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Zinc in PDB 1ed8: Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution

Enzymatic activity of Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution

All present enzymatic activity of Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution:
3.1.3.1;

Protein crystallography data

The structure of Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution, PDB code: 1ed8 was solved by B.Stec, K.M.Holtz, E.R.Kantrowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 195.150, 167.340, 76.800, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.8

Other elements in 1ed8:

The structure of Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution (pdb code 1ed8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution, PDB code: 1ed8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1ed8

Go back to Zinc Binding Sites List in 1ed8
Zinc binding site 1 out of 6 in the Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:14.8
occ:1.00
 O2 A:PO4456 1.8 18.2 1.0
NE2 A:HIS412 1.9 11.2 1.0
OD1 A:ASP327 2.0 14.4 1.0
NE2 A:HIS331 2.2 11.6 1.0
OD2 A:ASP327 2.4 15.3 1.0
CG A:ASP327 2.5 11.0 1.0
O3 A:PO4456 2.8 19.2 1.0
CE1 A:HIS412 2.9 11.8 1.0
P A:PO4456 2.9 19.0 1.0
CD2 A:HIS412 3.0 9.8 1.0
CD2 A:HIS331 3.1 12.4 1.0
CE1 A:HIS331 3.2 13.0 1.0
O4 A:PO4456 3.9 18.8 1.0
O1 A:PO4456 3.9 19.2 1.0
ZN A:ZN451 4.0 13.8 1.0
CE1 A:HIS370 4.0 9.1 1.0
NE2 A:HIS372 4.0 14.6 1.0
CB A:ASP327 4.0 9.9 1.0
ND1 A:HIS412 4.0 12.6 1.0
O A:HOH1093 4.1 68.8 1.0
CG A:HIS412 4.1 10.7 1.0
O A:HOH1603 4.1 42.5 1.0
NE2 A:HIS370 4.1 8.8 1.0
O A:HOH1045 4.2 16.5 1.0
ND1 A:HIS331 4.3 13.1 1.0
CG A:HIS331 4.3 12.7 1.0
OG A:SER102 4.4 17.8 0.6
OD1 A:ASP51 4.6 12.2 1.0
CD2 A:HIS372 4.7 16.7 1.0
O A:ASP327 4.9 11.2 1.0
CE1 A:HIS372 4.9 18.3 1.0

Zinc binding site 2 out of 6 in 1ed8

Go back to Zinc Binding Sites List in 1ed8
Zinc binding site 2 out of 6 in the Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:13.8
occ:1.00
 O3 A:PO4456 1.9 19.2 1.0
OD1 A:ASP51 1.9 12.2 1.0
NE2 A:HIS370 2.0 8.8 1.0
OD1 A:ASP369 2.0 17.6 1.0
OG A:SER102 2.1 17.8 0.6
CG A:ASP51 2.7 14.2 1.0
CG A:ASP369 2.9 15.9 1.0
OD2 A:ASP51 2.9 12.8 1.0
CD2 A:HIS370 2.9 9.9 1.0
CE1 A:HIS370 3.0 9.1 1.0
OD2 A:ASP369 3.1 11.4 1.0
P A:PO4456 3.3 19.0 1.0
CB A:SER102 3.4 14.8 0.6
OD1 A:ASP327 3.5 14.4 1.0
CB A:SER102 3.7 13.0 0.4
CG A:ASP327 3.9 11.0 1.0
OG A:SER102 4.0 11.9 0.4
CA A:SER102 4.0 13.8 0.6
ZN A:ZN450 4.0 14.8 1.0
CE1 A:HIS412 4.0 11.8 1.0
ND1 A:HIS370 4.0 10.8 1.0
CG A:HIS370 4.1 10.0 1.0
O1 A:PO4456 4.1 19.2 1.0
O4 A:PO4456 4.1 18.8 1.0
NE2 A:HIS412 4.1 11.2 1.0
CB A:ASP51 4.2 13.2 1.0
O2 A:PO4456 4.2 18.2 1.0
CA A:SER102 4.2 13.4 0.4
N A:GLY52 4.2 12.5 1.0
N A:SER102 4.3 14.3 0.6
CB A:ASP369 4.3 15.1 1.0
CB A:ASP327 4.3 9.9 1.0
N A:SER102 4.3 14.0 0.4
OD2 A:ASP327 4.4 15.3 1.0
O A:HOH499 4.5 10.5 0.6
CA A:ASP51 4.5 10.8 1.0
C A:ASP51 4.6 11.4 1.0
O A:HOH453 4.7 14.0 1.0
ZN A:ZN452 4.8 9.7 0.4
MG A:MG462 4.8 9.7 0.6
O A:HOH1045 4.9 16.5 1.0
ND1 A:HIS412 4.9 12.6 1.0
CA A:GLY52 4.9 16.1 1.0

