Zinc 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:

Sodium

(Na)

1 atom

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-5'-Monophosphate, PDB code: 8qjm:
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 Cytidine-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 Cytidine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:4.5 occ:1.00 NE2 A:HIS32 2.0 3.7 1.0 O2P A:C5P301 2.0 11.7 1.0 OD1 A:ASP145 2.1 3.7 1.0 N A:TRP27 2.2 4.6 1.0 O A:TRP27 2.2 4.8 1.0 CD2 A:HIS32 2.9 3.7 1.0 CE1 A:HIS32 2.9 3.8 1.0 C A:TRP27 2.9 4.4 1.0 CA A:TRP27 3.0 4.3 1.0 CG A:ASP145 3.1 3.5 1.0 P A:C5P301 3.3 10.1 1.0 OD2 A:ASP145 3.5 3.4 1.0 ZN A:ZN402 3.7 5.2 1.0 CB A:TRP27 3.7 4.3 1.0 OD2 A:ASP71 3.8 7.1 1.0 O1P A:C5P301 3.9 8.8 1.0 ND1 A:HIS32 4.0 3.6 1.0 CG A:HIS32 4.1 3.5 1.0 NE2 A:HIS141 4.1 3.8 1.0 CE1 A:HIS141 4.1 4.0 1.0 O5' A:C5P301 4.2 11.5 1.0 N A:GLY28 4.3 4.4 1.0 C5' A:C5P301 4.3 13.4 1.0 NE2 A:HIS151 4.3 5.5 1.0 CE1 A:HIS151 4.3 5.1 1.0 ZN A:ZN403 4.4 9.1 1.0 OD1 A:ASP179 4.4 6.7 1.0 O3P A:C5P301 4.4 13.4 1.0 CG A:TRP27 4.5 4.1 1.0 CB A:ASP145 4.5 3.5 1.0 CD1 A:TRP27 4.6 4.1 1.0 CG A:ASP71 4.6 6.2 1.0 OD1 A:ASP71 4.6 6.6 1.0 CA A:ASP145 4.7 3.7 1.0 CG A:ASP179 4.7 6.7 1.0 O A:GLY28 4.8 4.2 1.0 OD2 A:ASP179 4.8 8.0 1.0

Zinc binding site 2 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-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 Cytidine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:5.2 occ:1.00 ND1 A:HIS88 2.0 6.0 1.0 NE2 A:HIS141 2.0 3.8 1.0 OD2 A:ASP145 2.0 3.4 1.0 O1P A:C5P301 2.1 8.8 1.0 OD1 A:ASP71 2.2 6.6 1.0 CE1 A:HIS88 2.9 6.2 1.0 CE1 A:HIS141 3.0 4.0 1.0 CD2 A:HIS141 3.1 4.1 1.0 CG A:ASP145 3.1 3.5 1.0 CG A:ASP71 3.1 6.2 1.0 CG A:HIS88 3.2 5.7 1.0 P A:C5P301 3.2 10.1 1.0 OD2 A:ASP71 3.4 7.1 1.0 OD1 A:ASP145 3.5 3.7 1.0 O2P A:C5P301 3.5 11.7 1.0 CB A:HIS88 3.6 5.8 1.0 ZN A:ZN401 3.7 4.5 1.0 NH1 A:ARG74 3.9 8.7 1.0 O5' A:C5P301 3.9 11.5 1.0 NE2 A:HIS88 4.1 6.1 1.0 ND1 A:HIS141 4.1 4.0 1.0 NE2 A:HIS32 4.2 3.7 1.0 CG A:HIS141 4.2 3.8 1.0 CD2 A:HIS88 4.2 5.9 1.0 CB A:ASP145 4.4 3.5 1.0 CE1 A:HIS32 4.5 3.8 1.0 CB A:ASP71 4.5 6.5 1.0 CE1 A:HIS151 4.5 5.1 1.0 O3P A:C5P301 4.6 13.4 1.0 CA A:HIS88 4.7 6.0 1.0 CZ A:ARG74 4.8 9.0 1.0 CA A:ASP71 4.8 6.5 1.0 N A:ASP71 4.8 6.3 1.0 NH2 A:ARG74 4.9 9.2 1.0

