Zinc in PDB 1hp1: 5'-Nucleotidase (Open Form) Complex with Atp

All present enzymatic activity of 5'-Nucleotidase (Open Form) Complex with Atp:
3.1.3.5; 3.6.1.45;

The structure of 5'-Nucleotidase (Open Form) Complex with Atp, PDB code: 1hp1 was solved by T.Knoefel, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.59 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.700, 83.700, 181.800, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 19.9

The binding sites of Zinc atom in the 5'-Nucleotidase (Open Form) Complex with Atp (pdb code 1hp1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the 5'-Nucleotidase (Open Form) Complex with Atp, PDB code: 1hp1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the 5'-Nucleotidase (Open Form) Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 5'-Nucleotidase (Open Form) Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn600 b:20.4 occ:1.00 OD2 A:ASP41 2.1 8.7 1.0 NE2 A:HIS43 2.1 10.3 1.0 OE1 A:GLN254 2.3 19.1 1.0 OD2 A:ASP84 2.3 7.4 1.0 O1 A:CO3602 2.6 29.9 1.0 CE1 A:HIS43 3.0 10.0 1.0 CD2 A:HIS43 3.1 9.9 1.0 CG A:ASP41 3.1 10.3 1.0 CG A:ASP84 3.2 8.4 1.0 CD A:GLN254 3.4 17.6 1.0 ZN A:ZN601 3.4 15.7 1.0 CB A:ASP84 3.5 8.3 1.0 C A:CO3602 3.5 29.3 1.0 CB A:ASP41 3.6 8.1 1.0 O A:HOH1306 3.7 30.8 1.0 CG A:GLN254 3.9 14.1 1.0 ND1 A:HIS43 4.1 7.4 1.0 O2 A:CO3602 4.2 32.3 1.0 O3 A:CO3602 4.2 30.6 1.0 OD1 A:ASP41 4.2 9.9 1.0 CG A:HIS43 4.2 8.4 1.0 CD2 A:HIS117 4.2 7.9 1.0 CE1 A:HIS217 4.2 9.4 1.0 O A:HIS252 4.3 12.4 1.0 CA A:ASP41 4.3 8.0 1.0 NE2 A:HIS217 4.3 8.3 1.0 OD1 A:ASP84 4.4 8.8 1.0 NE2 A:GLN254 4.5 18.7 1.0 CA A:HIS252 4.5 11.9 1.0 NE2 A:HIS117 4.8 10.8 1.0 C A:HIS252 4.8 11.1 1.0 N A:HIS252 4.9 9.2 1.0 CA A:ASP84 5.0 7.2 1.0

Zinc binding site 2 out of 2 in the 5'-Nucleotidase (Open Form) Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 5'-Nucleotidase (Open Form) Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:15.7 occ:1.00 NE2 A:HIS217 2.1 8.3 1.0 OD1 A:ASN116 2.1 8.8 1.0 OD2 A:ASP84 2.2 7.4 1.0 ND1 A:HIS252 2.3 13.8 1.0 O1 A:CO3602 2.7 29.9 1.0 O3 A:CO3602 2.8 30.6 1.0 CE1 A:HIS217 3.1 9.4 1.0 CD2 A:HIS217 3.1 8.6 1.0 CG A:ASP84 3.1 8.4 1.0 CE1 A:HIS252 3.2 14.6 1.0 C A:CO3602 3.2 29.3 1.0 CG A:ASN116 3.2 10.9 1.0 ZN A:ZN600 3.4 20.4 1.0 CG A:HIS252 3.4 12.4 1.0 OD1 A:ASP84 3.5 8.8 1.0 CA A:HIS252 3.6 11.9 1.0 ND2 A:ASN116 3.7 11.0 1.0 CB A:HIS252 3.8 11.0 1.0 OD2 A:ASP41 3.9 8.7 1.0 CD2 A:HIS117 4.0 7.9 1.0 ND1 A:HIS217 4.2 9.7 1.0 CG A:HIS217 4.2 8.4 1.0 O A:HIS252 4.2 12.4 1.0 N A:ASN116 4.3 8.9 1.0 NE2 A:HIS252 4.3 14.1 1.0 CB A:ASP84 4.3 8.3 1.0 O2 A:CO3602 4.4 32.3 1.0 CB A:ASN116 4.4 9.1 1.0 C A:HIS252 4.4 11.1 1.0 CD2 A:HIS252 4.5 15.2 1.0 N A:HIS252 4.5 9.2 1.0 NE2 A:HIS117 4.7 10.8 1.0 N A:HIS117 4.9 8.3 1.0 CA A:ASN116 4.9 8.5 1.0

T.Knofel, N.Strater. Mechanism of Hydrolysis of Phosphate Esters By the Dimetal Center of 5'-Nucleotidase Based on Crystal Structures. J.Mol.Biol. V. 309 239 2001.
ISSN: ISSN 0022-2836
PubMed: 11491293
DOI: 10.1006/JMBI.2001.4656