Zinc in PDB 5h7w: Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra

The structure of Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra, PDB code: 5h7w was solved by C.Chang, C.-C.Lin, W.-G.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.98 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.089, 68.149, 139.815, 90.00, 95.73, 90.00
R / Rfree (%)	15.5 / 19.7

The structure of Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra (pdb code 5h7w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra, PDB code: 5h7w:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:17.6 occ:1.00 OD1 A:ASP37 2.1 17.5 1.0 NE2 A:HIS39 2.1 17.2 1.0 O A:HOH845 2.1 15.7 1.0 O A:HOH726 2.2 13.0 1.0 OD2 A:ASP85 2.3 15.7 1.0 O A:HOH741 2.6 28.8 1.0 CE1 A:HIS39 3.1 17.0 1.0 CD2 A:HIS39 3.1 14.4 1.0 CG A:ASP37 3.1 15.1 1.0 CG A:ASP85 3.3 16.9 1.0 ZN A:ZN606 3.3 17.1 1.0 CB A:ASP85 3.5 14.1 1.0 CB A:ASP37 3.6 12.0 1.0 O A:HOH888 4.1 16.5 1.0 OG A:SER521 4.1 25.5 1.0 ND1 A:HIS39 4.2 14.7 1.0 CE1 A:HIS220 4.2 14.9 1.0 OD2 A:ASP37 4.2 14.9 1.0 CG A:HIS39 4.3 12.9 1.0 NE2 A:HIS220 4.3 20.3 1.0 OD1 A:ASN245 4.3 21.5 1.0 O A:HIS243 4.3 16.7 1.0 CD2 A:HIS118 4.3 12.3 1.0 CA A:ASP37 4.3 12.4 1.0 OD1 A:ASP85 4.4 15.1 1.0 O A:HOH946 4.5 16.9 1.0 CA A:HIS243 4.6 15.7 1.0 O A:HOH765 4.7 14.7 1.0 C A:HIS243 4.8 14.7 1.0 NE2 A:HIS118 4.9 13.2 1.0 O A:HOH905 4.9 28.6 1.0 ND1 A:HIS243 4.9 17.9 1.0 OD1 A:ASN117 4.9 15.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:17.1 occ:1.00 NE2 A:HIS220 1.9 20.3 1.0 O A:HOH845 2.0 15.7 1.0 OD1 A:ASN117 2.1 15.0 1.0 ND1 A:HIS243 2.1 17.9 1.0 OD2 A:ASP85 2.3 15.7 1.0 CE1 A:HIS220 2.9 14.9 1.0 CD2 A:HIS220 2.9 20.9 1.0 CE1 A:HIS243 3.0 19.5 1.0 CG A:ASP85 3.1 16.9 1.0 CG A:ASN117 3.1 16.3 1.0 CG A:HIS243 3.2 14.7 1.0 ZN A:ZN605 3.3 17.6 1.0 O A:HOH888 3.4 16.5 1.0 CA A:HIS243 3.5 15.7 1.0 OD1 A:ASP85 3.5 15.1 1.0 ND2 A:ASN117 3.6 15.2 1.0 OD1 A:ASP37 3.6 17.5 1.0 CB A:HIS243 3.7 12.1 1.0 ND1 A:HIS220 4.0 16.9 1.0 CG A:HIS220 4.1 18.7 1.0 O A:HIS243 4.1 16.7 1.0 NE2 A:HIS243 4.2 20.5 1.0 CB A:ASP85 4.3 14.1 1.0 CD2 A:HIS243 4.3 17.8 1.0 C A:HIS243 4.3 14.7 1.0 N A:ASN117 4.4 15.2 1.0 O A:HOH741 4.5 28.8 1.0 CB A:ASN117 4.5 16.9 1.0 N A:HIS243 4.5 14.8 1.0 CD2 A:HIS118 4.6 12.3 1.0 CG A:ASP37 4.7 15.1 1.0 O A:HOH1014 4.9 22.4 1.0 O A:HOH726 4.9 13.0 1.0 NE2 A:HIS39 5.0 17.