Zinc in PDB 8qjq: SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine - 5' - Monophosphate As An Inhibitor.

The structure of SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine - 5' - Monophosphate As An Inhibitor., PDB code: 8qjq 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)	41.78 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.255, 73.166, 81.66, 90, 104.99, 90
R / Rfree (%)	16.6 / 20.3

The binding sites of Zinc atom in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine - 5' - Monophosphate As An Inhibitor. (pdb code 8qjq). 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 As An Inhibitor., PDB code: 8qjq:
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 As An Inhibitor.


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 As An Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:14.6 occ:1.00 O3P A:C5P404 1.9 17.8 0.8 NE2 A:HIS32 2.0 12.6 1.0 N A:TRP27 2.1 16.3 1.0 OD1 A:ASP145 2.1 13.7 1.0 O A:TRP27 2.2 15.7 1.0 O A:HOH503 2.2 3.3 0.2 O A:HOH501 2.8 2.4 0.2 C A:TRP27 2.9 15.5 1.0 CA A:TRP27 3.0 15.2 1.0 CD2 A:HIS32 3.0 13.1 1.0 CE1 A:HIS32 3.0 13.1 1.0 CG A:ASP145 3.2 11.8 1.0 P A:C5P404 3.3 16.3 0.8 OD2 A:ASP145 3.6 12.6 1.0 ZN A:ZN402 3.7 15.6 1.0 CB A:TRP27 3.8 14.6 1.0 O2P A:C5P404 3.8 17.0 0.8 OD2 A:ASP71 3.9 18.2 1.0 O5' A:C5P404 4.1 17.4 0.8 NE2 A:HIS141 4.1 13.7 1.0 ND1 A:HIS32 4.1 12.6 1.0 CG A:HIS32 4.1 13.1 1.0 CE1 A:HIS141 4.2 12.8 1.0 O1P A:C5P404 4.2 19.2 0.8 N A:GLY28 4.2 14.1 1.0 NE2 A:HIS151 4.3 15.0 1.0 CE1 A:HIS151 4.3 14.7 1.0 C5' A:C5P404 4.3 18.2 0.8 ZN A:ZN403 4.4 16.7 1.0 OD1 A:ASP179 4.4 15.5 1.0 CG A:TRP27 4.5 14.2 1.0 CB A:ASP145 4.5 11.7 1.0 CD1 A:TRP27 4.6 13.8 1.0 CG A:ASP71 4.7 17.8 1.0 CA A:ASP145 4.7 11.3 1.0 OD1 A:ASP71 4.7 16.9 1.0 O A:GLY28 4.8 15.3 1.0 CG A:ASP179 4.8 16.6 1.0 OD2 A:ASP179 4.9 15.7 1.0 CA A:GLY28 5.0 14.7 1.0

Zinc binding site 2 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine - 5' - Monophosphate As An Inhibitor.


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 As An Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:15.6 occ:1.00 ND1 A:HIS88 2.0 14.5 1.0 O A:HOH503 2.1 3.3 0.2 O2P A:C5P404 2.1 17.0 0.8 OD2 A:ASP145 2.1 12.6 1.0 NE2 A:HIS141 2.1 13.7 1.0 OD1 A:ASP71 2.3 16.9 1.0 CE1 A:HIS88 2.9 15.3 1.0 CD2 A:HIS141 3.0 13.5 1.0 CG A:ASP145 3.1 11.8 1.0 P A:C5P404 3.1 16.3 0.8 CE1 A:HIS141 3.1 12.8 1.0 CG A:HIS88 3.2 14.3 1.0 CG A:ASP71 3.3 17.8 1.0 O3P A:C5P404 3.3 17.8 0.8 OD1 A:ASP145 3.5 13.7 1.0 OD2 A:ASP71 3.5 18.2 1.0 CB A:HIS88 3.7 14.2 1.0 ZN A:ZN401 3.7 14.6 1.0 O5' A:C5P404 3.8 17.4 0.8 NH1 A:ARG74 3.9 22.9 1.0 NE2 A:HIS88 4.1 16.4 1.0 O A:HOH501 4.1 2.4 0.2 CG A:HIS141 4.2 13.0 1.0 ND1 A:HIS141 4.2 13.4 1.0 CD2 A:HIS88 4.2 15.7 1.0 NE2 A:HIS32 4.2 12.6 1.0 CB A:ASP145 4.4 11.7 1.0 CE1 A:HIS151 4.5 14.7 1.0 O1P A:C5P404 4.5 19.2 0.8 CE1 A:HIS32 4.6 13.1 1.0 CB A:ASP71 4.6 16.6 1.0 CA A:HIS88 4.7 14.7 1.0 CZ A:ARG74 4.8 20.7 1.0 O A:HOH502 4.9 15.0 0.2 CA A:ASP71 4.9 16.8 1.0 NH2 A:ARG74 4.9 20.4 1.0 N A:ASP71 5.0 15.8 1.0

