Zinc in PDB 2z1a: Crystal Structure of 5'-Nucleotidase Precursor From Thermus Thermophilus HB8

All present enzymatic activity of Crystal Structure of 5'-Nucleotidase Precursor From Thermus Thermophilus HB8:
3.1.3.5;

The structure of Crystal Structure of 5'-Nucleotidase Precursor From Thermus Thermophilus HB8, PDB code: 2z1a was solved by N.Nakagawa, S.Kishishita, S.Yokoyama, S.Kuramitsu, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.40 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.426, 57.832, 81.960, 90.00, 105.95, 90.00
R / Rfree (%)	17.9 / 20.9

The binding sites of Zinc atom in the Crystal Structure of 5'-Nucleotidase Precursor From Thermus Thermophilus HB8 (pdb code 2z1a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of 5'-Nucleotidase Precursor From Thermus Thermophilus HB8, PDB code: 2z1a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of 5'-Nucleotidase Precursor From Thermus Thermophilus HB8


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 Precursor From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5647 b:12.9 occ:1.00 O A:HOH6559 2.1 8.2 1.0 OD1 A:ASP37 2.2 6.2 1.0 NE2 A:HIS39 2.2 4.0 1.0 CE1 A:HIS240 2.3 4.5 1.0 O2 A:PO45646 2.3 9.3 1.0 OD2 A:ASP83 2.3 5.2 1.0 P A:PO45646 3.0 12.8 1.0 CE1 A:HIS39 3.1 5.2 1.0 NE2 A:HIS240 3.1 8.0 1.0 CG A:ASP37 3.1 5.8 1.0 CD2 A:HIS39 3.3 4.8 1.0 ND1 A:HIS240 3.3 8.5 1.0 ZN A:ZN5648 3.3 21.9 1.0 CG A:ASP83 3.3 5.3 1.0 CB A:ASP83 3.6 5.1 1.0 CB A:ASP37 3.7 5.6 1.0 O1 A:PO45646 3.7 6.2 1.0 OD2 A:ASP37 4.1 7.2 1.0 O3 A:PO45646 4.2 8.7 1.0 O4 A:PO45646 4.2 9.8 1.0 NH1 A:ARG345 4.2 13.5 1.0 ND1 A:HIS39 4.2 6.0 1.0 NH2 A:ARG383 4.3 6.6 1.0 CD2 A:HIS116 4.3 5.3 1.0 NE2 A:HIS215 4.3 9.9 1.0 CD2 A:HIS240 4.4 5.4 1.0 CG A:HIS39 4.4 6.2 1.0 CG A:HIS240 4.4 6.6 1.0 OD1 A:ASP83 4.5 6.0 1.0 O A:HIS238 4.5 6.0 1.0 CA A:ASP37 4.5 4.7 1.0 CE1 A:HIS215 4.5 4.1 1.0 CA A:HIS238 4.6 6.8 1.0 NE2 A:HIS116 4.8 4.9 1.0 C A:HIS238 4.9 8.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of 5'-Nucleotidase Precursor From Thermus Thermophilus HB8


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 Precursor From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5648 b:21.9 occ:1.00 OD1 A:ASN115 2.1 5.1 1.0 O A:HOH6559 2.2 8.2 1.0 CE1 A:HIS215 2.3 4.1 1.0 O1 A:PO45646 2.3 6.2 1.0 OD2 A:ASP83 2.3 5.2 1.0 ND1 A:HIS238 2.3 4.2 1.0 P A:PO45646 3.1 12.8 1.0 CE1 A:HIS238 3.1 7.2 1.0 NE2 A:HIS215 3.1 9.9 1.0 CG A:ASN115 3.1 6.8 1.0 CG A:ASP83 3.2 5.3 1.0 ZN A:ZN5647 3.3 12.9 1.0 ND1 A:HIS215 3.3 8.8 1.0 CG A:HIS238 3.4 5.8 1.0 ND2 A:ASN115 3.5 5.8 1.0 OD1 A:ASP83 3.6 6.0 1.0 CA A:HIS238 3.7 6.8 1.0 O2 A:PO45646 3.9 9.3 1.0 OD1 A:ASP37 3.9 6.2 1.0 CB A:HIS238 3.9 5.6 1.0 O A:HIS238 4.1 6.0 1.0 O3 A:PO45646 4.1 8.7 1.0 O4 A:PO45646 4.2 9.8 1.0 CD2 A:HIS116 4.2 5.3 1.0 NE2 A:HIS238 4.3 5.6 1.0 CD2 A:HIS215 4.3 3.8 1.0 C A:HIS238 4.4 8.2 1.0 CB A:ASP83 4.4 5.1 1.0 CG A:HIS215 4.4 5.9 1.0 CD2 A:HIS238 4.5 6.2 1.0 CB A:ASN115 4.5 4.9 1.0 N A:ASN115 4.5 3.9 1.0 N A:HIS238 4.7 7.5 1.0 NE2 A:HIS116 4.8 4.9 1.0 O A:HOH7097 5.0 11.7 1.0

N.Nakakaga, S.Kishishita, S.Yokoyama, S.Kuramitsu. Crystal Structure of 5'-Nucleotidase Precursor From Thermus Thermophilus HB8 To Be Published.