Zinc in PDB 1khk: E. Coli Alkaline Phosphatase Mutant (D153HD330N)

All present enzymatic activity of E. Coli Alkaline Phosphatase Mutant (D153HD330N):
3.1.3.1;

The structure of E. Coli Alkaline Phosphatase Mutant (D153HD330N), PDB code: 1khk was solved by M.H.Le Du, C.Lamoure, B.H.Muller, O.V.Bulgakov, E.Lajeunesse, A.Menez, J.C.Boulain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.50
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	163.511, 163.511, 138.025, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 20.7

The structure of E. Coli Alkaline Phosphatase Mutant (D153HD330N) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the E. Coli Alkaline Phosphatase Mutant (D153HD330N) (pdb code 1khk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the E. Coli Alkaline Phosphatase Mutant (D153HD330N), PDB code: 1khk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the E. Coli Alkaline Phosphatase Mutant (D153HD330N)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Alkaline Phosphatase Mutant (D153HD330N) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn450 b:22.9 occ:1.00 NE2 A:HIS412 2.0 12.2 1.0 NE2 A:HIS331 2.1 20.2 1.0 O A:HOH1007 2.3 30.1 1.0 OD2 A:ASP327 2.3 22.5 1.0 OD1 A:ASP327 2.6 20.4 1.0 CE1 A:HIS412 2.8 13.2 1.0 CG A:ASP327 2.8 21.5 1.0 CD2 A:HIS331 3.1 17.6 1.0 CD2 A:HIS412 3.1 16.3 1.0 CE1 A:HIS331 3.2 19.9 1.0 OG A:SER102 3.9 14.9 1.0 NE2 A:HIS372 3.9 12.4 1.0 ND1 A:HIS412 4.0 14.8 1.0 NE2 A:HIS370 4.0 14.1 1.0 O A:HOH1005 4.0 23.9 1.0 CE1 A:HIS370 4.2 14.8 1.0 CG A:HIS412 4.2 12.2 1.0 CG A:HIS331 4.3 16.1 1.0 CB A:ASP327 4.3 21.2 1.0 ND1 A:HIS331 4.3 18.7 1.0 O A:HOH1004 4.3 36.3 1.0 ZN A:ZN451 4.4 21.7 1.0 CD2 A:HIS372 4.5 10.0 1.0 OD2 A:ASP51 4.6 21.9 1.0 CE1 A:HIS372 4.8 10.0 1.0

Zinc binding site 2 out of 4 in the E. Coli Alkaline Phosphatase Mutant (D153HD330N)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Alkaline Phosphatase Mutant (D153HD330N) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn451 b:21.7 occ:1.00 OD1 A:ASP369 2.1 15.5 1.0 NE2 A:HIS370 2.2 14.1 1.0 OD2 A:ASP51 2.3 21.9 1.0 OG A:SER102 2.3 14.9 1.0 CD2 A:HIS370 2.7 13.4 1.0 CG A:ASP369 2.9 20.2 1.0 CG A:ASP51 3.0 24.0 1.0 CB A:SER102 3.0 18.1 1.0 OD1 A:ASP51 3.1 25.3 1.0 OD2 A:ASP369 3.1 20.2 1.0 CE1 A:HIS370 3.3 14.8 1.0 CA A:SER102 3.5 18.5 1.0 O A:HOH1156 3.9 15.2 1.0 CG A:HIS370 4.0 14.8 1.0 OD1 A:ASP327 4.0 20.4 1.0 N A:SER102 4.1 21.4 1.0 O A:HOH1003 4.1 48.3 1.0 CG A:ASP327 4.2 21.5 1.0 CB A:ASP369 4.2 17.7 1.0 O A:HOH1007 4.2 30.1 1.0 CE1 A:HIS412 4.2 13.2 1.0 ND1 A:HIS370 4.2 18.1 1.0 N A:GLY52 4.3 17.6 1.0 CB A:ASP51 4.3 21.6 1.0 ZN A:ZN450 4.4 22.9 1.0 OD2 A:ASP327 4.6 22.5 1.0 NE2 A:HIS412 4.7 12.2 1.0 CA A:ASP51 4.7 17.9 1.0 C A:ASP51 4.7 17.8 1.0 MG A:MG452 4.7 15.6 1.0 CB A:ASP327 4.8 21.2 1.0 C A:SER102 4.8 19.4 1.0 OG A:SER105 4.9 17.1 1.0 ND1 A:HIS412 4.9 14.8 1.0 C A:ASP101 4.9 18.0 1.0 CA A:GLY52 5.0 17.1 1.0

