Zinc in PDB 1zed: Alkaline Phosphatase From Human Placenta in Complex with P- Nitrophenyl-Phosphonate

All present enzymatic activity of Alkaline Phosphatase From Human Placenta in Complex with P- Nitrophenyl-Phosphonate:
3.1.3.1;

The structure of Alkaline Phosphatase From Human Placenta in Complex with P- Nitrophenyl-Phosphonate, PDB code: 1zed was solved by P.Llinas, E.A.Stura, A.Menez, Z.Kiss, T.Stigbrand, J.L.Millan, M.H.Le Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.92 / 1.57
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.346, 114.573, 106.568, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 18.8

The structure of Alkaline Phosphatase From Human Placenta in Complex with P- Nitrophenyl-Phosphonate also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Zinc atom in the Alkaline Phosphatase From Human Placenta in Complex with P- Nitrophenyl-Phosphonate (pdb code 1zed). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Alkaline Phosphatase From Human Placenta in Complex with P- Nitrophenyl-Phosphonate, PDB code: 1zed:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Alkaline Phosphatase From Human Placenta in Complex with P- Nitrophenyl-Phosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alkaline Phosphatase From Human Placenta in Complex with P- Nitrophenyl-Phosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:13.3 occ:1.00 O A:HOH1661 2.0 18.1 1.0 OD1 A:ASP316 2.0 11.9 1.0 NE2 A:HIS432 2.1 12.2 1.0 NE2 A:HIS320 2.1 11.3 1.0 O2 A:PO3907 2.2 13.6 1.0 OD2 A:ASP316 2.5 11.7 1.0 CG A:ASP316 2.6 12.4 1.0 CE1 A:HIS432 3.0 12.5 1.0 CD2 A:HIS320 3.0 11.4 1.0 CD2 A:HIS432 3.1 12.3 1.0 CE1 A:HIS320 3.1 10.6 1.0 P A:PO3907 3.2 15.1 1.0 O3 A:PO3907 3.6 15.1 1.0 O A:HOH1662 3.7 47.2 1.0 O A:HOH1290 3.9 42.9 1.0 O1 A:PO3907 3.9 14.8 1.0 O A:HOH1667 4.0 15.2 1.0 CB A:ASP316 4.1 12.2 1.0 ZN A:ZN904 4.1 12.5 1.0 ND1 A:HIS432 4.1 11.8 1.0 ND1 A:HIS320 4.2 12.4 1.0 CG A:HIS432 4.2 12.9 1.0 CE1 A:HIS358 4.2 12.7 1.0 CG A:HIS320 4.2 12.0 1.0 NE2 A:HIS358 4.3 12.1 1.0 CE1 A:HIS360 4.5 11.9 1.0 OG A:SER92 4.5 11.0 1.0 NE2 A:HIS360 4.6 12.0 1.0 OD1 A:ASP42 4.6 11.0 1.0 O2N A:PNP901 4.7 16.5 1.0 O A:ASP316 5.0 12.0 1.0 CA A:ASP316 5.0 12.0 1.0

Zinc binding site 2 out of 2 in the Alkaline Phosphatase From Human Placenta in Complex with P- Nitrophenyl-Phosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alkaline Phosphatase From Human Placenta in Complex with P- Nitrophenyl-Phosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:12.5 occ:1.00 OD1 A:ASP42 1.9 11.0 1.0 OD2 A:ASP357 2.0 9.3 1.0 NE2 A:HIS358 2.1 12.1 1.0 OG A:SER92 2.1 11.0 1.0 O2 A:PO3907 2.2 13.6 1.0 CG A:ASP42 2.7 12.5 1.0 OD2 A:ASP42 2.9 12.7 1.0 CG A:ASP357 2.9 11.1 1.0 P A:PO3907 2.9 15.1 1.0 CD2 A:HIS358 3.0 11.2 1.0 CE1 A:HIS358 3.0 12.7 1.0 OD1 A:ASP357 3.1 11.1 1.0 CB A:SER92 3.3 13.0 1.0 OD2 A:ASP316 3.7 11.7 1.0 O3 A:PO3907 3.8 15.1 1.0 CA A:SER92 3.9 12.7 1.0 O1 A:PO3907 3.9 14.8 1.0 CG A:ASP316 4.0 12.4 1.0 ZN A:ZN903 4.1 13.3 1.0 ND1 A:HIS358 4.1 12.0 1.0 CB A:ASP42 4.1 12.5 1.0 CG A:HIS358 4.1 10.3 1.0 CE1 A:HIS432 4.1 12.5 1.0 N A:SER92 4.2 12.9 1.0 NE2 A:HIS432 4.2 12.2 1.0 N A:GLY43 4.2 10.9 1.0 CB A:ASP357 4.3 10.9 1.0 OD1 A:ASP316 4.3 11.9 1.0 O A:HOH993 4.3 12.6 1.0 CA A:ASP42 4.5 12.2 1.0 C A:ASP42 4.5 11.9 1.0 CB A:ASP316 4.6 12.2 1.0 O A:HOH969 4.6 13.8 1.0 MG A:MG905 4.7 3.4 1.0 O A:HOH1667 4.7 15.2 1.0 ND1 A:HIS432 4.9 11.8 1.0 C A:ASP91 4.9 13.2 1.0 CA A:GLY43 4.9 11.0 1.0 OG A:SER155 5.0 13.2 1.0

P.Llinas, E.A.Stura, A.Menez, Z.Kiss, T.Stigbrand, J.L.Millan, M.H.Le Du. Structural Studies of Human Placental Alkaline Phosphatase in Complex with Functional Ligands. J.Mol.Biol. V. 350 441 2005.
ISSN: ISSN 0022-2836
PubMed: 15946677
DOI: 10.1016/J.JMB.2005.04.068