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Zinc in PDB 1ura: Alkaline Phosphatase (D51ZN)

Enzymatic activity of Alkaline Phosphatase (D51ZN)

All present enzymatic activity of Alkaline Phosphatase (D51ZN):
3.1.3.1;

Protein crystallography data

The structure of Alkaline Phosphatase (D51ZN), PDB code: 1ura was solved by T.T.Tibbitts, J.E.Murphy, E.R.Kantrowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.04
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 194.810, 166.870, 76.390, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Alkaline Phosphatase (D51ZN) (pdb code 1ura). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Alkaline Phosphatase (D51ZN), PDB code: 1ura:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ura

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Zinc binding site 1 out of 4 in the Alkaline Phosphatase (D51ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alkaline Phosphatase (D51ZN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:14.4
occ:1.00
NE2 A:HIS412 1.9 25.2 1.0
NE2 A:HIS331 2.0 15.9 1.0
O1 A:PO4453 2.1 23.4 0.8
OD1 A:ASP327 2.2 16.3 1.0
O2 A:PO4453 2.2 24.1 0.8
OD2 A:ASP327 2.4 12.9 1.0
CG A:ASP327 2.6 5.2 1.0
P A:PO4453 2.7 17.9 0.8
CE1 A:HIS412 2.7 15.1 1.0
CE1 A:HIS331 3.0 4.4 1.0
CD2 A:HIS331 3.0 5.5 1.0
CD2 A:HIS412 3.1 22.4 1.0
O3 A:PO4453 3.7 15.1 0.8
NE2 A:HIS372 3.7 5.3 1.0
O4 A:PO4453 3.8 14.8 0.8
CE1 A:HIS370 3.9 4.1 1.0
NE2 A:HIS370 3.9 18.2 1.0
ND1 A:HIS412 3.9 17.5 1.0
ZN A:ZN451 4.1 12.9 0.9
CG A:HIS412 4.1 14.3 1.0
CB A:ASP327 4.1 13.6 1.0
ND1 A:HIS331 4.1 12.3 1.0
CG A:HIS331 4.2 14.8 1.0
CD2 A:HIS372 4.5 6.8 1.0
OD1 A:ASN51 4.5 13.3 1.0
CE1 A:HIS372 4.6 6.5 1.0
O A:ASP327 4.9 8.3 1.0
O A:HOH526 4.9 28.8 1.0
C A:ASP327 4.9 10.6 1.0
OG A:SER102 4.9 14.0 1.0
CA A:ASP327 5.0 10.1 1.0

Zinc binding site 2 out of 4 in 1ura

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Zinc binding site 2 out of 4 in the Alkaline Phosphatase (D51ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alkaline Phosphatase (D51ZN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:12.9
occ:0.91
OD2 A:ASP369 2.0 15.3 1.0
NE2 A:HIS370 2.0 18.2 1.0
OD1 A:ASN51 2.1 13.3 1.0
O2 A:PO4453 2.2 24.1 0.8
OG A:SER102 2.2 14.0 1.0
CD2 A:HIS370 2.9 4.7 1.0
CG A:ASP369 2.9 15.1 1.0
CG A:ASN51 3.0 19.5 1.0
CE1 A:HIS370 3.1 4.1 1.0
OD1 A:ASP369 3.3 10.1 1.0
ND2 A:ASN51 3.3 12.5 1.0
P A:PO4453 3.5 17.9 0.8
CB A:SER102 3.5 10.3 1.0
OD1 A:ASP327 3.7 16.3 1.0
CA A:SER102 3.8 9.2 1.0
O4 A:PO4453 3.9 14.8 0.8
N A:SER102 3.9 6.1 1.0
O3 A:PO4453 4.0 15.1 0.8
CG A:ASP327 4.0 5.2 1.0
CG A:HIS370 4.0 2.0 1.0
ZN A:ZN450 4.1 14.4 1.0
ND1 A:HIS370 4.1 8.7 1.0
CE1 A:HIS412 4.2 15.1 1.0
CB A:ASP369 4.3 10.2 1.0
CB A:ASN51 4.4 15.2 1.0
OD2 A:ASP327 4.4 12.9 1.0
N A:GLY52 4.4 7.5 1.0
CB A:ASP327 4.6 13.6 1.0
NE2 A:HIS412 4.6 25.2 1.0
C A:ASP101 4.6 9.6 1.0
O1 A:PO4453 4.6 23.4 0.8
O A:HOH527 4.7 36.5 1.0
CA A:ASN51 4.7 15.4 1.0
C A:ASN51 4.8 11.2 1.0
ND1 A:HIS412 4.8 17.5 1.0

