Atomistry » Zinc » PDB 2rv5-2v1z » 2ush
Atomistry »
  Zinc »
    PDB 2rv5-2v1z »
      2ush »

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

Other elements in 2ush:

The structure of 5'-Nucleotidase From E. Coli also contains other interesting chemical elements:

Tungsten (W) 4 atoms

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

Go back to Zinc Binding Sites List in 2ush
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

Go back to Zinc Binding Sites List in 2ush
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

Go back to Zinc Binding Sites List in 2ush
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

Go back to Zinc Binding Sites List in 2ush
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

Go back to Zinc Binding Sites List in 2ush
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

Go back to Zinc Binding Sites List in 2ush
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

Go back to Zinc Binding Sites List in 2ush
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

Go back to Zinc Binding Sites List in 2ush
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

Go back to Zinc Binding Sites List in 2ush
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: Thu Oct 17 03:57:34 2024

Last articles

Al in 2YNM
Al in 2ZJY
Al in 2ZBG
Al in 2ZBD
Al in 2Y3I
Al in 2YBE
Al in 2XZO
Al in 2XZL
Al in 2WOJ
Al in 2X2F
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy