Zinc in PDB 7d0v: Crystal Structure of Taiwan Cobra 5'-Nucleotidase

All present enzymatic activity of Crystal Structure of Taiwan Cobra 5'-Nucleotidase:
3.1.3.5;

The structure of Crystal Structure of Taiwan Cobra 5'-Nucleotidase, PDB code: 7d0v was solved by M.-H.Tsai, I.-J.Lin, 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)	28.67 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.327, 68.127, 140.214, 90, 95.17, 90
R / Rfree (%)	n/a / 21.9

The structure of Crystal Structure of Taiwan Cobra 5'-Nucleotidase also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Taiwan Cobra 5'-Nucleotidase (pdb code 7d0v). 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 Taiwan Cobra 5'-Nucleotidase, PDB code: 7d0v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Taiwan Cobra 5'-Nucleotidase


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 Taiwan Cobra 5'-Nucleotidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:33.1 occ:1.00 NE2 A:HIS39 2.1 36.0 1.0 OD1 A:ASP37 2.1 34.1 1.0 O A:HOH914 2.2 21.9 1.0 O A:HOH815 2.3 21.4 1.0 OD2 A:ASP85 2.3 30.6 1.0 O A:HOH892 2.8 35.1 1.0 CE1 A:HIS39 3.0 34.1 1.0 CG A:ASP37 3.2 29.5 1.0 CD2 A:HIS39 3.2 34.6 1.0 ZN A:ZN702 3.2 25.9 1.0 CG A:ASP85 3.2 28.1 1.0 CB A:ASP85 3.5 26.1 1.0 CB A:ASP37 3.6 26.5 1.0 CE1 A:HIS220 4.1 29.9 1.0 OD1 A:ASN245 4.1 23.2 1.0 NE2 A:HIS220 4.2 30.5 1.0 ND1 A:HIS39 4.2 34.6 1.0 O A:HIS243 4.2 25.6 1.0 O A:HOH899 4.2 20.4 1.0 CD2 A:HIS118 4.2 23.5 1.0 OG A:SER521 4.3 26.6 1.0 OD2 A:ASP37 4.3 30.6 1.0 CG A:HIS39 4.3 34.0 1.0 CA A:ASP37 4.3 25.2 1.0 O A:HOH943 4.4 20.6 1.0 OD1 A:ASP85 4.4 29.2 1.0 CA A:HIS243 4.6 27.0 1.0 C A:HIS243 4.8 26.1 1.0 NE2 A:HIS118 4.8 23.3 1.0 O A:HOH881 4.8 27.8 1.0 ND1 A:HIS243 4.8 30.0 1.0 OD1 A:ASN117 4.8 32.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Taiwan Cobra 5'-Nucleotidase


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 Taiwan Cobra 5'-Nucleotidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:25.9 occ:1.00 NE2 A:HIS220 1.9 30.5 1.0 O A:HOH914 2.0 21.9 1.0 OD1 A:ASN117 2.0 32.5 1.0 ND1 A:HIS243 2.2 30.0 1.0 OD2 A:ASP85 2.2 30.6 1.0 CD2 A:HIS220 2.9 29.9 1.0 CE1 A:HIS220 2.9 29.9 1.0 CE1 A:HIS243 3.0 29.7 1.0 CG A:ASP85 3.1 28.1 1.0 CG A:ASN117 3.1 28.6 1.0 ZN A:ZN701 3.2 33.1 1.0 CG A:HIS243 3.3 29.2 1.0 O A:HOH899 3.4 20.4 1.0 OD1 A:ASP85 3.5 29.2 1.0 CA A:HIS243 3.5 27.0 1.0 ND2 A:ASN117 3.6 26.6 1.0 OD1 A:ASP37 3.7 34.1 1.0 CB A:HIS243 3.7 26.8 1.0 ND1 A:HIS220 4.0 30.2 1.0 CG A:HIS220 4.0 29.9 1.0 O A:HIS243 4.1 25.6 1.0 NE2 A:HIS243 4.2 29.8 1.0 CB A:ASP85 4.2 26.1 1.0 C A:HIS243 4.3 26.1 1.0 CD2 A:HIS243 4.3 29.7 1.0 N A:ASN117 4.4 24.4 1.0 CB A:ASN117 4.4 27.3 1.0 CD2 A:HIS118 4.4 23.5 1.0 O A:HOH892 4.5 35.1 1.0 N A:HIS243 4.5 27.0 1.0 CG A:ASP37 4.8 29.5 1.0 CA A:ASN117 5.0 26.1 1.0 NE2 A:HIS39 5.0 36.0 1.0 O A:HOH815 5.0 21.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Taiwan Cobra 5'-Nucleotidase


