Calcium in PDB 8db7: Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor

The structure of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor, PDB code: 8db7 was solved by S.N.Muellers, K.N.Allen, B.J.Stockman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.99 / 2.33
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.651, 74.537, 85.641, 83.02, 80.9, 89.9
R / Rfree (%)	19.6 / 25.6

The structure of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Calcium atom in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor (pdb code 8db7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor, PDB code: 8db7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:30.9 occ:1.00 O B:LEU125 2.3 28.4 1.0 OD2 B:ASP239 2.5 27.8 1.0 OD1 B:ASP13 2.5 33.8 1.0 OD1 B:ASP8 2.5 25.8 1.0 O B:HOH503 2.5 30.0 1.0 OD2 B:ASP13 2.5 34.5 1.0 O B:HOH507 2.6 28.8 1.0 O1 B:GOL401 2.7 31.1 1.0 CG B:ASP13 2.8 31.3 1.0 CG B:ASP239 3.4 32.7 1.0 C1 B:GOL401 3.5 35.5 1.0 CG B:ASP8 3.5 30.1 1.0 C B:LEU125 3.6 27.6 1.0 OD1 B:ASP239 3.7 31.2 1.0 ND2 B:ASN37 3.7 33.7 1.0 OD2 B:ASP8 3.9 34.0 1.0 O2 B:GOL401 3.9 31.9 1.0 CB B:LEU125 4.2 30.4 1.0 OD1 B:ASP12 4.3 33.2 1.0 C2 B:GOL401 4.3 39.2 1.0 CB B:ASP13 4.3 31.3 1.0 OD1 B:ASN168 4.3 31.3 1.0 CA B:LEU125 4.4 29.4 1.0 N B:ALA126 4.5 25.4 1.0 CA B:ALA126 4.5 32.9 1.0 ND2 B:ASN168 4.5 28.5 1.0 N B:ASP8 4.7 30.3 1.0 CG B:ASN37 4.8 34.0 1.0 CB B:ASP239 4.8 30.6 1.0 CB B:ASP8 4.8 24.6 1.0 OD2 B:ASP12 4.9 29.6 1.0 CG B:ASN168 4.9 30.2 1.0 N B:ASP13 4.9 29.1 1.0 CG B:ASP12 4.9 28.4 1.0 CA B:ASP13 5.0 33.2 1.0

Calcium binding site 2 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:34.6 occ:1.00 OD1 A:ASP8 2.4 26.9 1.0 C3 A:GOL401 2.4 47.2 1.0 O A:LEU125 2.4 30.6 1.0 O A:HOH517 2.6 33.8 1.0 OD2 A:ASP13 2.6 32.2 1.0 OD2 A:ASP239 2.6 32.4 1.0 O3 A:GOL401 2.7 42.8 1.0 OD1 A:ASP13 2.8 34.8 1.0 O2 A:GOL401 2.9 32.4 1.0 CG A:ASP13 3.0 31.6 1.0 C2 A:GOL401 3.2 41.3 1.0 CG A:ASP8 3.4 33.6 1.0 CG A:ASP239 3.5 34.3 1.0 C A:LEU125 3.6 31.8 1.0 ND2 A:ASN37 3.6 29.8 1.0 OD2 A:ASP8 3.8 28.7 1.0 OD1 A:ASP239 3.8 33.9 1.0 CB A:LEU125 4.2 30.7 1.0 CB A:ASP13 4.4 28.4 1.0 OD1 A:ASN168 4.4 29.5 1.0 O A:HOH502 4.4 32.8 1.0 CA A:LEU125 4.4 30.8 1.0 CA A:ALA126 4.5 32.6 1.0 N A:ALA126 4.5 33.6 1.0 C1 A:GOL401 4.5 41.6 1.0 OD1 A:ASP12 4.5 31.1 1.0 ND2 A:ASN168 4.6 31.3 1.0 CG A:ASN37 4.6 32.4 1.0 N A:ASP8 4.7 28.8 1.0 O A:ASP8 4.7 25.5 1.0 CB A:ASP8 4.7 26.1 1.0 CB A:ALA126 4.9 31.1 1.0 N A:ASP13 4.9 28.6 1.0 CB A:ASP239 4.9 28.1 1.0 C A:ASP8 4.9 32.2 1.0 OD1 A:ASN37 5.0 30.6 1.0 CG A:ASN168 5.0 30.9 1.0 OD2 A:ASP12 5.0 35.7 1.0 CA A:ASP13 5.0 32.4 1.0

