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Zinc in PDB 1kh5: E. Coli Alkaline Phosphatase Mutant (D330N) Mimic of the Transition States with Aluminium Fluoride

Enzymatic activity of E. Coli Alkaline Phosphatase Mutant (D330N) Mimic of the Transition States with Aluminium Fluoride

All present enzymatic activity of E. Coli Alkaline Phosphatase Mutant (D330N) Mimic of the Transition States with Aluminium Fluoride:
3.1.3.1;

Protein crystallography data

The structure of E. Coli Alkaline Phosphatase Mutant (D330N) Mimic of the Transition States with Aluminium Fluoride, PDB code: 1kh5 was solved by M.H.Le Du, C.Lamoure, B.H.Muller, O.V.Bulgakov, E.Lajeunesse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 163.620, 163.620, 138.880, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 22.8

Other elements in 1kh5:

The structure of E. Coli Alkaline Phosphatase Mutant (D330N) Mimic of the Transition States with Aluminium Fluoride also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the E. Coli Alkaline Phosphatase Mutant (D330N) Mimic of the Transition States with Aluminium Fluoride (pdb code 1kh5). 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 (D330N) Mimic of the Transition States with Aluminium Fluoride, PDB code: 1kh5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1kh5

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Zinc binding site 1 out of 4 in the E. Coli Alkaline Phosphatase Mutant (D330N) Mimic of the Transition States with Aluminium Fluoride


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 (D330N) Mimic of the Transition States with Aluminium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:21.0
occ:1.00
 F1 A:AF3453 1.9 33.1 1.0
NE2 A:HIS412 2.0 18.6 1.0
NE2 A:HIS331 2.1 15.0 1.0
O A:HOH1001 2.1 48.7 1.0
OD1 A:ASP327 2.3 22.4 1.0
OD2 A:ASP327 2.5 18.0 1.0
CG A:ASP327 2.7 18.7 1.0
AL A:AF3453 2.9 41.5 1.0
CE1 A:HIS412 2.9 16.1 1.0
CD2 A:HIS331 3.0 15.7 1.0
CE1 A:HIS331 3.2 16.8 1.0
CD2 A:HIS412 3.2 17.6 1.0
F3 A:AF3453 3.7 38.1 1.0
NE2 A:HIS372 3.9 13.4 1.0
F2 A:AF3453 4.0 37.8 1.0
OG A:SER102 4.1 30.4 1.0
ND1 A:HIS412 4.1 17.1 1.0
CE1 A:HIS370 4.2 9.7 1.0
CG A:HIS331 4.2 14.3 1.0
CB A:ASP327 4.2 15.1 1.0
NE2 A:HIS370 4.2 12.9 1.0
ND1 A:HIS331 4.2 15.7 1.0
CG A:HIS412 4.3 16.1 1.0
ZN A:ZN451 4.3 25.3 1.0
O A:HOH1003 4.3 15.7 1.0
O A:HOH1073 4.5 24.9 1.0
CD2 A:HIS372 4.6 12.5 1.0
OD1 A:ASP51 4.8 23.5 1.0
CE1 A:HIS372 4.9 10.5 1.0
O A:ASP327 4.9 19.3 1.0
C A:ASP327 5.0 15.9 1.0

Zinc binding site 2 out of 4 in 1kh5

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Zinc binding site 2 out of 4 in the E. Coli Alkaline Phosphatase Mutant (D330N) Mimic of the Transition States with Aluminium Fluoride


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 (D330N) Mimic of the Transition States with Aluminium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:25.3
occ:1.00
 OD1 A:ASP369 2.0 16.4 1.0
NE2 A:HIS370 2.1 12.9 1.0
OD1 A:ASP51 2.1 23.5 1.0
OG A:SER102 2.4 30.4 1.0
F1 A:AF3453 2.6 33.1 1.0
CG A:ASP51 2.9 21.9 1.0
CD2 A:HIS370 3.0 12.4 1.0
OD2 A:ASP51 3.0 24.2 1.0
CG A:ASP369 3.0 18.9 1.0
CB A:SER102 3.1 18.8 1.0
CE1 A:HIS370 3.2 9.7 1.0
OD2 A:ASP369 3.4 19.5 1.0
CA A:SER102 3.6 17.5 1.0
AL A:AF3453 3.7 41.5 1.0
OD1 A:ASP327 3.9 22.4 1.0
N A:SER102 4.1 16.5 1.0
CG A:HIS370 4.1 12.1 1.0
CG A:ASP327 4.1 18.7 1.0
ND1 A:HIS370 4.2 13.7 1.0
CE1 A:HIS412 4.3 16.1 1.0
ZN A:ZN450 4.3 21.0 1.0
CB A:ASP51 4.3 19.3 1.0
CB A:ASP369 4.3 13.5 1.0
O A:HOH1198 4.3 44.4 1.0
N A:GLY52 4.4 17.0 1.0
F2 A:AF3453 4.5 37.8 1.0
O A:HOH1002 4.5 20.8 1.0
OD2 A:ASP327 4.6 18.0 1.0
CB A:ASP327 4.6 15.1 1.0
NE2 A:HIS412 4.6 18.6 1.0
F3 A:AF3453 4.6 38.1 1.0
CA A:ASP51 4.7 18.8 1.0
C A:ASP51 4.7 17.2 1.0
C A:ASP101 4.8 12.8 1.0
MG A:MG452 4.8 12.5 1.0
C A:SER102 4.9 17.7 1.0
O A:HOH1003 5.0 15.7 1.0