Zinc binding site 3 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine - 5' - Monophosphate As An Inhibitor.


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 As An Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:16.7 occ:1.00 O1P A:C5P404 1.9 19.2 0.8 O A:HOH501 2.0 2.4 0.2 NE2 A:HIS151 2.0 15.0 1.0 NE2 A:HIS175 2.1 16.3 1.0 OD2 A:ASP179 2.1 15.7 1.0 O A:HOH502 2.3 15.0 0.2 OD1 A:ASP179 2.5 15.5 1.0 CG A:ASP179 2.6 16.6 1.0 CE1 A:HIS151 2.9 14.7 1.0 CD2 A:HIS175 3.0 16.7 1.0 P A:C5P404 3.1 16.3 0.8 CD2 A:HIS151 3.1 15.1 1.0 CE1 A:HIS175 3.1 16.3 1.0 O3P A:C5P404 3.1 17.8 0.8 ND1 A:HIS151 4.0 14.8 1.0 O2P A:C5P404 4.1 17.0 0.8 O5' A:C5P404 4.1 17.4 0.8 N A:TRP27 4.1 16.3 1.0 CB A:ASP179 4.1 16.4 1.0 CG A:HIS151 4.1 14.7 1.0 ND1 A:HIS175 4.2 16.3 1.0 CG A:HIS175 4.2 16.6 1.0 C5' A:C5P404 4.2 18.2 0.8 O A:HOH503 4.3 3.3 0.2 O A:HOH704 4.3 28.4 1.0 NE2 A:GLN148 4.3 14.9 1.0 ZN A:ZN401 4.4 14.6 1.0 O A:HOH536 4.4 24.7 1.0 O A:TRP27 4.8 15.7 1.0 OD1 A:ASP145 4.9 13.7 1.0 CA A:TRP27 4.9 15.2 1.0

Zinc binding site 4 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine - 5' - Monophosphate As An Inhibitor.


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 As An Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:23.9 occ:1.00 O3 B:PO4415 2.0 23.2 0.8 NE2 B:HIS32 2.0 23.0 1.0 OD1 B:ASP145 2.1 24.4 1.0 N B:TRP27 2.1 21.6 1.0 O B:TRP27 2.1 22.8 1.0 O4 B:PO4415 2.6 21.8 0.8 P B:PO4415 2.9 25.6 0.8 C B:TRP27 2.9 21.8 1.0 CD2 B:HIS32 3.0 23.4 1.0 CA B:TRP27 3.0 22.2 1.0 CE1 B:HIS32 3.1 25.0 1.0 CG B:ASP145 3.1 24.2 1.0 OD2 B:ASP145 3.5 25.2 1.0 ZN B:ZN402 3.6 22.6 0.8 CB B:TRP27 3.8 22.5 1.0 O2 B:PO4415 3.9 24.2 0.8 O1 B:PO4415 4.0 26.4 0.8 NE2 B:HIS141 4.0 23.1 1.0 OD2 B:ASP71 4.1 31.4 1.0 CG B:HIS32 4.1 23.9 1.0 ND1 B:HIS32 4.1 23.5 1.0 CE1 B:HIS141 4.2 27.5 1.0 N B:GLY28 4.2 21.5 1.0 CB B:ASP145 4.4 24.2 1.0 CG B:TRP27 4.4 22.5 1.0 CE1 B:HIS151 4.5 23.9 1.0 OD1 B:ASP179 4.5 20.6 1.0 NE2 B:HIS151 4.5 24.7 1.0 CD1 B:TRP27 4.5 22.5 1.0 ZN B:ZN403 4.6 23.9 0.9 CA B:ASP145 4.7 23.9 1.0 O B:GLY28 4.8 22.1 1.0 OD1 B:ASP71 4.8 31.6 1.0 CG B:ASP179 4.8 21.1 1.0 CG B:ASP71 4.9 32.2 1.0 OD2 B:ASP179 4.9 21.5 1.0 CA B:GLY28 5.0 24.3 1.0

Zinc binding site 5 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine - 5' - Monophosphate As An Inhibitor.