Calcium binding site 3 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:29.9 occ:1.00 O2 C:GOL401 2.2 27.8 1.0 O C:LEU125 2.3 27.7 1.0 OD1 C:ASP8 2.5 27.0 1.0 O3 C:GOL401 2.6 28.6 1.0 OD2 C:ASP239 2.6 33.0 1.0 OD2 C:ASP13 2.7 28.8 1.0 OD1 C:ASP13 2.8 30.7 1.0 CG C:ASP13 3.0 32.1 1.0 C2 C:GOL401 3.2 46.4 1.0 C3 C:GOL401 3.4 35.5 1.0 CG C:ASP239 3.5 36.4 1.0 CG C:ASP8 3.5 30.8 1.0 C C:LEU125 3.5 31.6 1.0 OD1 C:ASP239 3.6 30.9 1.0 ND2 C:ASN37 3.7 31.2 1.0 OD2 C:ASP8 3.8 32.8 1.0 CB C:LEU125 4.2 28.7 1.0 C1 C:GOL401 4.3 50.2 1.0 OD1 C:ASN168 4.3 32.7 1.0 O1 C:GOL401 4.4 40.4 1.0 CA C:ALA126 4.4 28.1 1.0 N C:ALA126 4.4 30.1 1.0 CA C:LEU125 4.4 27.5 1.0 CB C:ASP13 4.5 26.6 1.0 N C:ASP8 4.5 29.4 1.0 ND2 C:ASN168 4.6 29.5 1.0 OD1 C:ASP12 4.6 37.4 1.0 CB C:ALA126 4.6 27.8 1.0 CG C:ASN37 4.6 37.0 1.0 CB C:ASP8 4.8 28.7 1.0 OD2 C:ASP12 4.9 33.5 1.0 CB C:ASP239 4.9 29.7 1.0 CG C:ASN168 4.9 28.3 1.0 OD1 C:ASN37 4.9 42.4 1.0 O C:ASP8 5.0 28.3 1.0 C C:ASP8 5.0 30.8 1.0 CA C:ASP13 5.0 28.3 1.0

Calcium binding site 4 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca403 b:37.7 occ:1.00 O D:LEU125 2.3 35.3 1.0 OD1 D:ASP13 2.3 43.1 1.0 OD2 D:ASP239 2.4 38.2 1.0 O D:HOH508 2.5 36.8 1.0 O2 D:GOL401 2.9 48.1 1.0 CG D:ASP13 3.0 41.5 1.0 OD2 D:ASP13 3.0 40.8 1.0 OD1 D:ASP8 3.3 32.3 1.0 CG D:ASP239 3.3 39.8 1.0 C D:LEU125 3.5 38.4 1.0 OD1 D:ASP239 3.6 43.5 1.0 C2 D:GOL401 3.7 46.1 1.0 C1 D:GOL401 3.9 44.2 1.0 ND2 D:ASN37 4.1 40.5 1.0 OG1 D:THR7 4.1 36.9 1.0 CG D:ASP8 4.1 34.3 1.0 OD2 D:ASP8 4.2 39.8 1.0 CB D:LEU125 4.2 34.4 1.0 OD1 D:ASP12 4.4 46.3 1.0 ND2 D:ASN168 4.4 36.7 1.0 N D:ALA126 4.4 38.3 1.0 CA D:LEU125 4.4 32.2 1.0 OD1 D:ASN168 4.4 37.2 1.0 CB D:ASP13 4.4 43.1 1.0 CA D:ALA126 4.4 39.1 1.0 O1 D:GOL401 4.6 50.8 1.0 CB D:ASP239 4.7 42.4 1.0 OD2 D:ASP12 4.7 40.3 1.0 CG D:ASN168 4.8 34.5 1.0 CG D:ASP12 4.9 43.4 1.0 N D:ASP13 4.9 44.8 1.0 CA D:ASP13 4.9 44.0 1.0 CB D:ALA126 4.9 36.7 1.0

S.N.Muellers, M.M.Nyitray, N.Reynarowych, E.Saljanin, A.L.Benzie, A.R.Schoenfeld, B.J.Stockman, K.N.Allen. Structure-Guided Insight Into the Specificity and Mechanism of A Parasitic Nucleoside Hydrolase. Biochemistry V. 61 1853 2022.
ISSN: ISSN 0006-2960
PubMed: 35994320
DOI: 10.1021/ACS.BIOCHEM.2C00361