Zinc binding site 3 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-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 Cytidine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:9.1 occ:1.00 O3P A:C5P301 1.9 13.4 1.0 NE2 A:HIS151 2.0 5.5 1.0 NE2 A:HIS175 2.0 7.3 1.0 OD2 A:ASP179 2.1 8.0 1.0 OD1 A:ASP179 2.4 6.7 1.0 CG A:ASP179 2.6 6.7 1.0 O2P A:C5P301 2.8 11.7 1.0 CE1 A:HIS151 2.9 5.1 1.0 P A:C5P301 3.0 10.1 1.0 CE1 A:HIS175 3.0 7.4 1.0 CD2 A:HIS175 3.1 7.5 1.0 CD2 A:HIS151 3.1 5.8 1.0 N A:TRP27 4.0 4.6 1.0 ND1 A:HIS151 4.0 5.7 1.0 O5' A:C5P301 4.1 11.5 1.0 CB A:ASP179 4.1 6.2 1.0 CG A:HIS151 4.1 5.7 1.0 O1P A:C5P301 4.1 8.8 1.0 ND1 A:HIS175 4.2 7.6 1.0 CG A:HIS175 4.2 7.6 1.0 C5' A:C5P301 4.3 13.4 1.0 O A:HOH881 4.3 11.7 1.0 ZN A:ZN401 4.4 4.5 1.0 NE2 A:GLN148 4.4 5.2 1.0 O A:HOH800 4.6 20.5 1.0 OD1 A:ASP145 4.8 3.7 1.0 O A:TRP27 4.9 4.8 1.0 CA A:TRP27 4.9 4.3 1.0

Zinc binding site 4 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-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 Cytidine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:6.0 occ:1.00 O2P B:C5P301 1.9 19.3 1.0 N B:TRP27 2.0 4.2 1.0 NE2 B:HIS32 2.1 7.4 1.0 OD1 B:ASP145 2.1 4.5 1.0 O B:TRP27 2.2 4.9 1.0 C B:TRP27 2.9 4.3 1.0 CA B:TRP27 2.9 4.3 1.0 CD2 B:HIS32 3.0 6.7 1.0 O3P B:C5P301 3.1 18.3 1.0 CE1 B:HIS32 3.1 7.3 1.0 CG B:ASP145 3.1 4.7 1.0 P B:C5P301 3.1 17.6 1.0 OD2 B:ASP145 3.5 4.7 1.0 ZN B:ZN402 3.6 9.7 1.0 CB B:TRP27 3.7 4.4 1.0 OD2 B:ASP71 3.9 11.6 1.0 NE2 B:HIS141 4.0 6.9 1.0 O5' B:C5P301 4.1 16.4 1.0 O1P B:C5P301 4.1 15.8 1.0 ND1 B:HIS32 4.2 6.8 1.0 CG B:HIS32 4.2 6.7 1.0 N B:GLY28 4.2 4.3 1.0 CE1 B:HIS141 4.2 6.8 1.0 CE1 B:HIS151 4.3 6.4 1.0 NE2 B:HIS151 4.3 6.1 1.0 C5' B:C5P301 4.4 20.8 1.0 OD1 B:ASP179 4.4 6.3 1.0 CB B:ASP145 4.4 4.7 1.0 CG B:TRP27 4.5 4.5 1.0 ZN B:ZN403 4.5 13.1 1.0 CD1 B:TRP27 4.6 4.5 1.0 CA B:ASP145 4.7 4.6 1.0 OD1 B:ASP71 4.8 11.8 1.0 CG B:ASP71 4.8 11.5 1.0 O B:GLY28 4.8 4.2 1.0 CG B:ASP179 4.8 6.4 1.0 CA B:GLY28 5.0 4.4 1.0 CD2 B:HIS141 5.0 6.4 1.0

