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Zinc in PDB 2ga3: Structure of S102T E. Coli Alkaline Phosphatase-Phosphate Intermediate at 2.20A Resolution

Enzymatic activity of Structure of S102T E. Coli Alkaline Phosphatase-Phosphate Intermediate at 2.20A Resolution

All present enzymatic activity of Structure of S102T E. Coli Alkaline Phosphatase-Phosphate Intermediate at 2.20A Resolution:
3.1.3.1;

Protein crystallography data

The structure of Structure of S102T E. Coli Alkaline Phosphatase-Phosphate Intermediate at 2.20A Resolution, PDB code: 2ga3 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) 14.98 / 2.20
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 76.230, 164.970, 192.900, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.9

Other elements in 2ga3:

The structure of Structure of S102T E. Coli Alkaline Phosphatase-Phosphate Intermediate at 2.20A 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-Phosphate Intermediate at 2.20A Resolution (pdb code 2ga3). 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-Phosphate Intermediate at 2.20A Resolution, PDB code: 2ga3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2ga3

Go back to Zinc Binding Sites List in 2ga3
Zinc binding site 1 out of 4 in the Structure of S102T E. Coli Alkaline Phosphatase-Phosphate Intermediate at 2.20A 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-Phosphate Intermediate at 2.20A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:39.9
occ:0.95
 O3P A:TPO102 1.8 38.9 1.0
NE2 A:HIS412 2.0 32.4 1.0
NE2 A:HIS331 2.1 43.5 1.0
OD2 A:ASP327 2.5 36.6 1.0
OD1 A:ASP327 2.5 37.0 1.0
CE1 A:HIS412 2.8 32.6 1.0
CG A:ASP327 2.9 38.7 1.0
CE1 A:HIS331 3.1 41.9 1.0
CD2 A:HIS331 3.1 42.1 1.0
CD2 A:HIS412 3.2 33.6 1.0
P A:TPO102 3.2 36.3 1.0
O1P A:TPO102 3.7 34.9 1.0
ZN A:ZN451 3.7 38.7 1.0
NE2 A:HIS370 3.8 29.5 1.0
CE1 A:HIS370 3.9 28.6 1.0
NE2 A:HIS372 3.9 35.6 1.0
ND1 A:HIS412 4.0 33.4 1.0
O2P A:TPO102 4.1 34.2 1.0
O A:HOH564 4.1 41.2 1.0
CG A:HIS412 4.2 32.9 1.0
OG1 A:TPO102 4.2 30.5 1.0
ND1 A:HIS331 4.2 42.8 1.0
CG A:HIS331 4.3 43.3 1.0
OD2 A:ASP51 4.3 32.7 1.0
CB A:ASP327 4.4 37.7 1.0
CD2 A:HIS372 4.6 34.8 1.0
CE1 A:HIS372 4.9 34.3 1.0
O A:ASP327 5.0 37.2 1.0

Zinc binding site 2 out of 4 in 2ga3

Go back to Zinc Binding Sites List in 2ga3
Zinc binding site 2 out of 4 in the Structure of S102T E. Coli Alkaline Phosphatase-Phosphate Intermediate at 2.20A 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-Phosphate Intermediate at 2.20A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:38.7
occ:1.00
 NE2 A:HIS370 1.9 29.5 1.0
OD2 A:ASP51 2.0 32.7 1.0
OD1 A:ASP369 2.1 26.8 1.0
OG1 A:TPO102 2.4 30.5 1.0
O3P A:TPO102 2.8 38.9 1.0
CE1 A:HIS370 2.8 28.6 1.0
CD2 A:HIS370 2.9 26.5 1.0
CG A:ASP51 3.0 33.0 1.0
CG A:ASP369 3.1 24.7 1.0
P A:TPO102 3.2 36.3 1.0
OD1 A:ASP51 3.4 38.2 1.0
OD1 A:ASP327 3.4 37.0 1.0
OD2 A:ASP369 3.4 23.9 1.0
CG A:ASP327 3.6 38.7 1.0
CB A:TPO102 3.6 27.4 1.0
ZN A:ZN450 3.7 39.9 0.9
ND1 A:HIS370 3.9 28.9 1.0
OD2 A:ASP327 3.9 36.6 1.0
CG A:HIS370 3.9 25.9 1.0
CG2 A:TPO102 4.0 26.4 1.0
N A:GLY52 4.0 22.7 1.0
CE1 A:HIS412 4.1 32.6 1.0
CA A:TPO102 4.2 24.6 1.0
CB A:ASP51 4.2 26.5 1.0
O1P A:TPO102 4.3 34.9 1.0
O2P A:TPO102 4.3 34.2 1.0
CB A:ASP327 4.3 37.7 1.0
NE2 A:HIS412 4.3 32.4 1.0
CB A:ASP369 4.4 23.1 1.0
C A:ASP51 4.5 23.6 1.0
N A:TPO102 4.5 24.9 1.0
CA A:ASP51 4.5 25.3 1.0
CA A:GLY52 4.6 21.6 1.0
ND1 A:HIS412 4.9 33.4 1.0
O A:HOH564 4.9 41.2 1.0

