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Zinc in PDB 2ush: 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: 2ush 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 / 2.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.210, 116.290, 132.770, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the 5'-Nucleotidase From E. Coli (pdb code 2ush). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the 5'-Nucleotidase From E. Coli, PDB code: 2ush:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 2ush

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Zinc binding site 1 out of 9 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:Zn601

b:28.8
occ:1.00
O A:HOH883 2.0 34.7 1.0
OD2 A:ASP41 2.1 23.0 1.0
NE2 A:HIS43 2.2 19.0 1.0
OE1 A:GLN254 2.3 26.5 1.0
OD2 A:ASP84 2.3 24.6 1.0
CE1 A:HIS43 3.1 18.5 1.0
CD2 A:HIS43 3.2 15.2 1.0
CG A:ASP41 3.2 25.4 1.0
CG A:ASP84 3.2 20.4 1.0
CD A:GLN254 3.3 30.1 1.0
ZN A:ZN602 3.3 26.5 1.0
CB A:ASP84 3.5 18.0 1.0
CB A:ASP41 3.6 21.6 1.0
CG A:GLN254 3.9 27.5 1.0
CE1 A:HIS217 4.2 18.9 1.0
ND1 A:HIS43 4.2 24.4 1.0
O A:HIS252 4.3 23.1 1.0
OD1 A:ASP41 4.3 26.1 1.0
CG A:HIS43 4.3 20.6 1.0
CD2 A:HIS117 4.3 22.7 1.0
NE2 A:HIS217 4.3 19.6 1.0
CA A:ASP41 4.3 20.7 1.0
O A:HOH844 4.4 28.5 1.0
NE2 A:GLN254 4.4 30.8 1.0
OD1 A:ASP84 4.4 23.6 1.0
CA A:HIS252 4.5 21.3 1.0
OD1 A:ASN116 4.8 27.1 1.0
C A:HIS252 4.8 23.4 1.0
N A:HIS252 4.9 20.4 1.0
ND1 A:HIS252 5.0 25.7 1.0
CA A:ASP84 5.0 21.2 1.0
NE2 A:HIS117 5.0 24.4 1.0

Zinc binding site 2 out of 9 in 2ush

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Zinc binding site 2 out of 9 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:Zn602

b:26.5
occ:1.00
OD1 A:ASN116 2.0 27.1 1.0
NE2 A:HIS217 2.1 19.6 1.0
O A:HOH883 2.1 34.7 1.0
ND1 A:HIS252 2.2 25.7 1.0
OD2 A:ASP84 2.2 24.6 1.0
CE1 A:HIS217 3.0 18.9 1.0
CE1 A:HIS252 3.1 17.8 1.0
CD2 A:HIS217 3.1 15.5 1.0
CG A:ASN116 3.1 25.4 1.0
CG A:HIS252 3.2 25.3 1.0
CG A:ASP84 3.2 20.4 1.0
ZN A:ZN601 3.3 28.8 1.0
CA A:HIS252 3.5 21.3 1.0
O A:HOH844 3.5 28.5 1.0
CB A:HIS252 3.6 24.3 1.0
ND2 A:ASN116 3.6 24.4 1.0
OD1 A:ASP84 3.7 23.6 1.0
OD2 A:ASP41 3.9 23.0 1.0
O A:HIS252 4.1 23.1 1.0
ND1 A:HIS217 4.1 12.2 1.0
CG A:HIS217 4.2 18.0 1.0
NE2 A:HIS252 4.2 22.2 1.0
CD2 A:HIS117 4.2 22.7 1.0
C A:HIS252 4.3 23.4 1.0
N A:ASN116 4.3 26.6 1.0
CD2 A:HIS252 4.3 20.6 1.0
CB A:ASN116 4.3 21.9 1.0
N A:HIS252 4.4 20.4 1.0
CB A:ASP84 4.5 18.0 1.0
CA A:ASN116 4.9 25.8 1.0
N A:HIS117 4.9 26.0 1.0
NE2 A:HIS117 5.0 24.4 1.0