Zinc binding site 3 out of 6 in 1ed8

Go back to Zinc Binding Sites List in 1ed8
Zinc binding site 3 out of 6 in the Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn452

b:9.7
occ:0.40
 MG A:MG462 0.0 9.7 0.6
OE2 A:GLU322 2.0 11.4 1.0
OD2 A:ASP51 2.1 12.8 1.0
O A:HOH455 2.1 9.1 1.0
OG1 A:THR155 2.1 9.5 1.0
O A:HOH454 2.2 12.2 1.0
O A:HOH453 2.2 14.0 1.0
CD A:GLU322 3.0 13.8 1.0
CG A:ASP51 3.2 14.2 1.0
CB A:THR155 3.2 13.2 1.0
OE1 A:GLU322 3.4 9.6 1.0
CB A:ASP51 3.7 13.2 1.0
OD2 A:ASP153 3.8 17.1 1.0
OG A:SER102 4.0 11.9 0.4
O A:HOH1045 4.0 16.5 1.0
CG2 A:THR155 4.1 14.2 1.0
N A:THR155 4.1 12.7 1.0
OD1 A:ASP51 4.2 12.2 1.0
CA A:THR155 4.3 13.0 1.0
CG A:GLU322 4.3 14.5 1.0
OG A:SER102 4.4 17.8 0.6
O A:HOH499 4.4 10.5 0.6
CB A:ALA324 4.4 9.2 1.0
O1 A:PO4456 4.4 19.2 1.0
CB A:SER102 4.5 14.8 0.6
CB A:SER102 4.6 13.0 0.4
CA A:ALA324 4.6 15.8 1.0
O A:ALA324 4.7 23.4 1.0
CG A:ASP153 4.7 16.2 1.0
ZN A:ZN451 4.8 13.8 1.0
O3 A:PO4456 4.9 19.2 1.0
CD A:PRO156 5.0 18.8 1.0

Zinc binding site 4 out of 6 in 1ed8

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Zinc binding site 4 out of 6 in the Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn950

b:16.0
occ:1.00
 O2 B:PO4956 1.8 18.3 1.0
NE2 B:HIS912 2.1 15.7 1.0
OD1 B:ASP827 2.1 8.7 1.0
NE2 B:HIS831 2.3 16.1 1.0
OD2 B:ASP827 2.4 10.9 1.0
CG B:ASP827 2.6 9.6 1.0
O3 B:PO4956 2.8 23.5 1.0
P B:PO4956 2.8 24.5 1.0
CE1 B:HIS912 3.0 16.0 1.0
CD2 B:HIS912 3.1 15.7 1.0
CD2 B:HIS831 3.1 15.7 1.0
CE1 B:HIS831 3.3 16.3 1.0
O4 B:PO4956 3.8 21.7 1.0
O B:HOH1095 3.9 21.3 1.0
O1 B:PO4956 3.9 24.3 1.0
ZN B:ZN951 4.0 17.8 1.0
NE2 B:HIS872 4.0 17.8 1.0
CB B:ASP827 4.0 11.6 1.0
CE1 B:HIS870 4.1 16.1 1.0
ND1 B:HIS912 4.2 16.9 1.0
CG B:HIS912 4.2 16.5 1.0
O B:HOH1602 4.2 25.2 1.0
NE2 B:HIS870 4.2 15.5 1.0
OG B:SER602 4.3 22.7 0.6
CG B:HIS831 4.3 16.1 1.0
ND1 B:HIS831 4.3 17.0 1.0
CD2 B:HIS872 4.6 16.4 1.0
OD1 B:ASP551 4.6 18.9 1.0
O B:ASP827 4.7 15.2 1.0
C B:ASP827 4.9 13.8 1.0
CA B:ASP827 5.0 13.4 1.0