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 Taiwan Cobra 5'-Nucleotidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:31.9 occ:1.00 OD1 B:ASP37 2.1 34.3 1.0 NE2 B:HIS39 2.1 35.4 1.0 O B:HOH828 2.2 28.4 1.0 OD2 B:ASP85 2.2 29.6 1.0 O B:HOH723 2.3 13.9 1.0 CD2 B:HIS39 3.0 34.5 1.0 CG B:ASP37 3.0 31.0 1.0 CE1 B:HIS39 3.2 34.1 1.0 CG B:ASP85 3.2 26.6 1.0 ZN B:ZN603 3.2 23.2 1.0 CB B:ASP85 3.4 24.8 1.0 CB B:ASP37 3.5 28.7 1.0 CE1 B:HIS220 4.0 27.4 1.0 OD1 B:ASN245 4.1 26.6 1.0 NE2 B:HIS220 4.1 29.0 1.0 OD2 B:ASP37 4.1 31.4 1.0 O B:HOH794 4.1 27.2 1.0 CA B:ASP37 4.2 26.4 1.0 CG B:HIS39 4.2 33.7 1.0 ND1 B:HIS39 4.2 34.6 1.0 OD1 B:ASP85 4.3 26.6 1.0 CD2 B:HIS118 4.4 29.0 1.0 O B:HIS243 4.4 27.9 1.0 CA B:HIS243 4.5 26.6 1.0 OG B:SER521 4.7 37.6 1.0 C B:HIS243 4.8 26.9 1.0 OD1 B:ASN117 4.8 27.7 1.0 ND1 B:HIS243 4.8 30.6 1.0 O B:HOH886 4.9 40.3 1.0 CA B:ASP85 4.9 23.7 1.0 N B:HIS243 5.0 24.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Taiwan Cobra 5'-Nucleotidase


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 Taiwan Cobra 5'-Nucleotidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:23.2 occ:1.00 NE2 B:HIS220 1.8 29.0 1.0 OD1 B:ASN117 2.0 27.7 1.0 OD2 B:ASP85 2.2 29.6 1.0 ND1 B:HIS243 2.2 30.6 1.0 O B:HOH828 2.2 28.4 1.0 CE1 B:HIS220 2.8 27.4 1.0 CD2 B:HIS220 2.8 27.6 1.0 CE1 B:HIS243 3.0 29.6 1.0 CG B:ASN117 3.1 25.0 1.0 CG B:ASP85 3.1 26.6 1.0 ZN B:ZN602 3.2 31.9 1.0 CG B:HIS243 3.3 28.9 1.0 O B:HOH794 3.3 27.2 1.0 CA B:HIS243 3.5 26.6 1.0 OD1 B:ASP85 3.6 26.6 1.0 ND2 B:ASN117 3.6 25.0 1.0 OD1 B:ASP37 3.6 34.3 1.0 CB B:HIS243 3.7 27.5 1.0 ND1 B:HIS220 3.9 27.7 1.0 CG B:HIS220 3.9 27.6 1.0 O B:HIS243 4.1 27.9 1.0 NE2 B:HIS243 4.2 29.4 1.0 CB B:ASP85 4.3 24.8 1.0 CD2 B:HIS243 4.3 29.6 1.0 C B:HIS243 4.3 26.9 1.0 N B:ASN117 4.3 22.9 1.0 CB B:ASN117 4.4 24.2 1.0 N B:HIS243 4.4 24.7 1.0 CD2 B:HIS118 4.6 29.0 1.0 CG B:ASP37 4.8 31.0 1.0 O B:HOH723 4.9 13.9 1.0 NE2 B:HIS39 4.9 35.4 1.0 CA B:ASN117 5.0 24.2 1.0

M.-H.Tsai, I.-J.Lin, C.-C.Lin, W.-G.Wu. Crystal Structure of Taiwan Cobra 5'-Nucleotidase To Be Published.