Zinc binding site 3 out of 9 in 2ush

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Zinc binding site 3 out of 9 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 3 of 5'-Nucleotidase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn707

b:44.2
occ:1.00
OD2 B:ASP376 1.8 44.4 1.0
OD2 A:ASP374 1.9 40.3 1.0
OD2 A:ASP376 2.4 49.2 1.0
CG B:ASP376 2.7 42.8 1.0
CG A:ASP374 2.8 43.6 1.0
OD1 A:ASP374 3.0 40.8 1.0
OD1 B:ASP376 3.3 60.7 1.0
CG A:ASP376 3.5 52.7 1.0
CB B:ASP376 3.7 38.8 1.0
OD2 B:ASP374 4.0 56.2 1.0
CB A:ASP376 4.2 41.9 1.0
CB A:ASP374 4.2 38.7 1.0
OD1 A:ASP376 4.4 42.0 1.0
CG B:ASP374 4.8 47.2 1.0
CB B:ASP374 4.9 36.8 1.0
N A:ASP376 5.0 42.1 1.0

Zinc binding site 4 out of 9 in 2ush

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Zinc binding site 4 out of 9 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 4 of 5'-Nucleotidase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn708

b:50.0
occ:1.00
NZ A:LYS293 2.0 25.9 1.0
OE1 B:GLU326 2.3 52.6 1.0
NE2 A:HIS289 2.4 28.5 1.0
OE2 B:GLU326 2.7 50.3 1.0
CD B:GLU326 2.9 48.8 1.0
CE A:LYS293 3.2 25.8 1.0
CE1 A:HIS289 3.4 23.0 1.0
CD2 A:HIS289 3.4 24.2 1.0
CD A:LYS293 3.5 20.6 1.0
OE2 A:GLU290 3.6 27.0 1.0
O B:GLU326 4.1 41.3 1.0
CG B:GLU326 4.4 43.1 1.0
CD A:GLU290 4.5 26.4 1.0
C B:GLU326 4.5 42.9 1.0
ND1 A:HIS289 4.5 31.2 1.0
CG A:HIS289 4.6 30.4 1.0
CA B:ASP327 4.6 46.9 1.0
O A:HOH902 4.6 55.6 1.0
N B:ASP327 4.7 43.9 1.0
CG A:GLU290 4.8 23.9 1.0
CG A:LYS293 4.9 24.4 1.0

Zinc binding site 5 out of 9 in 2ush

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Zinc binding site 5 out of 9 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 5 of 5'-Nucleotidase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn709

b:31.9
occ:0.50
O4 A:WO4703 2.3 16.8 0.5
W A:WO4703 3.8 36.2 0.5
O4 B:WO4701 4.0 70.5 0.5
O3 B:WO4704 4.2 54.9 0.5
O1 A:WO4703 4.2 15.2 0.5
NH2 A:ARG410 4.7 38.8 1.0
O2 A:WO4703 4.9 38.0 0.5
O3 A:WO4703 4.9 36.1 0.5

Zinc binding site 6 out of 9 in 2ush

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Zinc binding site 6 out of 9 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 6 of 5'-Nucleotidase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:30.3
occ:1.00
O B:HOH880 1.9 27.4 1.0
NE2 B:HIS43 2.2 24.4 1.0
OE1 B:GLN254 2.2 30.1 1.0
OD1 B:ASP41 2.2 28.6 1.0
OD2 B:ASP84 2.4 25.0 1.0
CD2 B:HIS43 3.1 20.6 1.0
CE1 B:HIS43 3.2 22.3 1.0
CG B:ASP41 3.2 25.6 1.0
CD B:GLN254 3.3 23.2 1.0
ZN B:ZN602 3.3 31.2 1.0
CG B:ASP84 3.3 32.7 1.0
CB B:ASP41 3.5 20.5 1.0
CB B:ASP84 3.6 24.1 1.0
CG B:GLN254 3.9 21.5 1.0
CE1 B:HIS217 4.2 21.7 1.0
O B:HIS252 4.2 27.4 1.0
OD2 B:ASP41 4.2 24.7 1.0
ND1 B:HIS43 4.3 23.9 1.0
CD2 B:HIS117 4.3 22.2 1.0
CG B:HIS43 4.3 23.9 1.0
O B:HOH833 4.3 26.5 1.0
CA B:ASP41 4.3 24.2 1.0
NE2 B:GLN254 4.3 28.9 1.0
NE2 B:HIS217 4.4 26.6 1.0
CA B:HIS252 4.4 23.4 1.0
OD1 B:ASP84 4.5 28.5 1.0
C B:HIS252 4.8 24.2 1.0
OD1 B:ASN116 4.8 36.8 1.0
ND1 B:HIS252 4.9 25.2 1.0
NE2 B:HIS117 4.9 26.9 1.0
N B:HIS252 4.9 23.4 1.0