Zinc binding site 3 out of 4 in 1ura

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Zinc binding site 3 out of 4 in the Alkaline Phosphatase (D51ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alkaline Phosphatase (D51ZN) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn450

b:9.8
occ:0.90
NE2 B:HIS331 1.9 13.0 1.0
NE2 B:HIS412 2.0 25.9 1.0
O1 B:PO4453 2.1 16.7 0.8
OD1 B:ASP327 2.2 25.1 1.0
O2 B:PO4453 2.3 18.9 0.8
OD2 B:ASP327 2.3 18.8 1.0
CG B:ASP327 2.6 14.7 1.0
P B:PO4453 2.7 15.0 0.8
CE1 B:HIS412 2.8 15.7 1.0
CD2 B:HIS331 2.9 11.2 1.0
CE1 B:HIS331 2.9 6.8 1.0
CD2 B:HIS412 3.1 22.1 1.0
NE2 B:HIS372 3.7 14.4 1.0
O3 B:PO4453 3.7 9.2 0.8
O4 B:PO4453 3.8 13.5 0.8
CE1 B:HIS370 4.0 3.7 1.0
ND1 B:HIS412 4.0 14.6 1.0
NE2 B:HIS370 4.0 7.9 1.0
ND1 B:HIS331 4.1 13.1 1.0
CG B:HIS331 4.1 14.6 1.0
CB B:ASP327 4.1 17.1 1.0
ZN B:ZN451 4.1 15.6 0.8
CG B:HIS412 4.2 17.4 1.0
CD2 B:HIS372 4.5 5.1 1.0
CE1 B:HIS372 4.5 9.6 1.0
OD1 B:ASN51 4.6 16.7 1.0
O B:ASP327 4.7 10.5 1.0
C B:ASP327 4.8 12.8 1.0
CA B:ASP327 4.9 12.8 1.0
OG B:SER102 4.9 17.6 1.0

Zinc binding site 4 out of 4 in 1ura

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Zinc binding site 4 out of 4 in the Alkaline Phosphatase (D51ZN)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alkaline Phosphatase (D51ZN) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn451

b:15.6
occ:0.81
OD2 B:ASP369 2.0 19.4 1.0
OD1 B:ASN51 2.0 16.7 1.0
NE2 B:HIS370 2.1 7.9 1.0
OG B:SER102 2.2 17.6 1.0
O2 B:PO4453 2.2 18.9 0.8
CG B:ASN51 2.9 18.5 1.0
CD2 B:HIS370 2.9 2.7 1.0
CG B:ASP369 3.0 17.2 1.0
CE1 B:HIS370 3.1 3.7 1.0
ND2 B:ASN51 3.2 19.2 1.0
OD1 B:ASP369 3.2 21.5 1.0
CB B:SER102 3.5 11.9 1.0
P B:PO4453 3.5 15.0 0.8
OD1 B:ASP327 3.6 25.1 1.0
CA B:SER102 3.8 9.7 1.0
O4 B:PO4453 3.9 13.5 0.8
CG B:ASP327 4.0 14.7 1.0
N B:SER102 4.0 3.1 1.0
O3 B:PO4453 4.0 9.2 0.8
CG B:HIS370 4.1 2.0 1.0
ND1 B:HIS370 4.1 4.8 1.0
ZN B:ZN450 4.1 9.8 0.9
CE1 B:HIS412 4.2 15.7 1.0
CB B:ASN51 4.3 11.0 1.0
CB B:ASP369 4.3 13.1 1.0
OD2 B:ASP327 4.4 18.8 1.0
N B:GLY52 4.4 10.8 1.0
CB B:ASP327 4.5 17.1 1.0
NE2 B:HIS412 4.6 25.9 1.0
O1 B:PO4453 4.7 16.7 0.8
CA B:ASN51 4.7 11.0 1.0
C B:ASP101 4.7 8.8 1.0
C B:ASN51 4.7 9.6 1.0
ND1 B:HIS412 4.9 14.6 1.0
O B:HOH473 5.0 37.3 1.0

Reference:

T.T.Tibbitts, J.E.Murphy, E.R.Kantrowitz. Kinetic and Structural Consequences of Replacing the Aspartate Bridge By Asparagine in the Catalytic Metal Triad of Escherichia Coli Alkaline Phosphatase. J.Mol.Biol. V. 257 700 1996.
ISSN: ISSN 0022-2836
PubMed: 8648634
DOI: 10.1006/JMBI.1996.0195
Page generated: Mon Jan 25 16:14:42 2021

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