Zinc binding site 5 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-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 Cytidine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:9.7 occ:1.00 ND1 B:HIS88 2.0 7.0 1.0 OD2 B:ASP145 2.1 4.7 1.0 NE2 B:HIS141 2.1 6.9 1.0 O2P B:C5P301 2.3 19.3 1.0 OD1 B:ASP71 2.4 11.8 1.0 O1P B:C5P301 2.4 15.8 1.0 CE1 B:HIS88 2.8 6.9 1.0 P B:C5P301 2.9 17.6 1.0 CD2 B:HIS141 3.0 6.4 1.0 CG B:ASP145 3.1 4.7 1.0 CG B:HIS88 3.2 7.0 1.0 CE1 B:HIS141 3.2 6.8 1.0 CG B:ASP71 3.4 11.5 1.0 OD1 B:ASP145 3.5 4.5 1.0 OD2 B:ASP71 3.6 11.6 1.0 ZN B:ZN401 3.6 6.0 1.0 CB B:HIS88 3.7 7.1 1.0 O5' B:C5P301 3.9 16.4 1.0 NH2 B:ARG74 3.9 19.0 1.0 NE2 B:HIS88 4.0 6.6 1.0 O3P B:C5P301 4.1 18.3 1.0 NE2 B:HIS32 4.2 7.4 1.0 CD2 B:HIS88 4.2 7.4 1.0 CG B:HIS141 4.2 6.0 1.0 ND1 B:HIS141 4.3 6.6 1.0 CB B:ASP145 4.4 4.7 1.0 CE1 B:HIS151 4.5 6.4 1.0 CE1 B:HIS32 4.6 7.3 1.0 CA B:HIS88 4.7 7.4 1.0 CZ B:ARG74 4.7 20.3 1.0 CB B:ASP71 4.7 11.1 1.0 NH1 B:ARG74 4.8 22.8 1.0

Zinc binding site 6 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine-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 Cytidine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:13.1 occ:1.00 O3P B:C5P301 2.0 18.3 1.0 NE2 B:HIS151 2.1 6.1 1.0 NE2 B:HIS175 2.1 9.2 1.0 OD2 B:ASP179 2.2 7.2 1.0 OD1 B:ASP179 2.4 6.3 1.0 CG B:ASP179 2.6 6.4 1.0 CE1 B:HIS151 2.8 6.4 1.0 CD2 B:HIS175 3.0 8.6 1.0 CE1 B:HIS175 3.1 9.1 1.0 O3' B:C5P302 3.1 34.0 1.0 CD2 B:HIS151 3.2 6.4 1.0 P B:C5P301 3.4 17.6 1.0 ND1 B:HIS151 4.0 6.3 1.0 CB B:ASP179 4.1 5.8 1.0 O1P B:C5P301 4.1 15.8 1.0 N B:TRP27 4.1 4.2 1.0 CG B:HIS151 4.2 6.5 1.0 CG B:HIS175 4.2 8.1 1.0 ND1 B:HIS175 4.2 8.9 1.0 O5' B:C5P301 4.2 16.4 1.0 O2P B:C5P301 4.3 19.3 1.0 C1' B:C5P302 4.3 27.7 1.0 O4' B:C5P302 4.3 29.2 1.0 C3' B:C5P302 4.3 31.5 1.0 NE2 B:GLN148 4.4 5.8 1.0 C5' B:C5P301 4.4 20.8 1.0 C4' B:C5P302 4.5 32.2 1.0 ZN B:ZN401 4.5 6.0 1.0 O B:HOH719 4.5 24.7 1.0 C2' B:C5P302 4.8 30.6 1.0 O2' B:C5P302 4.8 26.4 1.0 O2 B:C5P302 4.8 26.5 1.0 O B:TRP27 4.9 4.9 1.0 CA B:TRP27 5.0 4.3 1.0 OD1 B:ASP145 5.0 4.5 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