Zinc binding site 3 out of 4 in 1kh5

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Zinc binding site 3 out of 4 in the E. Coli Alkaline Phosphatase Mutant (D330N) Mimic of the Transition States with Aluminium Fluoride


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 (D330N) Mimic of the Transition States with Aluminium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn950

b:16.6
occ:1.00
 F1 B:AF3953 1.5 26.2 1.0
NE2 B:HIS912 2.0 16.2 1.0
NE2 B:HIS831 2.0 12.1 1.0
OD1 B:ASP827 2.3 23.3 1.0
AL B:AF3953 2.5 33.7 1.0
OD2 B:ASP827 2.7 23.0 1.0
CG B:ASP827 2.8 19.9 1.0
CE1 B:HIS831 2.9 14.2 1.0
CE1 B:HIS912 2.9 17.7 1.0
CD2 B:HIS912 3.1 19.5 1.0
CD2 B:HIS831 3.1 12.9 1.0
F3 B:AF3953 3.6 34.5 1.0
F2 B:AF3953 3.8 32.0 1.0
OG B:SER602 3.9 28.4 1.0
NE2 B:HIS872 3.9 12.1 1.0
ND1 B:HIS912 4.1 18.1 1.0
ND1 B:HIS831 4.1 13.8 1.0
CE1 B:HIS870 4.1 11.8 1.0
NE2 B:HIS870 4.1 15.1 1.0
CG B:HIS912 4.2 14.6 1.0
ZN B:ZN951 4.2 25.5 1.0
CG B:HIS831 4.2 11.4 1.0
CB B:ASP827 4.3 19.4 1.0
O B:HOH1076 4.4 12.8 1.0
O B:HOH1200 4.4 50.0 1.0
CD2 B:HIS872 4.6 12.0 1.0
OD1 B:ASP551 4.7 21.2 1.0
CE1 B:HIS872 4.8 10.8 1.0

Zinc binding site 4 out of 4 in 1kh5

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Zinc binding site 4 out of 4 in the E. Coli Alkaline Phosphatase Mutant (D330N) Mimic of the Transition States with Aluminium Fluoride


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 (D330N) Mimic of the Transition States with Aluminium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn951

b:25.5
occ:1.00
 OD1 B:ASP869 2.1 17.8 1.0
OD1 B:ASP551 2.2 21.2 1.0
NE2 B:HIS870 2.2 15.1 1.0
OG B:SER602 2.6 28.4 1.0
F1 B:AF3953 2.8 26.2 1.0
CG B:ASP551 2.9 18.6 1.0
OD2 B:ASP551 2.9 16.7 1.0
CG B:ASP869 3.0 21.2 1.0
CB B:SER602 3.0 15.3 1.0
CD2 B:HIS870 3.0 15.6 1.0
CE1 B:HIS870 3.3 11.8 1.0
OD2 B:ASP869 3.3 19.0 1.0
CA B:SER602 3.5 16.6 1.0
OD1 B:ASP827 3.9 23.3 1.0
AL B:AF3953 3.9 33.7 1.0
F2 B:AF3953 4.0 32.0 1.0
N B:SER602 4.1 17.5 1.0
CG B:ASP827 4.1 19.9 1.0
CE1 B:HIS912 4.1 17.7 1.0
ZN B:ZN950 4.2 16.6 1.0
CG B:HIS870 4.2 13.6 1.0
CB B:ASP551 4.3 15.8 1.0
ND1 B:HIS870 4.3 13.5 1.0
O B:HOH1199 4.3 48.0 1.0
CB B:ASP869 4.3 16.4 1.0
O B:HOH1008 4.4 16.5 0.6
N B:GLY552 4.4 14.6 1.0
NE2 B:HIS912 4.4 16.2 1.0
OD2 B:ASP827 4.6 23.0 1.0
CB B:ASP827 4.6 19.4 1.0
MG B:MG952 4.6 6.1 1.0
F3 B:AF3953 4.7 34.5 1.0
CA B:ASP551 4.7 16.2 1.0
C B:ASP551 4.7 16.5 1.0
C B:ASP601 4.8 13.8 1.0
C B:SER602 4.9 18.7 1.0
CA B:GLY552 5.0 15.3 1.0

Reference:

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
Page generated: Sun Oct 13 04:22:39 2024

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