Zinc 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:

Sodium	(Na)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-5'-Monophosphate, PDB code: 8qjo:
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 Guanosine-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 Guanosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:16.3 occ:1.00 O3 A:PO4404 1.9 23.2 1.0 NE2 A:HIS32 2.0 12.9 1.0 OD1 A:ASP145 2.1 14.6 1.0 O A:TRP27 2.2 14.4 1.0 N A:TRP27 2.2 15.9 1.0 O2 A:PO4404 2.9 22.8 1.0 C A:TRP27 2.9 15.3 1.0 CD2 A:HIS32 2.9 13.5 1.0 P A:PO4404 3.0 21.3 1.0 CA A:TRP27 3.0 15.4 1.0 CE1 A:HIS32 3.0 13.3 1.0 CG A:ASP145 3.2 13.9 1.0 OD2 A:ASP145 3.6 15.1 1.0 ZN A:ZN402 3.6 17.2 1.0 CB A:TRP27 3.7 14.4 1.0 O4 A:PO4404 3.9 21.2 1.0 OD2 A:ASP71 3.9 20.7 1.0 NE2 A:HIS141 4.0 13.9 1.0 CE1 A:HIS141 4.0 14.7 1.0 O1 A:PO4404 4.1 23.3 1.0 CG A:HIS32 4.1 12.9 1.0 ND1 A:HIS32 4.1 13.0 1.0 N A:GLY28 4.2 15.2 1.0 CE1 A:HIS151 4.3 15.2 1.0 NE2 A:HIS151 4.3 14.2 1.0 CG A:TRP27 4.4 14.1 1.0 ZN A:ZN403 4.4 17.2 1.0 OD1 A:ASP179 4.5 16.6 1.0 CB A:ASP145 4.5 13.8 1.0 CD1 A:TRP27 4.5 14.3 1.0 CA A:ASP145 4.7 12.9 1.0 CG A:ASP71 4.8 21.3 1.0 OD1 A:ASP71 4.8 20.4 1.0 O A:GLY28 4.8 17.1 1.0 CG A:ASP179 5.0 17.2 1.0

Zinc binding site 2 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-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 Guanosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:17.2 occ:1.00 NE2 A:HIS141 2.1 13.9 1.0 OD2 A:ASP145 2.1 15.1 1.0 ND1 A:HIS88 2.1 15.6 1.0 O4 A:PO4404 2.2 21.2 1.0 O3 A:PO4404 2.3 23.2 1.0 OD1 A:ASP71 2.5 20.4 1.0 P A:PO4404 2.8 21.3 1.0 CE1 A:HIS88 3.0 16.3 1.0 CD2 A:HIS141 3.0 12.9 1.0 CG A:ASP145 3.1 13.9 1.0 CE1 A:HIS141 3.1 14.7 1.0 CG A:HIS88 3.2 15.1 1.0 CG A:ASP71 3.4 21.3 1.0 OD1 A:ASP145 3.4 14.6 1.0 ZN A:ZN401 3.6 16.3 1.0 OD2 A:ASP71 3.6 20.7 1.0 CB A:HIS88 3.7 15.7 1.0 O1 A:PO4404 3.8 23.3 1.0 O2 A:PO4404 3.9 22.8 1.0 NH1 A:ARG74 3.9 19.6 1.0 NE2 A:HIS88 4.1 15.0 1.0 CG A:HIS141 4.2 13.7 1.0 ND1 A:HIS141 4.2 13.9 1.0 NE2 A:HIS32 4.2 12.9 1.0 CD2 A:HIS88 4.3 15.5 1.0 CE1 A:HIS151 4.3 15.2 1.0 CB A:ASP145 4.4 13.8 1.0 CE1 A:HIS32 4.6 13.3 1.0 CA A:HIS88 4.7 16.0 1.0 CZ A:ARG74 4.8 21.4 1.0 CB A:ASP71 4.8 19.1 1.0 NH2 A:ARG74 4.9 21.4 1.0 O3' A:5GP405 4.9 22.9 1.0

