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Zinc in PDB 5c66: E. Coli Alkaline Phosphatase in Complex with Tungstate

Enzymatic activity of E. Coli Alkaline Phosphatase in Complex with Tungstate

All present enzymatic activity of E. Coli Alkaline Phosphatase in Complex with Tungstate:
3.1.3.1;

Protein crystallography data

The structure of E. Coli Alkaline Phosphatase in Complex with Tungstate, PDB code: 5c66 was solved by A.Peck, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.74 / 2.03
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 161.260, 161.260, 139.432, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 24

Other elements in 5c66:

The structure of E. Coli Alkaline Phosphatase in Complex with Tungstate also contains other interesting chemical elements:

Tungsten (W) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the E. Coli Alkaline Phosphatase in Complex with Tungstate (pdb code 5c66). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the E. Coli Alkaline Phosphatase in Complex with Tungstate, PDB code: 5c66:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5c66

Go back to Zinc Binding Sites List in 5c66
Zinc binding site 1 out of 6 in the E. Coli Alkaline Phosphatase in Complex with Tungstate


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 in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:32.2
occ:1.00
 OD2 A:ASP369 2.0 28.4 1.0
O A:HOH607 2.0 24.5 0.5
O1 A:WO4504 2.0 30.1 0.5
OD1 A:ASP51 2.0 31.9 1.0
NE2 A:HIS370 2.1 33.5 1.0
OG A:SER102 2.1 35.6 1.0
CG A:ASP51 2.8 33.2 1.0
CG A:ASP369 2.9 32.8 1.0
OD2 A:ASP51 2.9 31.9 1.0
CD2 A:HIS370 3.1 30.6 1.0
CE1 A:HIS370 3.1 31.4 1.0
OD1 A:ASP369 3.1 33.2 1.0
W A:WO4504 3.2 55.0 0.5
CB A:SER102 3.3 35.2 1.0
CA A:SER102 3.7 33.5 1.0
OD1 A:ASP327 3.9 32.4 1.0
ZN A:ZN502 4.0 31.3 1.0
CG A:ASP327 4.1 32.0 1.0
N A:SER102 4.1 31.4 1.0
CB A:ASP51 4.1 33.2 1.0
CE1 A:HIS412 4.2 34.6 1.0
ND1 A:HIS370 4.2 28.7 1.0
CG A:HIS370 4.2 32.7 1.0
CB A:ASP369 4.2 31.3 1.0
N A:GLY52 4.3 35.2 1.0
NE2 A:HIS412 4.3 33.0 1.0
O2 A:WO4504 4.3 25.1 0.5
OD2 A:ASP327 4.4 37.4 1.0
O3 A:WO4504 4.4 34.9 0.5
O A:HOH657 4.4 33.2 1.0
O A:HOH601 4.5 31.9 1.0
CB A:ASP327 4.5 31.0 1.0
CA A:ASP51 4.6 34.2 1.0
O A:HOH609 4.7 30.8 1.0
C A:ASP51 4.7 37.9 1.0
ZN A:ZN503 4.7 32.5 1.0
O A:HOH660 4.7 24.4 0.5
O4 A:WO4504 4.8 36.0 0.5
C A:ASP101 4.9 29.2 1.0
CA A:GLY52 5.0 31.5 1.0

Zinc binding site 2 out of 6 in 5c66

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Zinc binding site 2 out of 6 in the E. Coli Alkaline Phosphatase in Complex with Tungstate


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 in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:31.3
occ:1.00
 O A:HOH660 2.0 24.4 0.5
O4 A:WO4504 2.0 36.0 0.5
O A:HOH607 2.0 24.5 0.5
NE2 A:HIS331 2.0 28.2 1.0
O1 A:WO4504 2.1 30.1 0.5
NE2 A:HIS412 2.1 33.0 1.0
OD1 A:ASP327 2.1 32.4 1.0
OD2 A:ASP327 2.1 37.4 1.0
CG A:ASP327 2.5 32.0 1.0
W A:WO4504 2.9 55.0 0.5
CD2 A:HIS331 3.0 34.9 1.0
CD2 A:HIS412 3.1 30.6 1.0
CE1 A:HIS331 3.1 32.9 1.0
CE1 A:HIS412 3.1 34.6 1.0
NE2 A:HIS372 3.9 28.1 1.0
ZN A:ZN501 4.0 32.2 1.0
CB A:ASP327 4.0 31.0 1.0
CE1 A:HIS370 4.1 31.4 1.0
O A:HOH609 4.1 30.8 1.0
O2 A:WO4504 4.1 25.1 0.5
CG A:HIS331 4.1 31.6 1.0
ND1 A:HIS331 4.1 36.4 1.0
ND1 A:HIS412 4.2 32.9 1.0
CG A:HIS412 4.2 29.8 1.0
NE2 A:HIS370 4.3 33.5 1.0
OD1 A:ASP51 4.4 31.9 1.0
OG A:SER102 4.5 35.6 1.0
CD2 A:HIS372 4.5 29.4 1.0
O3 A:WO4504 4.6 34.9 0.5
O A:ASP327 4.8 30.5 1.0
CE1 A:HIS372 4.9 25.5 1.0
C A:ASP327 5.0 32.1 1.0
CA A:ASP327 5.0 30.2 1.0