Zinc binding site 3 out of 4 in 2ga3

Go back to Zinc Binding Sites List in 2ga3
Zinc binding site 3 out of 4 in the Structure of S102T E. Coli Alkaline Phosphatase-Phosphate Intermediate at 2.20A 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-Phosphate Intermediate at 2.20A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn450

b:44.9
occ:0.95
 O2P B:TPO102 1.8 42.8 1.0
NE2 B:HIS331 2.0 46.3 1.0
NE2 B:HIS412 2.0 29.6 1.0
OD1 B:ASP327 2.4 38.6 1.0
OD2 B:ASP327 2.5 36.6 1.0
CG B:ASP327 2.8 38.1 1.0
CE1 B:HIS412 2.9 30.9 1.0
CD2 B:HIS331 3.0 43.2 1.0
CE1 B:HIS331 3.1 44.8 1.0
CD2 B:HIS412 3.1 33.1 1.0
P B:TPO102 3.2 39.8 1.0
ZN B:ZN451 3.7 43.8 1.0
O3P B:TPO102 3.7 38.9 1.0
NE2 B:HIS372 3.9 32.5 1.0
O1P B:TPO102 3.9 40.3 1.0
NE2 B:HIS370 3.9 32.8 1.0
CE1 B:HIS370 4.0 29.7 1.0
ND1 B:HIS412 4.1 34.2 1.0
CG B:HIS331 4.1 42.7 1.0
ND1 B:HIS331 4.2 44.1 1.0
CG B:HIS412 4.2 32.7 1.0
O B:HOH1094 4.2 41.9 1.0
OG1 B:TPO102 4.3 34.8 1.0
CB B:ASP327 4.3 37.1 1.0
OD1 B:ASP51 4.4 33.8 1.0
CD2 B:HIS372 4.5 32.1 1.0
CE1 B:HIS372 4.9 32.0 1.0
O B:ASP327 4.9 38.2 1.0

Zinc binding site 4 out of 4 in 2ga3

Go back to Zinc Binding Sites List in 2ga3
Zinc binding site 4 out of 4 in the Structure of S102T E. Coli Alkaline Phosphatase-Phosphate Intermediate at 2.20A 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-Phosphate Intermediate at 2.20A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn451

b:43.8
occ:1.00
 OD1 B:ASP51 2.0 33.8 1.0
NE2 B:HIS370 2.0 32.8 1.0
OD1 B:ASP369 2.1 29.6 1.0
OG1 B:TPO102 2.5 34.8 1.0
O2P B:TPO102 2.7 42.8 1.0
CE1 B:HIS370 2.8 29.7 1.0
CG B:ASP51 3.0 32.8 1.0
CG B:ASP369 3.0 28.9 1.0
CD2 B:HIS370 3.0 30.0 1.0
P B:TPO102 3.2 39.8 1.0
OD2 B:ASP369 3.3 29.1 1.0
OD2 B:ASP51 3.3 38.4 1.0
OD1 B:ASP327 3.4 38.6 1.0
CG B:ASP327 3.6 38.1 1.0
ZN B:ZN450 3.7 44.9 0.9
CB B:TPO102 3.7 31.2 1.0
ND1 B:HIS370 3.9 29.7 1.0
CE1 B:HIS412 4.0 30.9 1.0
OD2 B:ASP327 4.0 36.6 1.0
CG B:HIS370 4.0 29.2 1.0
N B:GLY52 4.1 24.5 1.0
CG2 B:TPO102 4.1 29.1 1.0
CA B:TPO102 4.1 29.1 1.0
NE2 B:HIS412 4.1 29.6 1.0
O3P B:TPO102 4.2 38.9 1.0
CB B:ASP51 4.3 28.3 1.0
CB B:ASP327 4.3 37.1 1.0
O1P B:TPO102 4.3 40.3 1.0
CB B:ASP369 4.3 27.3 1.0
N B:TPO102 4.3 28.1 1.0
CA B:ASP51 4.6 25.8 1.0
C B:ASP51 4.6 24.9 1.0
CA B:GLY52 4.7 23.2 1.0
ND1 B:HIS412 4.8 34.2 1.0
O B:HOH961 4.8 40.5 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 00:06:37 2024

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