Zinc binding site 7 out of 9 in 2ush

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Zinc binding site 7 out of 9 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 7 of 5'-Nucleotidase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:31.2
occ:1.00
O B:HOH880 1.7 27.4 1.0
NE2 B:HIS217 2.0 26.6 1.0
OD1 B:ASN116 2.1 36.8 1.0
ND1 B:HIS252 2.1 25.2 1.0
OD2 B:ASP84 2.2 25.0 1.0
CE1 B:HIS217 2.8 21.7 1.0
CE1 B:HIS252 3.0 26.6 1.0
CD2 B:HIS217 3.1 18.5 1.0
CG B:ASN116 3.1 26.5 1.0
CG B:HIS252 3.2 24.2 1.0
CG B:ASP84 3.2 32.7 1.0
ZN B:ZN601 3.3 30.3 1.0
CA B:HIS252 3.5 23.4 1.0
CB B:HIS252 3.6 22.8 1.0
ND2 B:ASN116 3.6 28.5 1.0
O B:HOH833 3.7 26.5 1.0
OD1 B:ASP41 3.7 28.6 1.0
OD1 B:ASP84 3.7 28.5 1.0
ND1 B:HIS217 4.0 20.9 1.0
CG B:HIS217 4.1 21.6 1.0
CD2 B:HIS117 4.2 22.2 1.0
NE2 B:HIS252 4.2 24.8 1.0
O B:HIS252 4.2 27.4 1.0
CD2 B:HIS252 4.3 25.6 1.0
C B:HIS252 4.3 24.2 1.0
N B:ASN116 4.4 28.8 1.0
CB B:ASN116 4.4 23.6 1.0
CB B:ASP84 4.4 24.1 1.0
N B:HIS252 4.5 23.4 1.0
NE2 B:HIS117 4.9 26.9 1.0
CG B:ASP41 4.9 25.6 1.0
N B:HIS117 4.9 28.4 1.0
CA B:ASN116 4.9 28.5 1.0
NE2 B:HIS43 5.0 24.4 1.0

Zinc binding site 8 out of 9 in 2ush

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Zinc binding site 8 out of 9 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 8 of 5'-Nucleotidase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn705

b:40.7
occ:1.00
OE2 B:GLU235 1.8 46.3 1.0
NE2 B:HIS226 2.1 34.9 1.0
CD B:GLU235 2.6 40.5 1.0
OE1 B:GLU235 2.8 40.4 1.0
CD2 B:HIS226 3.0 35.4 1.0
CE1 B:HIS226 3.2 35.9 1.0
CG B:GLU235 4.0 36.8 1.0
CG B:HIS226 4.2 33.6 1.0
ND1 B:HIS226 4.3 34.9 1.0
CG B:PRO231 4.4 29.8 1.0
O B:GLY224 4.4 36.5 1.0
CB B:PRO231 5.0 33.4 1.0

Zinc binding site 9 out of 9 in 2ush

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Zinc binding site 9 out of 9 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 9 of 5'-Nucleotidase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn706

b:42.5
occ:1.00
OE1 B:GLU225 2.3 46.6 1.0
OE2 B:GLU225 2.4 48.0 1.0
CD B:GLU225 2.6 44.1 1.0
CG B:GLU225 4.1 45.8 1.0
CB B:GLU225 4.8 37.9 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: Sat Sep 26 03:55:44 2020
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