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Zinc in PDB 2g9y: Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution

Enzymatic activity of Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution

All present enzymatic activity of Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution:
3.1.3.1;

Protein crystallography data

The structure of Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution, PDB code: 2g9y was solved by J.Wang, E.R.Kantrowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.70 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 76.460, 164.490, 192.530, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.2

Other elements in 2g9y:

The structure of Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution (pdb code 2g9y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution, PDB code: 2g9y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2g9y

Go back to Zinc Binding Sites List in 2g9y
Zinc binding site 1 out of 4 in the Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A 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 S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:25.7
occ:1.00
 NE2 A:HIS331 2.0 22.5 1.0
NE2 A:HIS412 2.1 18.3 1.0
OD1 A:ASP327 2.1 16.2 1.0
O3 A:PO4656 2.3 42.7 1.0
O2 A:PO4656 2.4 43.9 0.9
OD2 A:ASP327 2.6 18.3 1.0
CG A:ASP327 2.7 18.0 1.0
P A:PO4656 2.9 44.0 0.8
CE1 A:HIS412 3.0 19.8 1.0
CD2 A:HIS331 3.0 21.7 1.0
CE1 A:HIS331 3.0 21.7 1.0
CD2 A:HIS412 3.1 21.9 1.0
NE2 A:HIS372 3.8 17.9 1.0
O1 A:PO4656 3.9 44.8 0.8
O4 A:PO4656 3.9 43.8 1.0
NE2 A:HIS370 4.0 19.4 1.0
CE1 A:HIS370 4.0 19.9 1.0
ZN A:ZN451 4.1 25.0 1.0
ND1 A:HIS412 4.1 20.4 1.0
ND1 A:HIS331 4.1 20.3 1.0
CG A:HIS331 4.1 21.2 1.0
CB A:ASP327 4.2 17.8 1.0
CG A:HIS412 4.2 20.8 1.0
O A:HOH721 4.2 28.4 1.0
OD1 A:ASP51 4.4 18.0 1.0
CD2 A:HIS372 4.5 19.4 1.0
CE1 A:HIS372 4.8 17.1 1.0
O A:ASP327 4.9 19.8 1.0
C A:ASP327 5.0 20.0 1.0

Zinc binding site 2 out of 4 in 2g9y

Go back to Zinc Binding Sites List in 2g9y
Zinc binding site 2 out of 4 in the Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A 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 S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:25.0
occ:1.00
 OD1 A:ASP369 1.9 16.3 1.0
OD1 A:ASP51 1.9 18.0 1.0
NE2 A:HIS370 2.0 19.4 1.0
CG A:ASP51 2.7 19.3 1.0
OD2 A:ASP51 2.8 19.4 1.0
CG A:ASP369 2.9 16.6 1.0
CD2 A:HIS370 2.9 20.6 1.0
CB A:THR102 3.0 27.9 1.0
CE1 A:HIS370 3.0 19.9 1.0
OD2 A:ASP369 3.1 17.5 1.0
O3 A:PO4656 3.3 42.7 1.0
OG1 A:THR102 3.3 30.8 1.0
OD1 A:ASP327 3.7 16.2 1.0
CA A:THR102 3.8 23.8 1.0
CG A:HIS370 4.0 20.6 1.0
CG A:ASP327 4.0 18.0 1.0
CB A:ASP51 4.1 16.5 1.0
ND1 A:HIS370 4.1 19.1 1.0
ZN A:ZN450 4.1 25.7 1.0
CE1 A:HIS412 4.1 19.8 1.0
CG2 A:THR102 4.2 30.2 1.0
N A:GLY52 4.2 17.3 1.0
CB A:ASP369 4.2 16.1 1.0
N A:THR102 4.3 23.3 1.0
NE2 A:HIS412 4.3 18.3 1.0
CA A:ASP51 4.5 17.0 1.0
CB A:ASP327 4.5 17.8 1.0
OD2 A:ASP327 4.5 18.3 1.0
C A:ASP51 4.6 18.1 1.0
O A:HOH977 4.7 46.8 1.0
MG A:MG452 4.7 20.7 1.0
P A:PO4656 4.7 44.0 0.8
CA A:GLY52 4.9 16.9 1.0
O A:HOH721 4.9 28.4 1.0
ND1 A:HIS412 5.0 20.4 1.0

