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Zinc in PDB 1ush: 5'-Nucleotidase From E. Coli

Enzymatic activity of 5'-Nucleotidase From E. Coli

All present enzymatic activity of 5'-Nucleotidase From E. Coli:
3.1.3.5;

Protein crystallography data

The structure of 5'-Nucleotidase From E. Coli, PDB code: 1ush was solved by T.Knofel, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.73
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.610, 83.610, 181.630, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the 5'-Nucleotidase From E. Coli (pdb code 1ush). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the 5'-Nucleotidase From E. Coli, PDB code: 1ush:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1ush

Go back to Zinc Binding Sites List in 1ush
Zinc binding site 1 out of 2 in the 5'-Nucleotidase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 5'-Nucleotidase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:29.0
occ:1.00
OD2 A:ASP41 2.1 8.6 1.0
NE2 A:HIS43 2.1 7.4 1.0
O1 A:CO3602 2.3 19.9 1.0
OD2 A:ASP84 2.3 5.1 1.0
OE1 A:GLN254 2.4 15.6 1.0
CE1 A:HIS43 3.1 6.4 1.0
CD2 A:HIS43 3.1 9.1 1.0
CG A:ASP41 3.2 8.8 1.0
C A:CO3602 3.2 23.1 1.0
CG A:ASP84 3.3 6.2 1.0
ZN A:ZN601 3.3 14.2 1.0
CD A:GLN254 3.4 15.1 1.0
CB A:ASP84 3.5 6.1 1.0
CB A:ASP41 3.6 6.9 1.0
O2 A:CO3602 3.8 25.8 1.0
CG A:GLN254 3.9 11.9 1.0
O3 A:CO3602 4.0 25.2 1.0
O A:HIS252 4.1 9.5 1.0
CD2 A:HIS117 4.2 6.8 1.0
ND1 A:HIS43 4.2 5.7 1.0
OD1 A:ASP41 4.2 7.8 1.0
CG A:HIS43 4.2 7.2 1.0
CE1 A:HIS217 4.2 7.2 1.0
NE2 A:HIS217 4.3 7.1 1.0
CA A:ASP41 4.4 6.3 1.0
CA A:HIS252 4.4 8.5 1.0
OD1 A:ASP84 4.4 7.2 1.0
NE2 A:GLN254 4.4 13.1 1.0
C A:HIS252 4.7 8.5 1.0
NE2 A:HIS117 4.7 7.3 1.0
ND1 A:HIS252 4.8 7.9 1.0
N A:HIS252 4.9 6.7 1.0
OD1 A:ASN116 4.9 7.6 1.0

Zinc binding site 2 out of 2 in 1ush

Go back to Zinc Binding Sites List in 1ush
Zinc binding site 2 out of 2 in the 5'-Nucleotidase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 5'-Nucleotidase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:14.2
occ:1.00
OD1 A:ASN116 2.0 7.6 1.0
NE2 A:HIS217 2.1 7.1 1.0
ND1 A:HIS252 2.2 7.9 1.0
OD2 A:ASP84 2.2 5.1 1.0
O1 A:CO3602 2.4 19.9 1.0
O3 A:CO3602 2.6 25.2 1.0
C A:CO3602 2.9 23.1 1.0
CE1 A:HIS252 3.0 10.3 1.0
CD2 A:HIS217 3.1 8.2 1.0
CE1 A:HIS217 3.1 7.2 1.0
CG A:ASP84 3.1 6.2 1.0
CG A:ASN116 3.1 6.0 1.0
CG A:HIS252 3.3 6.8 1.0
ZN A:ZN600 3.3 29.0 1.0
OD1 A:ASP84 3.5 7.2 1.0
CA A:HIS252 3.6 8.5 1.0
ND2 A:ASN116 3.7 6.8 1.0
CB A:HIS252 3.7 8.5 1.0
OD2 A:ASP41 3.9 8.6 1.0
CD2 A:HIS117 4.0 6.8 1.0
O2 A:CO3602 4.1 25.8 1.0
CG A:HIS217 4.2 7.6 1.0
ND1 A:HIS217 4.2 7.9 1.0
NE2 A:HIS252 4.2 8.2 1.0
O A:HIS252 4.2 9.5 1.0
N A:ASN116 4.3 7.1 1.0
CB A:ASP84 4.3 6.1 1.0
CD2 A:HIS252 4.4 7.3 1.0
CB A:ASN116 4.4 6.5 1.0
C A:HIS252 4.4 8.5 1.0
N A:HIS252 4.5 6.7 1.0
NE2 A:HIS117 4.7 7.3 1.0
N A:HIS117 4.8 6.8 1.0
CA A:ASN116 4.9 7.3 1.0
NE2 A:HIS43 4.9 7.4 1.0

Reference:

T.Knofel, N.Strater. X-Ray Structure of the Escherichia Coli Periplasmic 5'-Nucleotidase Containing A Dimetal Catalytic Site. Nat.Struct.Biol. V. 6 448 1999.
ISSN: ISSN 1072-8368
PubMed: 10331872
DOI: 10.1038/8253
Page generated: Mon Jan 25 16:14:42 2021

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