Zinc in PDB 1ura: Alkaline Phosphatase (D51ZN)

All present enzymatic activity of Alkaline Phosphatase (D51ZN):
3.1.3.1;

The structure of Alkaline Phosphatase (D51ZN), PDB code: 1ura was solved by T.T.Tibbitts, J.E.Murphy, E.R.Kantrowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.04
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	194.810, 166.870, 76.390, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23.4

The binding sites of Zinc atom in the Alkaline Phosphatase (D51ZN) (pdb code 1ura). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Alkaline Phosphatase (D51ZN), PDB code: 1ura:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Alkaline Phosphatase (D51ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alkaline Phosphatase (D51ZN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn450 b:14.4 occ:1.00 NE2 A:HIS412 1.9 25.2 1.0 NE2 A:HIS331 2.0 15.9 1.0 O1 A:PO4453 2.1 23.4 0.8 OD1 A:ASP327 2.2 16.3 1.0 O2 A:PO4453 2.2 24.1 0.8 OD2 A:ASP327 2.4 12.9 1.0 CG A:ASP327 2.6 5.2 1.0 P A:PO4453 2.7 17.9 0.8 CE1 A:HIS412 2.7 15.1 1.0 CE1 A:HIS331 3.0 4.4 1.0 CD2 A:HIS331 3.0 5.5 1.0 CD2 A:HIS412 3.1 22.4 1.0 O3 A:PO4453 3.7 15.1 0.8 NE2 A:HIS372 3.7 5.3 1.0 O4 A:PO4453 3.8 14.8 0.8 CE1 A:HIS370 3.9 4.1 1.0 NE2 A:HIS370 3.9 18.2 1.0 ND1 A:HIS412 3.9 17.5 1.0 ZN A:ZN451 4.1 12.9 0.9 CG A:HIS412 4.1 14.3 1.0 CB A:ASP327 4.1 13.6 1.0 ND1 A:HIS331 4.1 12.3 1.0 CG A:HIS331 4.2 14.8 1.0 CD2 A:HIS372 4.5 6.8 1.0 OD1 A:ASN51 4.5 13.3 1.0 CE1 A:HIS372 4.6 6.5 1.0 O A:ASP327 4.9 8.3 1.0 O A:HOH526 4.9 28.8 1.0 C A:ASP327 4.9 10.6 1.0 OG A:SER102 4.9 14.0 1.0 CA A:ASP327 5.0 10.1 1.0

Zinc binding site 2 out of 4 in the Alkaline Phosphatase (D51ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alkaline Phosphatase (D51ZN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn451 b:12.9 occ:0.91 OD2 A:ASP369 2.0 15.3 1.0 NE2 A:HIS370 2.0 18.2 1.0 OD1 A:ASN51 2.1 13.3 1.0 O2 A:PO4453 2.2 24.1 0.8 OG A:SER102 2.2 14.0 1.0 CD2 A:HIS370 2.9 4.7 1.0 CG A:ASP369 2.9 15.1 1.0 CG A:ASN51 3.0 19.5 1.0 CE1 A:HIS370 3.1 4.1 1.0 OD1 A:ASP369 3.3 10.1 1.0 ND2 A:ASN51 3.3 12.5 1.0 P A:PO4453 3.5 17.9 0.8 CB A:SER102 3.5 10.3 1.0 OD1 A:ASP327 3.7 16.3 1.0 CA A:SER102 3.8 9.2 1.0 O4 A:PO4453 3.9 14.8 0.8 N A:SER102 3.9 6.1 1.0 O3 A:PO4453 4.0 15.1 0.8 CG A:ASP327 4.0 5.2 1.0 CG A:HIS370 4.0 2.0 1.0 ZN A:ZN450 4.1 14.4 1.0 ND1 A:HIS370 4.1 8.7 1.0 CE1 A:HIS412 4.2 15.1 1.0 CB A:ASP369 4.3 10.2 1.0 CB A:ASN51 4.4 15.2 1.0 OD2 A:ASP327 4.4 12.9 1.0 N A:GLY52 4.4 7.5 1.0 CB A:ASP327 4.6 13.6 1.0 NE2 A:HIS412 4.6 25.2 1.0 C A:ASP101 4.6 9.6 1.0 O1 A:PO4453 4.6 23.4 0.8 O A:HOH527 4.7 36.5 1.0 CA A:ASN51 4.7 15.4 1.0 C A:ASN51 4.8 11.2 1.0 ND1 A:HIS412 4.8 17.5 1.0