Zinc binding site 3 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-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 Guanosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:17.2 occ:1.00 O2 A:PO4404 1.9 22.8 1.0 NE2 A:HIS151 2.0 14.2 1.0 NE2 A:HIS175 2.0 17.1 1.0 O3' A:5GP405 2.2 22.9 1.0 OD2 A:ASP179 2.3 15.8 1.0 OD1 A:ASP179 2.5 16.6 1.0 CG A:ASP179 2.7 17.2 1.0 CE1 A:HIS151 2.9 15.2 1.0 CD2 A:HIS175 3.0 17.0 1.0 CD2 A:HIS151 3.1 15.2 1.0 CE1 A:HIS175 3.1 16.4 1.0 P A:PO4404 3.3 21.3 1.0 C3' A:5GP405 3.5 26.8 1.0 C4' A:5GP405 3.8 29.2 1.0 O4 A:PO4404 3.8 21.2 1.0 O A:HOH626 3.9 38.6 1.0 O1 A:PO4404 4.0 23.3 1.0 ND1 A:HIS151 4.0 15.3 1.0 N A:TRP27 4.0 15.9 1.0 CG A:HIS151 4.1 14.9 1.0 ND1 A:HIS175 4.1 17.2 1.0 CG A:HIS175 4.2 17.4 1.0 NE2 A:GLN148 4.2 15.1 1.0 CB A:ASP179 4.2 16.7 1.0 O4' A:5GP405 4.3 28.6 1.0 O3 A:PO4404 4.4 23.2 1.0 C2' A:5GP405 4.4 26.5 1.0 ZN A:ZN401 4.4 16.3 1.0 C1' A:5GP405 4.5 27.7 1.0 O2' A:5GP405 4.5 24.7 1.0 O A:HOH606 4.7 39.9 1.0 O A:TRP27 4.9 14.4 1.0 CA A:TRP27 4.9 15.4 1.0 OD1 A:ASP145 5.0 14.6 1.0

Zinc binding site 4 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-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 Guanosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:21.0 occ:1.00 O4 B:PO4404 1.9 22.8 1.0 N B:TRP27 2.0 17.8 1.0 NE2 B:HIS32 2.0 19.3 1.0 OD1 B:ASP145 2.1 18.4 1.0 O B:TRP27 2.2 20.4 1.0 O2 B:PO4404 2.9 22.3 1.0 C B:TRP27 2.9 18.5 1.0 P B:PO4404 2.9 26.0 1.0 CA B:TRP27 2.9 18.6 1.0 CE1 B:HIS32 3.0 19.5 1.0 CD2 B:HIS32 3.0 18.3 1.0 CG B:ASP145 3.1 20.6 1.0 OD2 B:ASP145 3.5 21.1 1.0 ZN B:ZN402 3.5 27.3 1.0 CB B:TRP27 3.7 19.5 1.0 O1 B:PO4404 3.9 25.5 1.0 O3 B:PO4404 4.0 26.8 1.0 NE2 B:HIS141 4.0 20.9 1.0 OD2 B:ASP71 4.0 32.1 1.0 ND1 B:HIS32 4.1 18.7 1.0 CE1 B:HIS141 4.1 22.3 1.0 CG B:HIS32 4.1 19.9 1.0 N B:GLY28 4.2 20.2 1.0 CE1 B:HIS151 4.3 22.0 1.0 NE2 B:HIS151 4.4 21.3 1.0 CG B:TRP27 4.4 18.8 1.0 CB B:ASP145 4.4 19.4 1.0 CD1 B:TRP27 4.5 18.4 1.0 OD1 B:ASP179 4.6 19.1 1.0 ZN B:ZN403 4.6 24.5 1.0 CA B:ASP145 4.7 19.6 1.0 CG B:ASP71 4.9 33.1 1.0 OD1 B:ASP71 4.9 28.5 1.0 O B:GLY28 4.9 18.2 1.0 CG B:ASP179 5.0 19.6 1.0 CA B:GLY28 5.0 21.4 1.0 N B:ASP145 5.0 19.2 1.0