Zinc binding site 3 out of 6 in 5c66

Go back to Zinc Binding Sites List in 5c66
Zinc binding site 3 out of 6 in the E. Coli Alkaline Phosphatase in Complex with Tungstate


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 in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:32.5
occ:1.00
 O A:HOH651 2.0 29.1 1.0
OE2 A:GLU322 2.0 33.9 1.0
OG1 A:THR155 2.0 30.8 1.0
O A:HOH601 2.0 31.9 1.0
O A:HOH614 2.0 30.7 1.0
OD2 A:ASP51 2.0 31.9 1.0
CD A:GLU322 3.0 38.6 1.0
CG A:ASP51 3.1 33.2 1.0
CB A:THR155 3.1 31.3 1.0
OE1 A:GLU322 3.3 36.3 1.0
CB A:ASP51 3.6 33.2 1.0
OD2 A:ASP153 3.6 38.0 1.0
O A:HOH609 4.0 30.8 1.0
O3 A:WO4504 4.1 34.9 0.5
CG2 A:THR155 4.1 29.9 1.0
N A:THR155 4.1 36.4 1.0
OD1 A:ASP51 4.1 31.9 1.0
CA A:THR155 4.2 33.0 1.0
OG A:SER102 4.2 35.6 1.0
CG A:GLU322 4.3 35.6 1.0
O A:HOH657 4.4 33.2 1.0
CB A:ALA324 4.4 36.0 1.0
CB A:SER102 4.5 35.2 1.0
CA A:ALA324 4.6 34.5 1.0
CG A:ASP153 4.6 42.8 1.0
O A:ALA324 4.7 37.2 1.0
ZN A:ZN501 4.7 32.2 1.0
OD2 A:ASP369 4.8 28.4 1.0
CA A:ASP51 5.0 34.2 1.0
CD A:PRO156 5.0 31.5 1.0

Zinc binding site 4 out of 6 in 5c66

Go back to Zinc Binding Sites List in 5c66
Zinc binding site 4 out of 6 in the E. Coli Alkaline Phosphatase in Complex with Tungstate


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 in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:31.7
occ:1.00
 O B:HOH611 2.0 22.1 0.5
O B:HOH603 2.0 22.5 0.5
O4 B:WO4504 2.0 36.2 0.5
O1 B:WO4504 2.0 31.0 0.5
NE2 B:HIS331 2.0 28.4 1.0
OD1 B:ASP327 2.1 32.8 1.0
OD2 B:ASP327 2.2 32.9 1.0
NE2 B:HIS412 2.2 35.4 1.0
CG B:ASP327 2.5 33.1 1.0
W B:WO4504 2.9 58.2 0.5
CD2 B:HIS331 3.0 28.6 1.0
CE1 B:HIS331 3.0 31.0 1.0
CD2 B:HIS412 3.1 30.2 1.0
CE1 B:HIS412 3.1 35.7 1.0
NE2 B:HIS372 3.9 30.7 1.0
ZN B:ZN502 4.0 31.1 1.0
CE1 B:HIS370 4.0 31.1 1.0
CB B:ASP327 4.0 36.5 1.0
NE2 B:HIS370 4.1 31.4 1.0
O B:HOH601 4.1 37.8 1.0
O2 B:WO4504 4.1 25.3 0.5
ND1 B:HIS331 4.1 30.8 1.0
CG B:HIS331 4.2 29.6 1.0
ND1 B:HIS412 4.2 33.6 1.0
CG B:HIS412 4.3 30.6 1.0
OD1 B:ASP51 4.4 29.8 1.0
OG B:SER102 4.5 35.5 1.0
CD2 B:HIS372 4.5 31.2 1.0
O3 B:WO4504 4.5 27.7 0.5
O B:ASP327 4.9 33.3 1.0
CE1 B:HIS372 4.9 30.0 1.0
C B:ASP327 5.0 32.9 1.0
CA B:ASP327 5.0 32.8 1.0

