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Zinc in PDB 3dyc: Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate

Enzymatic activity of Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate

All present enzymatic activity of Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate:
3.1.3.1;

Protein crystallography data

The structure of Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate, PDB code: 3dyc was solved by J.G.Zalatan, T.D.Fenn, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.45 / 2.30
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 161.609, 161.609, 139.266, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 24.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate (pdb code 3dyc). 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 E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate, PDB code: 3dyc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3dyc

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Zinc binding site 1 out of 6 in the Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:33.5
occ:1.00
 NE2 A:HIS412 2.1 35.5 1.0
NE2 A:HIS331 2.2 32.2 1.0
O1 A:PO4452 2.2 37.6 1.0
OD1 A:ASP327 2.2 27.4 1.0
O2 A:PO4452 2.6 30.8 1.0
OD2 A:ASP327 2.6 28.1 1.0
CG A:ASP327 2.8 30.7 1.0
P A:PO4452 2.9 40.1 1.0
CE1 A:HIS412 2.9 27.5 1.0
CD2 A:HIS331 3.1 27.3 1.0
CD2 A:HIS412 3.2 38.0 1.0
CE1 A:HIS331 3.3 34.1 1.0
O4 A:PO4452 3.5 39.6 1.0
ZN A:ZN451 4.0 34.6 1.0
O A:HOH628 4.0 47.3 1.0
NE2 A:HIS372 4.1 34.5 1.0
ND1 A:HIS412 4.1 33.0 1.0
NE2 A:HIS370 4.2 23.1 1.0
CE1 A:HIS370 4.2 27.7 1.0
O3 A:PO4452 4.2 38.0 1.0
CG A:HIS412 4.2 28.8 1.0
CB A:ASP327 4.2 32.9 1.0
CG A:HIS331 4.3 31.9 1.0
ND1 A:HIS331 4.3 41.5 1.0
O A:HOH615 4.4 48.9 1.0
OD1 A:ASP51 4.6 34.1 1.0
CD2 A:HIS372 4.6 33.0 1.0
O A:HOH595 4.8 52.3 1.0
O A:ASP327 4.9 29.6 1.0

Zinc binding site 2 out of 6 in 3dyc

Go back to Zinc Binding Sites List in 3dyc
Zinc binding site 2 out of 6 in the Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:34.6
occ:1.00
 O2 A:PO4452 2.0 30.8 1.0
OD1 A:ASP51 2.1 34.1 1.0
NE2 A:HIS370 2.2 23.1 1.0
OD2 A:ASP369 2.2 31.9 1.0
OG A:SER102 2.6 57.9 1.0
CG A:ASP51 2.8 32.6 1.0
OD2 A:ASP51 2.8 29.7 1.0
CD2 A:HIS370 3.0 22.6 1.0
CG A:ASP369 3.0 39.4 1.0
CE1 A:HIS370 3.2 27.7 1.0
OD1 A:ASP369 3.3 31.7 1.0
P A:PO4452 3.4 40.1 1.0
OD1 A:ASP327 3.6 27.4 1.0
CB A:SER102 3.8 41.0 1.0
CE1 A:HIS412 3.9 27.5 1.0
O4 A:PO4452 3.9 39.6 1.0
ZN A:ZN450 4.0 33.5 1.0
CG A:ASP327 4.0 30.7 1.0
CA A:SER102 4.0 37.3 1.0
N A:SER102 4.1 33.5 1.0
O3 A:PO4452 4.1 38.0 1.0
CG A:HIS370 4.1 29.0 1.0
ND1 A:HIS370 4.2 25.5 1.0
CB A:ASP51 4.2 33.9 1.0
NE2 A:HIS412 4.3 35.5 1.0
N A:GLY52 4.4 31.9 1.0
CB A:ASP369 4.4 26.2 1.0
O1 A:PO4452 4.4 37.6 1.0
CB A:ASP327 4.5 32.9 1.0
O A:HOH521 4.6 58.3 1.0
OD2 A:ASP327 4.6 28.1 1.0
CA A:ASP51 4.6 32.9 1.0
ND1 A:HIS412 4.6 33.0 1.0
C A:ASP51 4.7 30.2 1.0
C A:ASP101 4.8 32.4 1.0

Zinc binding site 3 out of 6 in 3dyc

Go back to Zinc Binding Sites List in 3dyc
Zinc binding site 3 out of 6 in the Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn453

b:79.5
occ:1.00
 NE2 A:HIS125 2.3 45.4 1.0
CD2 A:HIS125 3.1 40.8 1.0
CE1 A:HIS125 3.3 35.6 1.0
OG1 B:THR17 4.1 24.3 1.0
CG A:HIS125 4.3 39.2 1.0
ND1 A:HIS125 4.4 37.0 1.0
O B:HOH585 4.4 44.2 1.0
O A:HOH580 4.5 41.9 1.0
OD2 B:ASP15 4.7 46.4 1.0