Zinc binding site 3 out of 4 in the E. Coli Alkaline Phosphatase Mutant (D153HD330N)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E. Coli Alkaline Phosphatase Mutant (D153HD330N) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn450 b:31.6 occ:1.00 NE2 B:HIS331 2.0 14.4 1.0 NE2 B:HIS412 2.1 12.5 1.0 O B:HOH1015 2.2 21.7 1.0 OD2 B:ASP327 2.3 36.2 1.0 OD1 B:ASP327 2.6 25.4 1.0 CG B:ASP327 2.8 26.6 1.0 CD2 B:HIS331 2.9 9.6 1.0 CE1 B:HIS331 3.0 14.9 1.0 CE1 B:HIS412 3.0 17.1 1.0 CD2 B:HIS412 3.2 23.1 1.0 O B:HOH1014 3.9 33.3 1.0 NE2 B:HIS372 4.0 16.2 1.0 OG B:SER102 4.0 22.3 1.0 ND1 B:HIS331 4.1 16.9 1.0 CG B:HIS331 4.1 4.5 1.0 NE2 B:HIS370 4.1 21.7 1.0 ND1 B:HIS412 4.2 13.7 1.0 O B:HOH1013 4.3 47.1 1.0 CE1 B:HIS370 4.3 20.1 1.0 CB B:ASP327 4.3 26.0 1.0 CG B:HIS412 4.3 13.5 1.0 ZN B:ZN451 4.5 24.0 1.0 OD2 B:ASP51 4.6 27.4 1.0 CD2 B:HIS372 4.7 14.5 1.0 CE1 B:HIS372 4.9 8.3 1.0 O B:HOH1032 4.9 45.4 1.0

Zinc binding site 4 out of 4 in the E. Coli Alkaline Phosphatase Mutant (D153HD330N)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E. Coli Alkaline Phosphatase Mutant (D153HD330N) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn451 b:24.0 occ:1.00 OD1 B:ASP369 2.1 23.6 1.0 OG B:SER102 2.1 22.3 1.0 OD2 B:ASP51 2.3 27.4 1.0 NE2 B:HIS370 2.3 21.7 1.0 CG B:ASP369 2.9 20.3 1.0 CG B:ASP51 3.0 22.4 1.0 CD2 B:HIS370 3.0 14.6 1.0 CB B:SER102 3.0 24.2 1.0 OD1 B:ASP51 3.1 33.2 1.0 OD2 B:ASP369 3.2 16.1 1.0 CE1 B:HIS370 3.4 20.1 1.0 CA B:SER102 3.6 27.4 1.0 O B:HOH1015 3.9 21.7 1.0 OD1 B:ASP327 4.0 25.4 1.0 O B:HOH1157 4.1 11.6 1.0 O B:HOH1012 4.1 61.8 1.0 N B:SER102 4.1 21.0 1.0 CG B:HIS370 4.1 16.2 1.0 CE1 B:HIS412 4.2 17.1 1.0 CG B:ASP327 4.2 26.6 1.0 CB B:ASP369 4.2 16.9 1.0 CB B:ASP51 4.3 22.2 1.0 N B:GLY52 4.3 19.4 1.0 ND1 B:HIS370 4.3 22.6 1.0 ZN B:ZN450 4.5 31.6 1.0 OD2 B:ASP327 4.5 36.2 1.0 CA B:ASP51 4.5 22.0 1.0 NE2 B:HIS412 4.6 12.5 1.0 MG B:MG452 4.6 15.9 1.0 C B:ASP51 4.6 12.1 1.0 CB B:ASP327 4.7 26.0 1.0 C B:SER102 4.9 26.9 1.0 OG B:SER105 4.9 21.7 1.0 C B:ASP101 4.9 19.3 1.0 ND1 B:HIS412 5.0 13.7 1.0 OG1 B:THR155 5.0 16.0 1.0

M.H.Le Du, C.Lamoure, B.H.Muller, O.V.Bulgakov, E.Lajeunesse, A.Menez, J.C.Boulain. Artificial Evolution of An Enzyme Active Site: Structural Studies of Three Highly Active Mutants of Escherichia Coli Alkaline Phosphatase. J.Mol.Biol. V. 316 941 2002.
ISSN: ISSN 0022-2836
PubMed: 11884134
DOI: 10.1006/JMBI.2001.5384