Zinc in PDB 9emg: SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-5'-Monophosphate As A Product of C-Di-Gmp Cleavage

The structure of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-5'-Monophosphate As A Product of C-Di-Gmp Cleavage, PDB code: 9emg 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 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.34, 72.637, 82.94, 90, 102.1, 90
R / Rfree (%)	11.1 / 13.1

The binding sites of Zinc atom in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-5'-Monophosphate As A Product of C-Di-Gmp Cleavage (pdb code 9emg). 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 As A Product of C-Di-Gmp Cleavage, PDB code: 9emg:
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 As A Product of C-Di-Gmp Cleavage


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 As A Product of C-Di-Gmp Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:5.9 occ:1.00 O A:HOH617 1.9 7.9 1.0 NE2 A:HIS32 2.0 5.1 1.0 OD1 A:ASP145 2.1 5.3 1.0 N A:TRP27 2.1 5.4 1.0 O A:TRP27 2.3 6.0 1.0 C A:TRP27 3.0 5.2 1.0 CA A:TRP27 3.0 5.0 1.0 CE1 A:HIS32 3.0 4.3 1.0 CG A:ASP145 3.1 4.2 1.0 CD2 A:HIS32 3.1 4.9 1.0 ZN A:ZN402 3.3 5.8 0.9 OD2 A:ASP145 3.4 5.6 1.0 OD2 A:ASP71 3.6 8.1 1.0 CB A:TRP27 3.6 5.1 1.0 CE1 A:HIS151 3.9 5.6 1.0 NE2 A:HIS141 3.9 5.2 1.0 CE1 A:HIS141 4.1 5.2 1.0 ND1 A:HIS32 4.1 4.7 1.0 NE2 A:HIS151 4.2 5.3 1.0 CG A:HIS32 4.2 4.6 1.0 N A:GLY28 4.3 5.7 1.0 CB A:ASP145 4.4 4.2 1.0 CG A:TRP27 4.4 4.5 1.0 CD1 A:TRP27 4.5 5.2 1.0 CG A:ASP71 4.5 6.3 1.0 OD1 A:ASP71 4.6 7.2 1.0 ND1 A:HIS151 4.7 5.2 1.0 ZN A:ZN403 4.7 5.3 0.8 CA A:ASP145 4.7 4.1 1.0 OD1 A:ASP179 4.7 8.2 1.0 CD2 A:HIS141 4.9 5.3 1.0 OD2 A:ASP179 4.9 9.4 1.0 O A:HOH773 4.9 39.7 1.0 O A:GLY28 4.9 5.8 1.0 CG A:ASP179 5.0 6.5 1.0

Zinc binding site 2 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-5'-Monophosphate As A Product of C-Di-Gmp Cleavage


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 As A Product of C-Di-Gmp Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:5.8 occ:0.95 O A:HOH617 1.9 7.9 1.0 ND1 A:HIS88 2.0 6.2 1.0 NE2 A:HIS141 2.1 5.2 1.0 OD2 A:ASP145 2.1 5.6 1.0 OD1 A:ASP71 2.4 7.2 1.0 CE1 A:HIS88 2.9 6.5 1.0 CG A:ASP145 3.1 4.2 1.0 CD2 A:HIS141 3.1 5.3 1.0 CE1 A:HIS141 3.1 5.2 1.0 CG A:ASP71 3.2 6.3 1.0 CG A:HIS88 3.2 5.7 1.0 ZN A:ZN401 3.3 5.9 1.0 OD2 A:ASP71 3.4 8.1 1.0 OD1 A:ASP145 3.4 5.3 1.0 CB A:HIS88 3.7 5.8 1.0 NE2 A:HIS32 4.0 5.1 1.0 NE2 A:HIS88 4.1 7.6 1.0 O A:HOH713 4.1 22.6 1.0 ND1 A:HIS141 4.2 5.1 1.0 CG A:HIS141 4.2 4.7 1.0 CE1 A:HIS151 4.2 5.6 1.0 CD2 A:HIS88 4.2 7.0 1.0 CE1 A:HIS32 4.4 4.3 1.0 CB A:ASP145 4.4 4.2 1.0 CB A:ASP71 4.6 8.0 1.0 CA A:HIS88 4.8 5.5 1.0 ND1 A:HIS151 4.8 5.2 1.0 O A:TRP27 4.9 6.0 1.0 CD2 A:HIS32 4.9 4.9 1.0