Zinc binding site 4 out of 6 in 3dyc

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Zinc binding site 4 out of 6 in the Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn454

b:0.0
occ:0.88
 NE2 B:HIS125 2.8 47.0 1.0
OG1 A:THR17 3.3 33.1 1.0
CD2 B:HIS125 3.6 40.9 1.0
CE1 B:HIS125 3.8 43.9 1.0
OD2 A:ASP15 4.2 42.8 1.0
CB A:THR17 4.2 37.1 1.0
O B:HOH602 4.6 39.5 1.0
O A:THR17 4.8 39.2 1.0
C A:THR17 4.8 38.8 1.0
CG B:HIS125 4.8 38.1 1.0
ND1 B:HIS125 4.9 42.2 1.0

Zinc binding site 5 out of 6 in 3dyc

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Zinc binding site 5 out of 6 in the Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn450

b:36.8
occ:1.00
 OD2 B:ASP369 2.0 38.1 1.0
OD1 B:ASP51 2.1 37.3 1.0
NE2 B:HIS370 2.1 31.8 1.0
O2 B:PO4452 2.1 37.6 1.0
OG B:SER102 2.6 53.1 1.0
CG B:ASP51 2.8 34.9 1.0
OD2 B:ASP51 2.8 39.6 1.0
CD2 B:HIS370 3.0 34.5 1.0
CG B:ASP369 3.0 40.7 1.0
CE1 B:HIS370 3.1 31.2 1.0
OD1 B:ASP369 3.3 38.7 1.0
P B:PO4452 3.4 35.5 1.0
OD1 B:ASP327 3.5 34.2 1.0
CB B:SER102 3.8 38.1 1.0
O3 B:PO4452 3.9 28.0 1.0
CG B:ASP327 3.9 33.7 1.0
CE1 B:HIS412 4.0 34.4 1.0
O1 B:PO4452 4.0 43.0 1.0
ZN B:ZN451 4.0 33.0 1.0
CA B:SER102 4.0 34.2 1.0
N B:SER102 4.1 31.0 1.0
CG B:HIS370 4.1 31.1 1.0
ND1 B:HIS370 4.1 30.9 1.0
CB B:ASP51 4.2 31.1 1.0
NE2 B:HIS412 4.3 24.8 1.0
CB B:ASP369 4.3 29.7 1.0
N B:GLY52 4.4 29.2 1.0
CB B:ASP327 4.4 35.1 1.0
O B:HOH527 4.5 44.7 1.0
OD2 B:ASP327 4.5 33.6 1.0
O4 B:PO4452 4.6 41.7 1.0
CA B:ASP51 4.7 27.7 1.0
C B:ASP51 4.7 28.3 1.0
ND1 B:HIS412 4.7 32.4 1.0
C B:ASP101 4.8 27.1 1.0

Zinc binding site 6 out of 6 in 3dyc

Go back to Zinc Binding Sites List in 3dyc
Zinc binding site 6 out of 6 in the Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn451

b:33.0
occ:1.00
 NE2 B:HIS331 2.0 33.6 1.0
NE2 B:HIS412 2.1 24.8 1.0
OD1 B:ASP327 2.2 34.2 1.0
O4 B:PO4452 2.3 41.7 1.0
O2 B:PO4452 2.4 37.6 1.0
OD2 B:ASP327 2.7 33.6 1.0
CG B:ASP327 2.8 33.7 1.0
P B:PO4452 2.8 35.5 1.0
CD2 B:HIS331 2.9 25.9 1.0
CE1 B:HIS412 3.0 34.4 1.0
CE1 B:HIS331 3.0 32.4 1.0
CD2 B:HIS412 3.1 29.2 1.0
O B:HOH596 3.5 60.8 1.0
O3 B:PO4452 3.7 28.0 1.0
NE2 B:HIS372 3.9 33.4 1.0
ZN B:ZN450 4.0 36.8 1.0
ND1 B:HIS331 4.1 31.8 1.0
CG B:HIS331 4.1 24.6 1.0
O1 B:PO4452 4.1 43.0 1.0
ND1 B:HIS412 4.1 32.4 1.0
CE1 B:HIS370 4.2 31.2 1.0
CG B:HIS412 4.2 27.2 1.0
NE2 B:HIS370 4.2 31.8 1.0
CB B:ASP327 4.3 35.1 1.0
O B:HOH527 4.5 44.7 1.0
CD2 B:HIS372 4.6 26.4 1.0
OD1 B:ASP51 4.7 37.3 1.0
O B:ASP327 4.8 28.6 1.0
CE1 B:HIS372 4.9 30.1 1.0
O B:HOH636 4.9 55.0 1.0
C B:ASP327 5.0 27.6 1.0

Reference:

J.G.Zalatan, T.D.Fenn, D.Herschlag. Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of An Active-Site Metal Ion. J.Mol.Biol. V. 384 1174 2008.
ISSN: ISSN 0022-2836
PubMed: 18851975
DOI: 10.1016/J.JMB.2008.09.059
Page generated: Wed Dec 16 04:14:16 2020

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