Zinc in PDB 7p9t: Crystal Structure of CD73 in Complex with Dcmp in the Open Form

Enzymatic activity of Crystal Structure of CD73 in Complex with Dcmp in the Open Form

All present enzymatic activity of Crystal Structure of CD73 in Complex with Dcmp in the Open Form:
3.1.3.5;

Protein crystallography data

The structure of Crystal Structure of CD73 in Complex with Dcmp in the Open Form, PDB code: 7p9t was solved by E.R.Scaletti, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 1.79
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.104, 132.846, 67.404, 90, 90, 90
R / Rfree (%) 18.5 / 21.7

Other elements in 7p9t:

The structure of Crystal Structure of CD73 in Complex with Dcmp in the Open Form also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of CD73 in Complex with Dcmp in the Open Form (pdb code 7p9t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of CD73 in Complex with Dcmp in the Open Form, PDB code: 7p9t:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7p9t

Go back to Zinc Binding Sites List in 7p9t
Zinc binding site 1 out of 2 in the Crystal Structure of CD73 in Complex with Dcmp in the Open Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of CD73 in Complex with Dcmp in the Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:14.7
occ:1.00
OD1 A:ASP36 1.9 14.0 1.0
O A:HOH726 2.1 12.6 1.0
NE2 A:HIS38 2.1 10.6 1.0
OD2 A:ASP85 2.2 12.7 1.0
CG A:ASP36 3.0 12.2 1.0
CD2 A:HIS38 3.1 11.5 1.0
CE1 A:HIS38 3.1 10.8 1.0
CG A:ASP85 3.1 12.5 1.0
CB A:ASP85 3.3 11.8 1.0
ZN A:ZN602 3.4 14.8 1.0
CB A:ASP36 3.5 11.7 1.0
OD2 A:ASP36 4.1 12.9 1.0
CA A:ASP36 4.1 11.4 1.0
ND1 A:HIS38 4.2 11.5 1.0
CG A:HIS38 4.2 10.6 1.0
CD2 A:HIS118 4.2 14.7 1.0
OD1 A:ASN245 4.2 13.2 1.0
OD1 A:ASP85 4.3 13.0 1.0
CE1 A:HIS220 4.3 12.8 1.0
NE2 A:HIS220 4.3 12.8 1.0
O A:HOH886 4.3 21.7 1.0
O A:HIS243 4.4 19.7 1.0
CA A:HIS243 4.7 14.7 1.0
NE2 A:HIS118 4.8 14.8 1.0
CA A:ASP85 4.8 11.6 1.0
OG A:SER520 5.0 20.0 0.5
ND1 A:HIS243 5.0 17.7 1.0
OD1 A:ASN117 5.0 15.8 1.0

Zinc binding site 2 out of 2 in 7p9t

Go back to Zinc Binding Sites List in 7p9t
Zinc binding site 2 out of 2 in the Crystal Structure of CD73 in Complex with Dcmp in the Open Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of CD73 in Complex with Dcmp in the Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:14.8
occ:1.00
OD1 A:ASN117 2.0 15.8 1.0
ND1 A:HIS243 2.1 17.7 1.0
NE2 A:HIS220 2.1 12.8 1.0
OD2 A:ASP85 2.2 12.7 1.0
CE1 A:HIS243 2.9 19.4 1.0
CD2 A:HIS220 3.0 12.7 1.0
CG A:ASP85 3.1 12.5 1.0
CG A:ASN117 3.1 15.2 1.0
CE1 A:HIS220 3.2 12.8 1.0
CG A:HIS243 3.2 16.6 1.0
ZN A:ZN601 3.4 14.7 1.0
OD1 A:ASP85 3.5 13.0 1.0
CA A:HIS243 3.6 14.7 1.0
ND2 A:ASN117 3.6 14.9 1.0
CB A:HIS243 3.6 15.6 1.0
OD1 A:ASP36 3.6 14.0 1.0
O A:HIS243 4.1 19.7 1.0
NE2 A:HIS243 4.1 17.1 1.0
CD2 A:HIS118 4.2 14.7 1.0
CG A:HIS220 4.2 13.5 1.0
ND1 A:HIS220 4.3 13.4 1.0
CD2 A:HIS243 4.3 18.1 1.0
CB A:ASP85 4.3 11.8 1.0
N A:ASN117 4.4 14.8 1.0
C A:HIS243 4.4 16.6 1.0
CB A:ASN117 4.4 13.4 1.0
N A:HIS243 4.5 13.2 1.0
CG A:ASP36 4.8 12.2 1.0
O A:HOH726 4.9 12.6 1.0
NE2 A:HIS118 4.9 14.8 1.0
CA A:ASN117 4.9 13.9 1.0

Reference:

E.Scaletti, F.U.Huschmann, U.Mueller, M.S.Weiss, N.Strater. Substrate Binding Modes of Purine and Pyrimidine Nucleotides to Human Ecto-5'-Nucleotidase (CD73) and Inhibition By Their Bisphosphonic Acid Derivatives. Purinergic Signal 2021.
ISSN: ISSN 1573-9546
PubMed: 34403084
DOI: 10.1007/S11302-021-09802-W
Page generated: Fri Nov 5 17:00:09 2021

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