Zinc in PDB 1b8j: Alkaline Phosphatase Complexed with Vanadate

All present enzymatic activity of Alkaline Phosphatase Complexed with Vanadate:
3.1.3.1;

The structure of Alkaline Phosphatase Complexed with Vanadate, PDB code: 1b8j was solved by K.M.Holtz, B.Stec, E.R.Kantrowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	195.410, 167.810, 76.520, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 19.6

The structure of Alkaline Phosphatase Complexed with Vanadate also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Vanadium	(V)	2 atoms

The binding sites of Zinc atom in the Alkaline Phosphatase Complexed with Vanadate (pdb code 1b8j). 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 Complexed with Vanadate, PDB code: 1b8j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Alkaline Phosphatase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alkaline Phosphatase Complexed with Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn450 b:25.1 occ:1.00 NE2 A:HIS412 2.1 16.9 1.0 O2 A:SVA102 2.1 47.5 1.0 NE2 A:HIS331 2.1 17.4 1.0 OD2 A:ASP327 2.2 17.9 1.0 O4 A:SVA102 2.4 41.6 1.0 OD1 A:ASP327 2.5 15.3 1.0 CG A:ASP327 2.7 19.6 1.0 CE1 A:HIS412 2.9 21.2 1.0 V A:SVA102 3.0 42.4 1.0 CE1 A:HIS331 3.1 16.4 1.0 CD2 A:HIS331 3.1 23.3 1.0 CD2 A:HIS412 3.2 24.0 1.0 O3 A:SVA102 3.7 41.5 1.0 NE2 A:HIS372 3.8 20.8 1.0 OG A:SVA102 4.1 34.5 1.0 CE1 A:HIS370 4.1 13.8 1.0 NE2 A:HIS370 4.1 16.8 1.0 ZN A:ZN451 4.1 20.1 1.0 ND1 A:HIS412 4.1 24.1 1.0 CB A:ASP327 4.2 20.3 1.0 O1 A:SVA102 4.2 44.8 1.0 ND1 A:HIS331 4.2 17.1 1.0 O A:HOH1028 4.3 56.2 1.0 CG A:HIS412 4.3 23.1 1.0 CG A:HIS331 4.3 22.0 1.0 O A:HOH1471 4.5 19.2 1.0 CD2 A:HIS372 4.5 16.7 1.0 OD1 A:ASP51 4.6 23.4 1.0 CE1 A:HIS372 4.7 16.6 1.0 O A:ASP327 4.8 22.2 1.0 O A:HOH1026 4.8 58.9 1.0 C A:ASP327 4.9 14.8 1.0

Zinc binding site 2 out of 4 in the Alkaline Phosphatase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alkaline Phosphatase Complexed with Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn451 b:20.1 occ:1.00 OD2 A:ASP369 1.9 16.1 1.0 OG A:SVA102 1.9 34.5 1.0 OD1 A:ASP51 2.1 23.4 1.0 NE2 A:HIS370 2.1 16.8 1.0 O2 A:SVA102 2.2 47.5 1.0 CG A:ASP51 2.9 20.2 1.0 CB A:SVA102 2.9 8.6 1.0 OD2 A:ASP51 3.0 22.7 1.0 CD2 A:HIS370 3.0 10.0 1.0 CG A:ASP369 3.0 17.1 1.0 V A:SVA102 3.1 42.4 1.0 CE1 A:HIS370 3.2 13.8 1.0 OD1 A:ASP369 3.4 11.6 1.0 CA A:SVA102 3.5 8.1 1.0 OD2 A:ASP327 3.7 17.9 1.0 O1 A:SVA102 3.9 44.8 1.0 N A:SVA102 4.0 6.7 1.0 CG A:ASP327 4.1 19.6 1.0 O A:HOH1472 4.1 16.0 1.0 ZN A:ZN450 4.1 25.1 1.0 CG A:HIS370 4.2 8.3 1.0 CE1 A:HIS412 4.2 21.2 1.0 O3 A:SVA102 4.2 41.5 1.0 ND1 A:HIS370 4.2 16.7 1.0 O A:HOH1473 4.2 11.5 1.0 CB A:ASP369 4.3 8.2 1.0 CB A:ASP51 4.3 18.7 1.0 NE2 A:HIS412 4.5 16.9 1.0 MG A:MG452 4.6 14.8 1.0 N A:GLY52 4.6 4.8 1.0 CB A:ASP327 4.6 20.3 1.0 OD1 A:ASP327 4.6 15.3 1.0 O4 A:SVA102 4.7 41.6 1.0 CA A:ASP51 4.8 13.4 1.0 C A:ASP101 4.8 6.5 1.0 C A:ASP51 4.8 12.0 1.0 C A:SVA102 4.9 8.9 1.0