Zinc binding site 3 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-5'-Monophosphate As A Product of C-Di-Gmp Cleavage


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 As A Product of C-Di-Gmp Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:5.3 occ:0.85 OD2 A:ASP179 2.0 9.4 1.0 NE2 A:HIS175 2.0 6.5 1.0 NE2 A:HIS151 2.0 5.3 1.0 CG A:ASP179 2.7 6.5 1.0 OD1 A:ASP179 2.9 8.2 1.0 CE1 A:HIS151 3.0 5.6 1.0 CD2 A:HIS175 3.0 5.8 1.0 CD2 A:HIS151 3.0 5.2 1.0 CE1 A:HIS175 3.0 6.5 1.0 ND1 A:HIS151 4.1 5.2 1.0 O A:HOH595 4.1 42.9 1.0 ND1 A:HIS175 4.2 6.0 1.0 CG A:HIS175 4.2 5.3 1.0 CG A:HIS151 4.2 5.2 1.0 CB A:ASP179 4.2 6.2 1.0 N A:TRP27 4.2 5.4 1.0 O A:HOH617 4.3 7.9 1.0 O A:HOH698 4.5 43.1 1.0 NE2 A:GLN148 4.5 5.6 0.4 CE1 A:TYR89 4.7 9.5 0.8 ZN A:ZN401 4.7 5.9 1.0 O A:TRP27 4.9 6.0 1.0 CA A:TRP27 4.9 5.0 1.0 C A:TRP27 5.0 5.2 1.0

Zinc binding site 4 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-5'-Monophosphate As A Product of C-Di-Gmp Cleavage


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 As A Product of C-Di-Gmp Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:12.2 occ:1.00 O B:HOH1030 1.9 14.1 1.0 NE2 B:HIS32 2.0 11.4 1.0 OD1 B:ASP145 2.1 10.8 1.0 N B:TRP27 2.1 10.8 1.0 O B:TRP27 2.3 12.1 1.0 CE1 B:HIS32 3.0 10.8 1.0 C B:TRP27 3.0 10.6 1.0 CA B:TRP27 3.0 9.7 1.0 CD2 B:HIS32 3.0 11.6 1.0 CG B:ASP145 3.1 9.5 1.0 O B:HOH1008 3.2 23.1 1.0 ZN B:ZN402 3.3 12.2 0.9 OD2 B:ASP145 3.5 12.0 1.0 CB B:TRP27 3.7 10.2 1.0 OD2 B:ASP71 3.7 15.4 1.0 NE2 B:HIS141 3.9 11.1 1.0 CE1 B:HIS141 4.1 10.8 1.0 ND1 B:HIS32 4.1 10.7 1.0 CG B:HIS32 4.2 10.7 1.0 CE1 B:HIS151 4.2 12.1 1.0 N B:GLY28 4.3 11.4 1.0 NE2 B:HIS151 4.3 11.6 1.0 CG B:TRP27 4.4 10.4 1.0 CB B:ASP145 4.4 9.7 1.0 CD1 B:TRP27 4.5 9.8 1.0 O B:HOH1039 4.5 39.2 1.0 CG B:ASP71 4.6 13.1 1.0 OD1 B:ASP179 4.6 10.7 1.0 OD1 B:ASP71 4.6 15.9 1.0 CA B:ASP145 4.7 9.5 1.0 ZN B:ZN403 4.8 11.7 0.7 CD2 B:HIS141 4.9 10.8 1.0 O B:GLY28 4.9 11.3 1.0 ND1 B:HIS151 5.0 10.9 1.0 O B:HOH1245 5.0 36.7 1.0

Zinc binding site 5 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-5'-Monophosphate As A Product of C-Di-Gmp Cleavage