Zinc binding site 3 out of 4 in 2g9y

Go back to Zinc Binding Sites List in 2g9y
Zinc binding site 3 out of 4 in the Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A 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 S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn450

b:27.3
occ:1.00
 NE2 B:HIS412 2.0 27.9 1.0
O2 B:PO4956 2.0 47.2 1.0
NE2 B:HIS331 2.1 18.3 1.0
OD1 B:ASP327 2.3 28.2 1.0
O3 B:PO4956 2.5 47.1 0.8
OD2 B:ASP327 2.5 25.5 1.0
CG B:ASP327 2.7 26.6 1.0
P B:PO4956 2.7 47.0 1.0
CE1 B:HIS412 2.9 26.9 1.0
CD2 B:HIS331 3.0 20.3 1.0
CD2 B:HIS412 3.1 26.8 1.0
CE1 B:HIS331 3.1 21.1 1.0
O1 B:PO4956 3.7 46.8 1.0
CE1 B:HIS372 3.8 20.0 1.0
O4 B:PO4956 3.9 47.7 0.5
ZN B:ZN451 4.0 27.1 1.0
CE1 B:HIS370 4.0 21.3 1.0
ND1 B:HIS412 4.1 28.7 1.0
OG1 B:THR102 4.1 30.9 1.0
NE2 B:HIS370 4.1 21.9 1.0
CG B:HIS331 4.2 22.5 1.0
CG B:HIS412 4.2 26.4 1.0
ND1 B:HIS331 4.2 21.7 1.0
O B:HOH1107 4.2 31.3 1.0
CB B:ASP327 4.2 24.7 1.0
OD1 B:ASP51 4.4 21.9 1.0
ND1 B:HIS372 4.5 23.1 1.0
NE2 B:HIS372 4.7 21.8 1.0
O B:ASP327 4.9 23.7 1.0

Zinc binding site 4 out of 4 in 2g9y

Go back to Zinc Binding Sites List in 2g9y
Zinc binding site 4 out of 4 in the Structure of S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A 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 S102T E. Coli Alkaline Phosphatase in Presence of Phosphate at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn451

b:27.1
occ:1.00
 OD1 B:ASP369 1.9 20.4 1.0
OD1 B:ASP51 2.0 21.9 1.0
NE2 B:HIS370 2.1 21.9 1.0
OG1 B:THR102 2.2 30.9 1.0
CG B:ASP51 2.8 23.8 1.0
CG B:ASP369 2.8 22.4 1.0
OD2 B:ASP51 2.9 28.1 1.0
CD2 B:HIS370 3.0 20.4 1.0
CE1 B:HIS370 3.1 21.3 1.0
OD2 B:ASP369 3.1 21.4 1.0
CB B:THR102 3.3 28.9 1.0
O2 B:PO4956 3.3 47.2 1.0
CG2 B:THR102 3.6 26.4 1.0
OD1 B:ASP327 3.6 28.2 1.0
CA B:THR102 3.8 27.1 1.0
CG B:ASP327 3.9 26.6 1.0
ZN B:ZN450 4.0 27.3 1.0
CG B:HIS370 4.1 20.9 1.0
CE1 B:HIS412 4.1 26.9 1.0
ND1 B:HIS370 4.1 22.9 1.0
CB B:ASP51 4.2 20.8 1.0
CB B:ASP369 4.2 20.9 1.0
N B:GLY52 4.2 21.6 1.0
N B:THR102 4.3 26.9 1.0
NE2 B:HIS412 4.3 27.9 1.0
OD2 B:ASP327 4.4 25.5 1.0
CB B:ASP327 4.5 24.7 1.0
CA B:ASP51 4.6 21.2 1.0
P B:PO4956 4.6 47.0 1.0
O B:HOH1191 4.6 49.0 1.0
MG B:MG452 4.6 21.0 1.0
C B:ASP51 4.7 22.3 1.0
O1 B:PO4956 4.7 46.8 1.0
CA B:GLY52 4.9 20.9 1.0
ND1 B:HIS412 4.9 28.7 1.0

Reference:

J.Wang, E.R.Kantrowitz. Trapping the Tetrahedral Intermediate in the Alkaline Phosphatase Reaction By Substitution of the Active Site Serine with Threonine. Protein Sci. V. 15 2395 2006.
ISSN: ISSN 0961-8368
PubMed: 17008720
DOI: 10.1110/PS.062351506
Page generated: Thu Oct 17 00:05:48 2024

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