Zinc binding site 3 out of 4 in the Alkaline Phosphatase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alkaline Phosphatase Complexed with Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn450 b:27.4 occ:1.00 O2 B:SVA102 2.1 41.3 1.0 NE2 B:HIS412 2.1 23.2 1.0 NE2 B:HIS331 2.1 18.6 1.0 OD2 B:ASP327 2.3 26.8 1.0 O4 B:SVA102 2.4 33.4 1.0 OD1 B:ASP327 2.4 29.4 1.0 CG B:ASP327 2.6 25.6 1.0 CE1 B:HIS412 3.0 27.7 1.0 V B:SVA102 3.0 34.7 1.0 CD2 B:HIS331 3.1 20.5 1.0 CE1 B:HIS331 3.2 16.8 1.0 CD2 B:HIS412 3.2 27.4 1.0 NE2 B:HIS372 3.7 25.2 1.0 O3 B:SVA102 3.8 36.8 1.0 O B:HOH1320 3.9 45.3 1.0 CE1 B:HIS370 3.9 11.8 1.0 O B:HOH1330 4.0 53.6 1.0 NE2 B:HIS370 4.1 10.3 1.0 OG B:SVA102 4.1 42.2 1.0 O1 B:SVA102 4.1 36.2 1.0 ZN B:ZN451 4.1 23.3 1.0 CB B:ASP327 4.1 22.6 1.0 ND1 B:HIS412 4.2 23.4 1.0 O B:HOH1224 4.2 66.4 1.0 CG B:HIS331 4.3 17.1 1.0 CG B:HIS412 4.3 25.1 1.0 ND1 B:HIS331 4.3 19.0 1.0 CD2 B:HIS372 4.4 16.8 1.0 OD1 B:ASP51 4.5 28.8 1.0 CE1 B:HIS372 4.6 20.5 1.0 O B:ASP327 4.8 16.5 1.0 C B:ASP327 4.9 18.9 1.0

Zinc binding site 4 out of 4 in the Alkaline Phosphatase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alkaline Phosphatase Complexed with Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn451 b:23.3 occ:1.00 OG B:SVA102 1.9 42.2 1.0 OD2 B:ASP369 2.0 12.8 1.0 OD1 B:ASP51 2.1 28.8 1.0 NE2 B:HIS370 2.1 10.3 1.0 O2 B:SVA102 2.1 41.3 1.0 CG B:ASP51 2.8 24.6 1.0 CB B:SVA102 2.9 8.1 1.0 OD2 B:ASP51 2.9 24.9 1.0 CD2 B:HIS370 3.0 7.3 1.0 CG B:ASP369 3.0 17.8 1.0 V B:SVA102 3.1 34.7 1.0 CE1 B:HIS370 3.1 11.8 1.0 OD1 B:ASP369 3.4 19.5 1.0 CA B:SVA102 3.5 11.2 1.0 OD2 B:ASP327 3.7 26.8 1.0 O1 B:SVA102 3.9 36.2 1.0 O B:HOH1407 4.0 19.2 1.0 N B:SVA102 4.0 8.0 1.0 ZN B:ZN450 4.1 27.4 1.0 CG B:ASP327 4.1 25.6 1.0 CG B:HIS370 4.2 8.7 1.0 O3 B:SVA102 4.2 36.8 1.0 CB B:ASP51 4.2 21.8 1.0 ND1 B:HIS370 4.2 10.2 1.0 CE1 B:HIS412 4.3 27.7 1.0 O B:HOH1409 4.3 20.8 1.0 CB B:ASP369 4.3 9.9 1.0 N B:GLY52 4.5 9.2 1.0 NE2 B:HIS412 4.5 23.2 1.0 CB B:ASP327 4.6 22.6 1.0 MG B:MG452 4.6 21.4 1.0 O4 B:SVA102 4.6 33.4 1.0 OD1 B:ASP327 4.6 29.4 1.0 CA B:ASP51 4.7 13.5 1.0 C B:ASP51 4.8 14.1 1.0 C B:ASP101 4.8 7.2 1.0 O B:HOH1320 4.9 45.3 1.0 C B:SVA102 4.9 10.8 1.0

K.M.Holtz, B.Stec, E.R.Kantrowitz. A Model of the Transition State in the Alkaline Phosphatase Reaction. J.Biol.Chem. V. 274 8351 1999.
ISSN: ISSN 0021-9258
PubMed: 10085061
DOI: 10.1074/JBC.274.13.8351