Zinc binding site 5 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-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 Guanosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:27.3 occ:1.00 OD2 B:ASP145 2.0 21.1 1.0 NE2 B:HIS141 2.1 20.9 1.0 ND1 B:HIS88 2.1 25.0 1.0 O4 B:PO4404 2.3 22.8 1.0 O3 B:PO4404 2.5 26.8 1.0 OD1 B:ASP71 2.6 28.5 1.0 P B:PO4404 2.9 26.0 1.0 CE1 B:HIS88 2.9 25.6 1.0 CG B:ASP145 3.0 20.6 1.0 CD2 B:HIS141 3.0 21.8 1.0 CE1 B:HIS141 3.1 22.3 1.0 CG B:HIS88 3.3 24.9 1.0 OD1 B:ASP145 3.5 18.4 1.0 CG B:ASP71 3.5 33.1 1.0 ZN B:ZN401 3.5 21.0 1.0 OD2 B:ASP71 3.7 32.1 1.0 CB B:HIS88 3.7 24.3 1.0 O1 B:PO4404 3.9 25.5 1.0 O2 B:PO4404 4.1 22.3 1.0 NE2 B:HIS32 4.1 19.3 1.0 NE2 B:HIS88 4.1 25.4 1.0 NH2 B:ARG74 4.1 49.6 1.0 ND1 B:HIS141 4.2 20.7 1.0 CG B:HIS141 4.2 21.5 1.0 CD2 B:HIS88 4.3 26.1 1.0 CB B:ASP145 4.3 19.4 1.0 CE1 B:HIS151 4.5 22.0 1.0 CE1 B:HIS32 4.5 19.5 1.0 CA B:HIS88 4.7 26.2 1.0 CZ B:ARG74 4.8 54.8 1.0 CB B:ASP71 4.9 30.3 1.0 NH1 B:ARG74 4.9 55.9 1.0

Zinc binding site 6 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-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 Guanosine-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:24.5 occ:1.00 O2 B:PO4404 2.0 22.3 1.0 NE2 B:HIS151 2.1 21.3 1.0 NE2 B:HIS175 2.1 20.9 1.0 O3' B:5GP405 2.2 29.5 1.0 OD2 B:ASP179 2.2 20.9 1.0 OD1 B:ASP179 2.4 19.1 1.0 CG B:ASP179 2.6 19.6 1.0 CE1 B:HIS151 2.9 22.0 1.0 CD2 B:HIS175 3.0 21.0 1.0 CD2 B:HIS151 3.2 21.6 1.0 CE1 B:HIS175 3.2 23.5 1.0 P B:PO4404 3.4 26.0 1.0 C3' B:5GP405 3.5 32.9 1.0 O3 B:PO4404 3.8 26.8 1.0 C4' B:5GP405 3.8 33.7 1.0 ND1 B:HIS151 4.0 20.0 1.0 O1 B:PO4404 4.1 25.5 1.0 CG B:HIS175 4.1 21.4 1.0 CB B:ASP179 4.1 19.2 1.0 N B:TRP27 4.2 17.8 1.0 CG B:HIS151 4.2 21.1 1.0 ND1 B:HIS175 4.2 22.4 1.0 O4' B:5GP405 4.2 31.2 1.0 C1' B:5GP405 4.4 32.1 1.0 NE2 B:GLN148 4.4 21.9 1.0 C2' B:5GP405 4.4 33.1 1.0 O4 B:PO4404 4.5 22.8 1.0 ZN B:ZN401 4.6 21.0 1.0 O2' B:5GP405 4.6 33.1 1.0 CA B:TRP27 4.9 18.6 1.0 O B:TRP27 5.0 20.4 1.0 OD1 B:ASP145 5.0 18.4 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