Zinc binding site 3 out of 4 in the Alkaline Phosphatase (D51ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alkaline Phosphatase (D51ZN) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn450 b:9.8 occ:0.90 NE2 B:HIS331 1.9 13.0 1.0 NE2 B:HIS412 2.0 25.9 1.0 O1 B:PO4453 2.1 16.7 0.8 OD1 B:ASP327 2.2 25.1 1.0 O2 B:PO4453 2.3 18.9 0.8 OD2 B:ASP327 2.3 18.8 1.0 CG B:ASP327 2.6 14.7 1.0 P B:PO4453 2.7 15.0 0.8 CE1 B:HIS412 2.8 15.7 1.0 CD2 B:HIS331 2.9 11.2 1.0 CE1 B:HIS331 2.9 6.8 1.0 CD2 B:HIS412 3.1 22.1 1.0 NE2 B:HIS372 3.7 14.4 1.0 O3 B:PO4453 3.7 9.2 0.8 O4 B:PO4453 3.8 13.5 0.8 CE1 B:HIS370 4.0 3.7 1.0 ND1 B:HIS412 4.0 14.6 1.0 NE2 B:HIS370 4.0 7.9 1.0 ND1 B:HIS331 4.1 13.1 1.0 CG B:HIS331 4.1 14.6 1.0 CB B:ASP327 4.1 17.1 1.0 ZN B:ZN451 4.1 15.6 0.8 CG B:HIS412 4.2 17.4 1.0 CD2 B:HIS372 4.5 5.1 1.0 CE1 B:HIS372 4.5 9.6 1.0 OD1 B:ASN51 4.6 16.7 1.0 O B:ASP327 4.7 10.5 1.0 C B:ASP327 4.8 12.8 1.0 CA B:ASP327 4.9 12.8 1.0 OG B:SER102 4.9 17.6 1.0

Zinc binding site 4 out of 4 in the Alkaline Phosphatase (D51ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alkaline Phosphatase (D51ZN) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn451 b:15.6 occ:0.81 OD2 B:ASP369 2.0 19.4 1.0 OD1 B:ASN51 2.0 16.7 1.0 NE2 B:HIS370 2.1 7.9 1.0 OG B:SER102 2.2 17.6 1.0 O2 B:PO4453 2.2 18.9 0.8 CG B:ASN51 2.9 18.5 1.0 CD2 B:HIS370 2.9 2.7 1.0 CG B:ASP369 3.0 17.2 1.0 CE1 B:HIS370 3.1 3.7 1.0 ND2 B:ASN51 3.2 19.2 1.0 OD1 B:ASP369 3.2 21.5 1.0 CB B:SER102 3.5 11.9 1.0 P B:PO4453 3.5 15.0 0.8 OD1 B:ASP327 3.6 25.1 1.0 CA B:SER102 3.8 9.7 1.0 O4 B:PO4453 3.9 13.5 0.8 CG B:ASP327 4.0 14.7 1.0 N B:SER102 4.0 3.1 1.0 O3 B:PO4453 4.0 9.2 0.8 CG B:HIS370 4.1 2.0 1.0 ND1 B:HIS370 4.1 4.8 1.0 ZN B:ZN450 4.1 9.8 0.9 CE1 B:HIS412 4.2 15.7 1.0 CB B:ASN51 4.3 11.0 1.0 CB B:ASP369 4.3 13.1 1.0 OD2 B:ASP327 4.4 18.8 1.0 N B:GLY52 4.4 10.8 1.0 CB B:ASP327 4.5 17.1 1.0 NE2 B:HIS412 4.6 25.9 1.0 O1 B:PO4453 4.7 16.7 0.8 CA B:ASN51 4.7 11.0 1.0 C B:ASP101 4.7 8.8 1.0 C B:ASN51 4.7 9.6 1.0 ND1 B:HIS412 4.9 14.6 1.0 O B:HOH473 5.0 37.3 1.0

T.T.Tibbitts, J.E.Murphy, E.R.Kantrowitz. Kinetic and Structural Consequences of Replacing the Aspartate Bridge By Asparagine in the Catalytic Metal Triad of Escherichia Coli Alkaline Phosphatase. J.Mol.Biol. V. 257 700 1996.
ISSN: ISSN 0022-2836
PubMed: 8648634
DOI: 10.1006/JMBI.1996.0195