Zinc in PDB 2x98: H.Salinarum Alkaline Phosphatase

All present enzymatic activity of H.Salinarum Alkaline Phosphatase:
3.1.3.1;

The structure of H.Salinarum Alkaline Phosphatase, PDB code: 2x98 was solved by A.Wende, P.Johansson, M.Grininger, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.143, 152.524, 86.799, 90.00, 110.00, 90.00
R / Rfree (%)	16.042 / 19.771

The structure of H.Salinarum Alkaline Phosphatase also contains other interesting chemical elements:

Magnesium	(Mg)	11 atoms
Chlorine	(Cl)	13 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the H.Salinarum Alkaline Phosphatase (pdb code 2x98). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the H.Salinarum Alkaline Phosphatase, PDB code: 2x98:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of H.Salinarum Alkaline Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1475 b:8.4 occ:1.00 NE2 A:HIS308 2.0 5.1 1.0 NE2 A:HIS435 2.0 4.3 1.0 O3 A:PO41474 2.1 15.3 1.0 OD1 A:ASP304 2.2 11.9 1.0 OD2 A:ASP304 2.3 11.1 1.0 CG A:ASP304 2.6 6.9 1.0 O2 A:PO41474 2.8 14.3 1.0 CD2 A:HIS308 3.0 5.1 1.0 CE1 A:HIS435 3.0 7.6 1.0 CE1 A:HIS308 3.0 7.9 1.0 P A:PO41474 3.0 11.4 1.0 CD2 A:HIS435 3.0 3.5 1.0 O1 A:PO41474 3.9 6.5 1.0 CE1 A:HIS347 4.0 5.0 1.0 O4 A:PO41474 4.1 10.2 1.0 ND1 A:HIS308 4.1 5.8 1.0 ND1 A:HIS435 4.1 5.2 1.0 CG A:HIS308 4.1 4.4 1.0 CB A:ASP304 4.1 6.4 1.0 CG A:HIS435 4.2 4.5 1.0 ZN A:ZN1476 4.2 9.6 1.0 NE2 A:HIS347 4.2 5.0 1.0 O A:HOH2463 4.2 15.1 1.0 SG A:CYS349 4.4 10.5 1.0 OG A:SER115 4.5 5.6 0.5 OD1 A:ASP56 4.8 7.5 1.0 O A:ASP304 4.8 6.1 1.0 CB A:CYS349 5.0 8.4 1.0 CA A:ASP304 5.0 5.2 1.0

Zinc binding site 2 out of 4 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of H.Salinarum Alkaline Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1476 b:9.6 occ:1.00 NE2 A:HIS347 1.9 5.0 1.0 OD2 A:ASP346 2.0 12.8 1.0 OD1 A:ASP56 2.0 7.5 1.0 O2 A:PO41474 2.0 14.3 1.0 OG A:SER115 2.1 5.6 0.5 CG A:ASP56 2.8 8.4 1.0 CG A:ASP346 2.9 12.2 1.0 CD2 A:HIS347 2.9 5.8 1.0 CE1 A:HIS347 2.9 5.0 1.0 OD2 A:ASP56 3.0 8.3 1.0 OD1 A:ASP346 3.1 8.4 1.0 CB A:SER115 3.2 6.4 0.5 P A:PO41474 3.4 11.4 1.0 CB A:SER115 3.4 8.0 0.5 OD1 A:ASP304 3.7 11.9 1.0 CA A:SER115 3.8 6.3 0.5 CA A:SER115 3.8 7.6 0.5 CG A:ASP304 4.0 6.9 1.0 ND1 A:HIS347 4.0 6.5 1.0 O4 A:PO41474 4.0 10.2 1.0 CE1 A:HIS435 4.0 7.6 1.0 CG A:HIS347 4.0 6.1 1.0 N A:SER115 4.1 6.6 0.5 O1 A:PO41474 4.1 6.5 1.0 N A:SER115 4.1 6.0 0.5 CB A:ASP56 4.1 4.7 1.0 ZN A:ZN1475 4.2 8.4 1.0 N A:GLY57 4.2 4.7 1.0 NE2 A:HIS435 4.3 4.3 1.0 CB A:ASP346 4.3 9.8 1.0 O3 A:PO41474 4.4 15.3 1.0 OD2 A:ASP304 4.4 11.1 1.0 OG A:SER115 4.4 11.9 0.5 CB A:ASP304 4.5 6.4 1.0 CA A:ASP56 4.5 5.2 1.0 O A:HOH2087 4.5 15.5 1.0 C A:ASP56 4.6 4.2 1.0 O A:HOH2138 4.7 10.9 1.0 MG A:MG1477 4.8 7.4 1.0 O A:HOH2463 4.8 15.1 1.0 ND1 A:HIS435 4.8 5.2 1.0 C A:ASP114 4.8 6.9 1.0