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 As An Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:22.6 occ:0.80 OD2 B:ASP145 2.0 25.2 1.0 NE2 B:HIS141 2.1 23.1 1.0 ND1 B:HIS88 2.1 28.4 1.0 O2 B:PO4415 2.3 24.2 0.8 O3 B:PO4415 2.3 23.2 0.8 OD1 B:ASP71 2.5 31.6 1.0 P B:PO4415 2.8 25.6 0.8 CD2 B:HIS141 3.0 24.8 1.0 CE1 B:HIS88 3.0 31.1 1.0 CG B:ASP145 3.0 24.2 1.0 CE1 B:HIS141 3.2 27.5 1.0 CG B:HIS88 3.2 30.3 1.0 OD1 B:ASP145 3.5 24.4 1.0 CG B:ASP71 3.5 32.2 1.0 CB B:HIS88 3.6 30.5 1.0 ZN B:ZN401 3.6 23.9 1.0 OD2 B:ASP71 3.7 31.4 1.0 O1 B:PO4415 3.9 26.4 0.8 O4 B:PO4415 3.9 21.8 0.8 CG B:HIS141 4.2 24.7 1.0 NE2 B:HIS32 4.2 23.0 1.0 NE2 B:HIS88 4.2 31.2 1.0 ND1 B:HIS141 4.2 25.1 1.0 CD2 B:HIS88 4.3 29.0 1.0 CB B:ASP145 4.3 24.2 1.0 O B:HOH532 4.6 40.1 1.0 CE1 B:HIS32 4.6 25.0 1.0 CE1 B:HIS151 4.6 23.9 1.0 CA B:HIS88 4.7 30.6 1.0 CB B:ASP71 4.9 31.4 1.0

Zinc binding site 6 out of 6 in the SMNUC1 Nuclease From Stenotrophomonas Maltophilia in Complex with Cytidine - 5' - Monophosphate As An Inhibitor.


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 As An Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:23.9 occ:0.90 O1P B:C5P404 2.0 36.8 1.0 OD2 B:ASP179 2.1 21.5 1.0 NE2 B:HIS151 2.1 24.7 1.0 NE2 B:HIS175 2.1 23.6 1.0 O4 B:PO4415 2.2 21.8 0.8 OD1 B:ASP179 2.6 20.6 1.0 CG B:ASP179 2.7 21.1 1.0 CE1 B:HIS151 2.9 23.9 1.0 CD2 B:HIS175 3.0 24.5 1.0 CD2 B:HIS151 3.2 25.5 1.0 CE1 B:HIS175 3.2 25.2 1.0 P B:PO4415 3.4 25.6 0.8 P B:C5P404 3.5 44.5 1.0 O1 B:PO4415 3.9 26.4 0.8 O2 B:PO4415 3.9 24.2 0.8 C5' B:C5P404 4.0 41.2 1.0 O5' B:C5P404 4.0 39.9 1.0 ND1 B:HIS151 4.0 23.6 1.0 CB B:ASP179 4.2 22.1 1.0 CG B:HIS175 4.2 24.3 1.0 O3P B:C5P404 4.2 45.2 1.0 CG B:HIS151 4.2 25.6 1.0 N B:TRP27 4.3 21.6 1.0 ND1 B:HIS175 4.3 23.9 1.0 O B:HOH558 4.4 38.6 1.0 NE2 B:GLN148 4.5 24.5 1.0 ZN B:ZN401 4.6 23.9 1.0 O2P B:C5P404 4.6 39.0 1.0 O3 B:PO4415 4.6 23.2 0.8 O B:HOH532 4.8 40.1 1.0 O B:TRP27 4.9 22.8 1.0 OD1 B:ASP145 4.9 24.4 1.0 CA B:TRP27 5.0 22.2 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