Zinc binding site 5 out of 6 in 1ed8

Go back to Zinc Binding Sites List in 1ed8
Zinc binding site 5 out of 6 in the Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn951

b:17.8
occ:1.00
 O3 B:PO4956 1.9 23.5 1.0
OD1 B:ASP551 2.0 18.9 1.0
OD1 B:ASP869 2.0 17.1 1.0
OG B:SER602 2.1 22.7 0.6
NE2 B:HIS870 2.1 15.5 1.0
CG B:ASP551 2.8 18.6 1.0
CG B:ASP869 2.9 15.8 1.0
OD2 B:ASP551 2.9 19.9 1.0
CD2 B:HIS870 3.0 14.2 1.0
CE1 B:HIS870 3.1 16.1 1.0
OD2 B:ASP869 3.1 16.9 1.0
CB B:SER602 3.3 21.3 0.6
P B:PO4956 3.4 24.5 1.0
CB B:SER602 3.5 19.5 0.4
OD1 B:ASP827 3.6 8.7 1.0
CA B:SER602 3.9 19.1 0.6
CG B:ASP827 4.0 9.6 1.0
OG B:SER602 4.0 18.8 0.4
ZN B:ZN950 4.0 16.0 1.0
CA B:SER602 4.0 18.8 0.4
CE1 B:HIS912 4.1 16.0 1.0
O1 B:PO4956 4.1 24.3 1.0
O4 B:PO4956 4.1 21.7 1.0
CG B:HIS870 4.2 14.7 1.0
ND1 B:HIS870 4.2 15.1 1.0
NE2 B:HIS912 4.2 15.7 1.0
CB B:ASP551 4.2 16.5 1.0
N B:GLY552 4.2 13.3 1.0
O2 B:PO4956 4.2 18.3 1.0
N B:SER602 4.2 17.8 0.4
N B:SER602 4.3 17.2 0.6
CB B:ASP869 4.3 13.9 1.0
O B:HOH999 4.4 10.1 0.6
CB B:ASP827 4.4 11.6 1.0
OD2 B:ASP827 4.5 10.9 1.0
CA B:ASP551 4.6 13.9 1.0
C B:ASP551 4.6 14.6 1.0
O B:HOH953 4.7 15.8 1.0
ZN B:ZN952 4.8 20.2 0.4
MG B:MG962 4.8 20.2 0.6
CA B:GLY552 4.8 11.6 1.0
O B:HOH1095 4.8 21.3 1.0
ND1 B:HIS912 4.9 16.9 1.0

Zinc binding site 6 out of 6 in 1ed8

Go back to Zinc Binding Sites List in 1ed8
Zinc binding site 6 out of 6 in the Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of E. Coli Alkaline Phosphatase Inhibited By the Inorganic Phosphate at 1.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn952

b:20.2
occ:0.42
 MG B:MG962 0.0 20.2 0.6
OE1 B:GLU822 1.9 12.9 1.0
O B:HOH953 2.0 15.8 1.0
OD2 B:ASP551 2.1 19.9 1.0
O B:HOH954 2.1 13.4 1.0
OG1 B:THR655 2.2 18.4 1.0
O B:HOH955 2.3 20.1 1.0
CD B:GLU822 3.0 13.9 1.0
CB B:THR655 3.0 18.1 1.0
CG B:ASP551 3.1 18.6 1.0
OE2 B:GLU822 3.3 12.3 1.0
CB B:ASP551 3.6 16.5 1.0
OD2 B:ASP653 3.7 25.4 1.0
OG B:SER602 3.9 18.8 0.4
CG2 B:THR655 4.0 20.6 1.0
O B:HOH1546 4.0 0.9 1.0
O B:HOH999 4.0 10.1 0.6
N B:THR655 4.1 16.4 1.0
CA B:THR655 4.2 15.9 1.0
OD1 B:ASP551 4.2 18.9 1.0
CG B:GLU822 4.3 16.5 1.0
O B:HOH1095 4.3 21.3 1.0
CB B:SER602 4.5 21.3 0.6
CB B:SER602 4.5 19.5 0.4
CB B:ALA824 4.5 18.1 1.0
OG B:SER602 4.5 22.7 0.6
O1 B:PO4956 4.6 24.3 1.0
CG B:ASP653 4.6 23.2 1.0
CA B:ALA824 4.7 19.0 1.0
ZN B:ZN951 4.8 17.8 1.0
O B:ALA824 4.8 14.3 1.0
CA B:ASP551 5.0 13.9 1.0

Reference:

B.Stec, K.M.Holtz, E.R.Kantrowitz. A Revised Mechanism For the Alkaline Phosphatase Reaction Involving Three Metal Ions. J.Mol.Biol. V. 299 1303 2000.
ISSN: ISSN 0022-2836
PubMed: 10873454
DOI: 10.1006/JMBI.2000.3799
Page generated: Sun Oct 13 00:09:46 2024

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