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:16.4 occ:1.00 OD2 B:ASP37 2.0 15.7 1.0 NE2 B:HIS39 2.1 14.3 1.0 O B:HOH810 2.1 13.9 1.0 O B:HOH835 2.1 15.0 1.0 OD2 B:ASP85 2.2 12.6 1.0 O B:HOH858 2.9 33.5 1.0 CD2 B:HIS39 3.0 15.9 1.0 CG B:ASP37 3.1 16.1 1.0 CE1 B:HIS39 3.1 15.2 1.0 CG B:ASP85 3.2 13.9 1.0 ZN B:ZN605 3.2 17.5 1.0 CB B:ASP85 3.5 13.1 1.0 CB B:ASP37 3.6 13.2 1.0 O B:HOH1005 4.1 17.6 1.0 OD1 B:ASP37 4.1 14.9 1.0 CG B:HIS39 4.2 15.0 1.0 ND1 B:HIS39 4.2 15.6 1.0 CE1 B:HIS220 4.2 13.7 1.0 NE2 B:HIS220 4.2 13.0 1.0 OD1 B:ASN245 4.2 19.8 1.0 CA B:ASP37 4.3 11.3 1.0 CD2 B:HIS118 4.3 13.8 1.0 OD1 B:ASP85 4.3 13.8 1.0 O B:HIS243 4.4 16.9 1.0 CA B:HIS243 4.6 12.3 1.0 O B:HOH972 4.7 24.3 1.0 ND1 B:HIS243 4.8 14.0 1.0 O B:HOH966 4.8 39.2 1.0 OD1 B:ASN117 4.8 12.5 1.0 C B:HIS243 4.9 14.8 1.0 OG B:SER521 4.9 35.7 1.0 NE2 B:HIS118 4.9 16.8 1.0 O B:HOH954 4.9 34.5 1.0 CA B:ASP85 5.0 11.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 5'-Nucleotidase From Venom of Naja Atra within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn605 b:17.5 occ:1.00 NE2 B:HIS220 2.0 13.0 1.0 O B:HOH835 2.0 15.0 1.0 OD1 B:ASN117 2.0 12.5 1.0 ND1 B:HIS243 2.1 14.0 1.0 OD2 B:ASP85 2.3 12.6 1.0 CE1 B:HIS243 2.9 16.4 1.0 CD2 B:HIS220 3.0 11.8 1.0 CE1 B:HIS220 3.0 13.7 1.0 CG B:ASP85 3.1 13.9 1.0 CG B:ASN117 3.2 12.7 1.0 ZN B:ZN604 3.2 16.4 1.0 CG B:HIS243 3.2 15.2 1.0 O B:HOH1005 3.4 17.6 1.0 OD1 B:ASP85 3.5 13.8 1.0 CA B:HIS243 3.6 12.3 1.0 OD2 B:ASP37 3.6 15.7 1.0 CB B:HIS243 3.7 14.2 1.0 ND2 B:ASN117 3.7 12.4 1.0 NE2 B:HIS243 4.1 17.0 1.0 ND1 B:HIS220 4.1 11.1 1.0 CG B:HIS220 4.2 11.8 1.0 O B:HOH858 4.2 33.5 1.0 O B:HIS243 4.2 16.9 1.0 CD2 B:HIS243 4.3 16.7 1.0 N B:ASN117 4.3 11.4 1.0 CB B:ASP85 4.3 13.1 1.0 C B:HIS243 4.4 14.8 1.0 CB B:ASN117 4.5 14.4 1.0 CD2 B:HIS118 4.5 13.8 1.0 N B:HIS243 4.5 15.0 1.0 O B:HOH810 4.7 13.9 1.0 CG B:ASP37 4.8 16.1 1.0 NE2 B:HIS39 4.9 14.3 1.0 CA B:ASN117 5.0 14.4 1.0

C.Chang, C.-C.Lin, W.-G.Wu. Crystal Strucuture of Taiwan Cobra (Naja Atra) Venom 5'-Nucleotidase at 1.9 Angstroms Resolution. To Be Published.