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 As A Product of C-Di-Gmp Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:12.2 occ:0.90 O B:HOH1030 2.0 14.1 1.0 ND1 B:HIS88 2.0 12.8 1.0 OD2 B:ASP145 2.1 12.0 1.0 NE2 B:HIS141 2.1 11.1 1.0 OD1 B:ASP71 2.4 15.9 1.0 O B:HOH1039 2.7 39.2 1.0 CE1 B:HIS88 2.9 13.2 1.0 CG B:ASP145 3.0 9.5 1.0 CD2 B:HIS141 3.1 10.8 1.0 CE1 B:HIS141 3.1 10.8 1.0 CG B:HIS88 3.2 12.9 1.0 CG B:ASP71 3.2 13.1 1.0 ZN B:ZN401 3.3 12.2 1.0 OD1 B:ASP145 3.4 10.8 1.0 OD2 B:ASP71 3.4 15.4 1.0 CB B:HIS88 3.7 12.0 1.0 NE2 B:HIS32 4.0 11.4 1.0 NE2 B:HIS88 4.1 15.6 1.0 O B:HOH1182 4.1 42.5 1.0 ND1 B:HIS141 4.2 11.3 1.0 CG B:HIS141 4.2 11.1 1.0 CD2 B:HIS88 4.2 14.7 1.0 O B:HOH1008 4.3 23.1 1.0 CE1 B:HIS151 4.3 12.1 1.0 O B:HOH1128 4.4 41.8 1.0 CB B:ASP145 4.4 9.7 1.0 CE1 B:HIS32 4.4 10.8 1.0 CB B:ASP71 4.6 15.5 1.0 CA B:HIS88 4.8 11.4 1.0 O B:TRP27 5.0 12.1 1.0 ND1 B:HIS151 5.0 10.9 1.0

Zinc binding site 6 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Guanosine-5'-Monophosphate As A Product of C-Di-Gmp Cleavage


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 As A Product of C-Di-Gmp Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:11.7 occ:0.70 NE2 B:HIS175 2.0 12.9 1.0 O B:HOH1008 2.1 23.1 1.0 OD2 B:ASP179 2.1 14.7 1.0 NE2 B:HIS151 2.1 11.6 1.0 O3' B:5GP405 2.1 23.0 0.8 OD1 B:ASP179 2.6 10.7 1.0 CG B:ASP179 2.6 11.1 1.0 CE1 B:HIS151 3.0 12.1 1.0 CD2 B:HIS175 3.0 10.7 1.0 CE1 B:HIS175 3.1 11.7 1.0 CD2 B:HIS151 3.2 10.8 1.0 C3' B:5GP405 3.5 22.4 0.8 C4' B:5GP405 3.8 21.4 0.8 ND1 B:HIS151 4.1 10.9 1.0 CB B:ASP179 4.1 10.1 1.0 O4' B:5GP405 4.2 21.3 0.8 ND1 B:HIS175 4.2 9.6 1.0 CG B:HIS175 4.2 8.7 1.0 CG B:HIS151 4.2 9.6 1.0 O B:HOH1245 4.2 36.7 1.0 C1' B:5GP405 4.3 22.5 0.8 N B:TRP27 4.3 10.8 1.0 C2' B:5GP405 4.3 24.0 0.8 O B:HOH1039 4.3 39.2 1.0 O2' B:5GP405 4.3 30.6 0.8 O B:HOH1128 4.4 41.8 1.0 O B:HOH1030 4.5 14.1 1.0 NE2 B:GLN148 4.5 8.8 1.0 O B:HOH1147 4.6 30.7 0.5 ZN B:ZN401 4.8 12.2 1.0

K.Adamkova, M.Trundova, T.Koval, B.Hustakova, P.Kolenko, J.Duskova, T.Skalova, J.Dohnalek. Substrate Preference, Rna Binding and Active Site Versatility of Stenotrophomonas Maltophilia Nuclease SMNUC1, Explained By A Structural Study. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 39361520
DOI: 10.1111/FEBS.17265