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Zinc in PDB 4h2b: Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with Baicalin

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

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

Protein crystallography data

The structure of Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with Baicalin, PDB code: 4h2b was solved by M.Zebisch, J.Pippel, K.Knapp, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.263, 131.056, 66.238, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18

Other elements in 4h2b:

The structure of Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with Baicalin 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 Baicalin (pdb code 4h2b). 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 Baicalin, PDB code: 4h2b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4h2b

Go back to Zinc Binding Sites List in 4h2b
Zinc binding site 1 out of 2 in the Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with Baicalin


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 Baicalin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:10.5
occ:1.00
O A:HOH727 2.0 10.6 1.0
OD1 A:ASN117 2.0 10.9 1.0
NE2 A:HIS220 2.1 9.4 1.0
ND1 A:HIS243 2.2 12.7 1.0
OD2 A:ASP85 2.2 10.8 1.0
CE1 A:HIS243 3.0 13.7 1.0
CD2 A:HIS220 3.0 9.9 1.0
CE1 A:HIS220 3.1 9.4 1.0
CG A:ASP85 3.1 8.2 1.0
CG A:ASN117 3.1 11.6 1.0
O A:HOH702 3.2 12.5 1.0
ZN A:ZN602 3.2 11.1 1.0
CG A:HIS243 3.2 11.1 1.0
OD1 A:ASP85 3.5 9.4 1.0
CA A:HIS243 3.6 9.6 1.0
OD1 A:ASP36 3.6 9.9 1.0
CB A:HIS243 3.6 9.8 1.0
ND2 A:ASN117 3.7 11.7 1.0
O A:HIS243 4.1 12.0 1.0
ND1 A:HIS220 4.2 8.9 1.0
CG A:HIS220 4.2 8.9 1.0
NE2 A:HIS243 4.2 14.5 1.0
CB A:ASP85 4.2 8.6 1.0
CD2 A:HIS243 4.3 13.5 1.0
CD2 A:HIS118 4.3 10.8 1.0
C A:HIS243 4.3 10.3 1.0
N A:ASN117 4.4 10.1 1.0
CB A:ASN117 4.4 10.1 1.0
N A:HIS243 4.5 8.4 1.0
O A:HOH748 4.8 10.8 1.0
CG A:ASP36 4.8 10.6 1.0
CA A:ASN117 4.9 10.4 1.0
NE2 A:HIS38 4.9 11.2 1.0
N A:HIS118 5.0 10.5 1.0

Zinc binding site 2 out of 2 in 4h2b

Go back to Zinc Binding Sites List in 4h2b
Zinc binding site 2 out of 2 in the Human Ecto-5'-Nucleotidase (CD73): Crystal Form II (Open) in Complex with Baicalin


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 Baicalin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:11.1
occ:1.00
OD1 A:ASP36 2.0 9.9 1.0
O A:HOH727 2.0 10.6 1.0
O A:HOH748 2.1 10.8 1.0
NE2 A:HIS38 2.1 11.2 1.0
OD2 A:ASP85 2.2 10.8 1.0
CE1 A:HIS38 3.0 10.8 1.0
CG A:ASP36 3.1 10.6 1.0
CD2 A:HIS38 3.1 9.7 1.0
CG A:ASP85 3.2 8.2 1.0
ZN A:ZN601 3.2 10.5 1.0
CB A:ASP85 3.4 8.6 1.0
CB A:ASP36 3.7 8.8 1.0
OG A:SER520 3.7 15.9 0.5
OD1 A:ASN245 4.1 14.3 1.0
O A:HOH702 4.1 12.5 1.0
OD2 A:ASP36 4.1 9.4 1.0
O A:HIS243 4.2 12.0 1.0
ND1 A:HIS38 4.2 10.3 1.0
O A:HOH745 4.2 16.0 1.0
CG A:HIS38 4.2 10.1 1.0
CA A:ASP36 4.2 8.4 1.0
NE2 A:HIS220 4.3 9.4 1.0
CE1 A:HIS220 4.3 9.4 1.0
CD2 A:HIS118 4.3 10.8 1.0
OD1 A:ASP85 4.4 9.4 1.0
O A:HOH735 4.4 15.6 1.0
CA A:HIS243 4.5 9.6 1.0
C A:HIS243 4.7 10.3 1.0
ND1 A:HIS243 4.8 12.7 1.0
CB A:SER520 4.8 13.1 0.5
OD1 A:ASN117 4.8 10.9 1.0
NE2 A:HIS118 4.9 12.4 1.0
CA A:ASP85 4.9 9.2 1.0

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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