Zinc binding site 5 out of 6 in 5c66

Go back to Zinc Binding Sites List in 5c66
Zinc binding site 5 out of 6 in the E. Coli Alkaline Phosphatase in Complex with Tungstate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of E. Coli Alkaline Phosphatase in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:31.1
occ:1.00
 O B:HOH603 2.0 22.5 0.5
O1 B:WO4504 2.0 31.0 0.5
OD1 B:ASP51 2.0 29.8 1.0
OD2 B:ASP369 2.0 33.0 1.0
OG B:SER102 2.1 35.5 1.0
NE2 B:HIS370 2.1 31.4 1.0
CG B:ASP51 2.8 32.2 1.0
CG B:ASP369 2.9 33.5 1.0
OD2 B:ASP51 2.9 31.2 1.0
CD2 B:HIS370 2.9 33.6 1.0
W B:WO4504 3.2 58.2 0.5
OD1 B:ASP369 3.2 34.2 1.0
CE1 B:HIS370 3.2 31.1 1.0
CB B:SER102 3.3 34.2 1.0
CA B:SER102 3.7 33.1 1.0
OD1 B:ASP327 3.8 32.8 1.0
ZN B:ZN501 4.0 31.7 1.0
CG B:ASP327 4.0 33.1 1.0
N B:SER102 4.1 32.0 1.0
CG B:HIS370 4.1 32.2 1.0
CE1 B:HIS412 4.2 35.7 1.0
ND1 B:HIS370 4.2 33.3 1.0
CB B:ASP51 4.2 32.8 1.0
O2 B:WO4504 4.3 25.3 0.5
CB B:ASP369 4.3 36.1 1.0
O B:HOH654 4.3 29.0 1.0
N B:GLY52 4.3 29.3 1.0
OD2 B:ASP327 4.3 32.9 1.0
NE2 B:HIS412 4.3 35.4 1.0
O B:HOH611 4.4 22.1 0.5
O3 B:WO4504 4.4 27.7 0.5
CB B:ASP327 4.5 36.5 1.0
O B:HOH602 4.5 32.1 1.0
CA B:ASP51 4.6 32.8 1.0
ZN B:ZN503 4.7 32.5 1.0
C B:ASP51 4.7 32.9 1.0
O B:HOH601 4.7 37.8 1.0
O4 B:WO4504 4.8 36.2 0.5
C B:ASP101 4.9 30.8 1.0

Zinc binding site 6 out of 6 in 5c66

Go back to Zinc Binding Sites List in 5c66
Zinc binding site 6 out of 6 in the E. Coli Alkaline Phosphatase in Complex with Tungstate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of E. Coli Alkaline Phosphatase in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:32.5
occ:1.00
 OE2 B:GLU322 2.0 31.4 1.0
O B:HOH602 2.0 32.1 1.0
OG1 B:THR155 2.0 29.2 1.0
OD2 B:ASP51 2.0 31.2 1.0
O B:HOH636 2.0 33.7 1.0
O B:HOH660 2.0 26.6 1.0
CD B:GLU322 3.0 36.8 1.0
CG B:ASP51 3.1 32.2 1.0
CB B:THR155 3.1 27.6 1.0
OE1 B:GLU322 3.5 34.9 1.0
OD2 B:ASP153 3.6 34.2 1.0
CB B:ASP51 3.6 32.8 1.0
CG2 B:THR155 4.1 27.2 1.0
O B:HOH601 4.1 37.8 1.0
OD1 B:ASP51 4.1 29.8 1.0
N B:THR155 4.1 35.3 1.0
O3 B:WO4504 4.2 27.7 0.5
CA B:THR155 4.2 29.9 1.0
OG B:SER102 4.3 35.5 1.0
CG B:GLU322 4.3 36.3 1.0
O B:HOH654 4.3 29.0 1.0
CB B:ALA324 4.4 38.0 1.0
CB B:SER102 4.5 34.2 1.0
CA B:ALA324 4.6 34.5 1.0
CG B:ASP153 4.6 36.8 1.0
O B:ALA324 4.6 37.8 1.0
ZN B:ZN502 4.7 31.1 1.0
OD2 B:ASP369 4.8 33.0 1.0
CA B:ASP51 5.0 32.8 1.0

Reference:

A.Peck, F.Sunden, L.D.Andrews, V.S.Pande, D.Herschlag. Tungstate As A Transition State Analog For Catalysis By Alkaline Phosphatase. J.Mol.Biol. V. 428 2758 2016.
ISSN: ESSN 1089-8638
PubMed: 27189921
DOI: 10.1016/J.JMB.2016.05.007
Page generated: Sun Oct 27 13:53:26 2024

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