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Zinc in PDB 4h1y: Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552

Enzymatic activity of Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552

All present enzymatic activity of Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552:
3.1.3.5;

Protein crystallography data

The structure of Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552, PDB code: 4h1y was solved by J.Pippel, M.Zebisch, K.Knapp, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.75 / 1.58
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.483, 131.893, 66.333, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.6

Other elements in 4h1y:

The structure of Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552 (pdb code 4h1y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552, PDB code: 4h1y:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4h1y

Go back to Zinc Binding Sites List in 4h1y
Zinc binding site 1 out of 2 in the Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn601

b:9.8
occ:0.90
O P:HOH733 2.0 10.1 1.0
NE2 P:HIS220 2.0 6.5 1.0
OD1 P:ASN117 2.0 11.3 1.0
ND1 P:HIS243 2.1 12.3 1.0
OD2 P:ASP85 2.3 8.4 1.0
CD2 P:HIS220 3.0 7.4 1.0
CE1 P:HIS220 3.0 8.0 1.0
CE1 P:HIS243 3.0 15.1 1.0
CG P:ASP85 3.1 7.5 1.0
CG P:ASN117 3.1 9.2 1.0
CG P:HIS243 3.2 11.3 1.0
ZN P:ZN602 3.3 8.4 0.7
O P:HOH710 3.3 15.2 1.0
OD1 P:ASP85 3.6 8.0 1.0
CA P:HIS243 3.6 9.4 1.0
OD1 P:ASP36 3.6 6.9 1.0
CB P:HIS243 3.6 10.3 1.0
ND2 P:ASN117 3.6 10.2 1.0
O P:HOH1055 4.1 5.9 0.5
CG P:HIS220 4.1 7.2 1.0
ND1 P:HIS220 4.1 7.5 1.0
O P:HIS243 4.1 11.9 1.0
NE2 P:HIS243 4.2 17.2 1.0
CB P:ASP85 4.2 7.2 1.0
CD2 P:HIS243 4.3 14.8 1.0
N P:ASN117 4.4 8.4 1.0
C P:HIS243 4.4 10.4 1.0
CD2 P:HIS118 4.4 8.2 1.0
CB P:ASN117 4.4 9.1 1.0
N P:HIS243 4.6 8.2 1.0
CG P:ASP36 4.8 7.7 1.0
O P:HOH960 4.8 8.1 0.2
O P:HOH769 4.8 11.1 1.0
CA P:ASN117 5.0 8.6 1.0
NE2 P:HIS38 5.0 7.9 1.0

Zinc binding site 2 out of 2 in 4h1y

Go back to Zinc Binding Sites List in 4h1y
Zinc binding site 2 out of 2 in the Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with PSB11552 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn602

b:8.4
occ:0.70
OD1 P:ASP36 2.0 6.9 1.0
NE2 P:HIS38 2.0 7.9 1.0
O P:HOH769 2.1 11.1 1.0
OD2 P:ASP85 2.2 8.4 1.0
O P:HOH733 2.2 10.1 1.0
O P:HOH1055 2.3 5.9 0.5
CE1 P:HIS38 3.0 7.6 1.0
CD2 P:HIS38 3.1 7.8 1.0
CG P:ASP36 3.1 7.7 1.0
CG P:ASP85 3.2 7.5 1.0
ZN P:ZN601 3.3 9.8 0.9
CB P:ASP85 3.4 7.2 1.0
CB P:ASP36 3.7 7.5 1.0
OG P:SER520 3.9 13.1 0.5
ND1 P:HIS38 4.1 7.7 1.0
O P:HOH710 4.2 15.2 1.0
OD1 P:ASN245 4.2 15.1 1.0
CG P:HIS38 4.2 7.3 1.0
OD2 P:ASP36 4.2 7.8 1.0
CD2 P:HIS118 4.2 8.2 1.0
NE2 P:HIS220 4.3 6.5 1.0
CE1 P:HIS220 4.3 8.0 1.0
O P:HIS243 4.3 11.9 1.0
CA P:ASP36 4.3 7.1 1.0
O P:HOH715 4.3 13.6 1.0
OD1 P:ASP85 4.4 8.0 1.0
CA P:HIS243 4.6 9.4 1.0
O P:HOH883 4.7 28.3 1.0
CB P:SER520 4.8 12.8 0.5
C P:HIS243 4.9 10.4 1.0
NE2 P:HIS118 4.9 9.1 1.0
OD1 P:ASN117 4.9 11.3 1.0
ND1 P:HIS243 4.9 12.3 1.0
CA P:ASP85 4.9 6.9 1.0
O P:HOH960 5.0 6.6 0.2

Reference:

K.Knapp, M.Zebisch, J.Pippel, A.El-Tayeb, C.E.Muller, N.Strater. Crystal Structure of the Human Ecto-5'-Nucleotidase (CD73): Insights Into the Regulation of Purinergic Signaling. Structure V. 20 2161 2012.
ISSN: ISSN 0969-2126
PubMed: 23142347
DOI: 10.1016/J.STR.2012.10.001
Page generated: Wed Dec 16 05:21:26 2020

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