:ASP71 3.3 9.7 1.0 ZN A:ZN401 3.3 8.8 1.0 OD1 A:ASP145 3.4 8.2 1.0 OD2 A:ASP71 3.5 11.0 1.0 CB A:HIS88 3.6 8.9 1.0 NE2 A:HIS32 4.1 7.8 1.0 NE2 A:HIS88 4.1 12.1 1.0 O A:HOH674 4.2 30.2 1.0 CD2 A:HIS88 4.2 11.8 1.0 CG A:HIS141 4.2 6.8 1.0 ND1 A:HIS141 4.3 7.2 1.0 CE1 A:HIS151 4.3 9.7 1.0 O A:HOH662 4.3 13.4 1.0 CB A:ASP145 4.4 7.8 1.0 CE1 A:HIS32 4.5 7.6 1.0 O A:HOH890 4.6 29.3 1.0 CB A:ASP71 4.7 10.0 1.0 CA A:HIS88 4.8 8.5 1.0 O A:HOH717 4.9 24.7 1.0 O A:TRP27 4.9 8.6 1.0 ND1 A:HIS151 5.0 9.4 1.0

Zinc binding site 3 out of 3 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:11.9 occ:0.90 OD2 A:ASP179 2.1 12.7 1.0 O A:HOH741 2.1 13.8 1.0 O A:HOH662 2.1 13.4 1.0 NE2 A:HIS151 2.1 8.8 1.0 NE2 A:HIS175 2.1 9.9 1.0 OD1 A:ASP179 2.5 9.6 1.0 CG A:ASP179 2.6 10.2 1.0 CE1 A:HIS151 3.0 9.7 1.0 CD2 A:HIS175 3.1 9.3 1.0 CE1 A:HIS175 3.1 9.8 1.0 CD2 A:HIS151 3.2 9.3 1.0 CB A:ASP179 4.1 9.1 1.0 ND1 A:HIS151 4.1 9.4 1.0 O A:HOH767 4.2 21.5 1.0 O A:HOH804 4.2 20.4 1.0 CG A:HIS175 4.2 9.9 1.0 O A:HOH890 4.2 29.3 1.0 CG A:HIS151 4.2 8.5 1.0 ND1 A:HIS175 4.2 9.9 1.0 O A:HOH585 4.3 20.4 1.0 N A:TRP27 4.3 8.4 1.0 O A:HOH748 4.4 22.9 1.0 NE2 A:GLN148 4.4 9.3 1.0 O A:HOH544 4.5 8.9 1.0 ZN A:ZN401 4.8 8.8 1.0 O A:HOH938 4.9 42.2 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