Zinc binding site 3 out of 4 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of H.Salinarum Alkaline Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1475 b:8.6 occ:1.00 NE2 B:HIS435 2.0 5.5 1.0 O3 B:PO41474 2.0 14.8 1.0 NE2 B:HIS308 2.0 6.2 1.0 OD1 B:ASP304 2.3 10.4 1.0 OD2 B:ASP304 2.4 12.8 1.0 CG B:ASP304 2.6 7.3 1.0 O2 B:PO41474 2.7 13.2 1.0 CE1 B:HIS435 3.0 8.0 1.0 CD2 B:HIS308 3.0 7.6 1.0 P B:PO41474 3.0 13.2 1.0 CD2 B:HIS435 3.0 4.3 1.0 CE1 B:HIS308 3.0 6.5 1.0 O1 B:PO41474 3.9 9.3 1.0 CE1 B:HIS347 4.0 7.3 1.0 ND1 B:HIS435 4.1 4.5 1.0 O B:HOH2307 4.1 16.3 1.0 O4 B:PO41474 4.1 9.9 1.0 ND1 B:HIS308 4.1 7.4 1.0 CG B:HIS308 4.2 6.9 1.0 CB B:ASP304 4.2 6.1 1.0 CG B:HIS435 4.2 4.7 1.0 ZN B:ZN1476 4.2 10.2 1.0 NE2 B:HIS347 4.2 7.4 1.0 SG B:CYS349 4.4 10.0 1.0 OG B:SER115 4.5 4.7 0.5 OD1 B:ASP56 4.8 5.1 1.0 O B:ASP304 4.8 6.0 1.0

Zinc binding site 4 out of 4 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of H.Salinarum Alkaline Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1476 b:10.2 occ:1.00 OD1 B:ASP56 2.0 5.1 1.0 OD2 B:ASP346 2.0 11.2 1.0 O2 B:PO41474 2.0 13.2 1.0 NE2 B:HIS347 2.0 7.4 1.0 OG B:SER115 2.1 4.7 0.5 CG B:ASP56 2.7 7.7 1.0 OD2 B:ASP56 2.9 9.9 1.0 CG B:ASP346 2.9 10.6 1.0 CE1 B:HIS347 3.0 7.3 1.0 CD2 B:HIS347 3.0 8.2 1.0 OD1 B:ASP346 3.2 7.7 1.0 CB B:SER115 3.2 6.6 0.5 CB B:SER115 3.3 8.4 0.5 P B:PO41474 3.4 13.2 1.0 OD1 B:ASP304 3.8 10.4 1.0 CA B:SER115 3.8 6.2 0.5 CA B:SER115 3.8 7.7 0.5 CG B:ASP304 3.9 7.3 1.0 O4 B:PO41474 4.0 9.9 1.0 N B:SER115 4.1 6.7 0.5 ND1 B:HIS347 4.1 9.5 1.0 CE1 B:HIS435 4.1 8.0 1.0 O1 B:PO41474 4.1 9.3 1.0 N B:SER115 4.1 5.9 0.5 CG B:HIS347 4.1 7.0 1.0 CB B:ASP56 4.1 5.5 1.0 ZN B:ZN1475 4.2 8.6 1.0 N B:GLY57 4.2 6.4 1.0 OG B:SER115 4.2 12.9 0.5 NE2 B:HIS435 4.3 5.5 1.0 CB B:ASP346 4.3 8.1 1.0 O3 B:PO41474 4.4 14.8 1.0 OD2 B:ASP304 4.4 12.8 1.0 CB B:ASP304 4.4 6.1 1.0 CA B:ASP56 4.5 5.9 1.0 O B:HOH2150 4.5 17.1 1.0 C B:ASP56 4.6 6.1 1.0 O B:HOH2480 4.6 12.4 1.0 O B:HOH2307 4.7 16.3 1.0 MG B:MG1477 4.7 8.7 1.0 C B:ASP114 4.9 6.0 1.0 ND1 B:HIS435 4.9 4.5 1.0

A.Wende, P.Johansson, R.Vollrath, M.Dyall-Smith, D.Oesterhelt, M.Grininger. Structural and Biochemical Characterization of A Halophilic Archaeal Alkaline Phosphatase. J.Mol.Biol. V. 400 52 2010.
ISSN: ISSN 0022-2836
PubMed: 20438737
DOI: 10.1016/J.JMB.2010.04.057