Calcium in PDB 8db9: Adenosine/Guanosine Nucleoside Hydrolase Bound to Inhibitor

The structure of Adenosine/Guanosine Nucleoside Hydrolase Bound to Inhibitor, PDB code: 8db9 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)	38.13 / 2.89
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.406, 75.382, 88.856, 65.47, 80.79, 87.32
R / Rfree (%)	26 / 34.1

The binding sites of Calcium atom in the Adenosine/Guanosine Nucleoside Hydrolase Bound to Inhibitor (pdb code 8db9). 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 Inhibitor, PDB code: 8db9:
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 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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:45.9 occ:1.00 OD1 A:ASP8 2.5 45.3 1.0 O A:LEU125 2.6 46.9 1.0 OD1 A:ASP13 2.8 47.5 1.0 OD2 A:ASP13 2.8 47.3 1.0 OD2 A:ASP8 3.1 45.3 1.0 CG A:ASP8 3.2 46.4 1.0 CG A:ASP13 3.2 46.7 1.0 OD2 A:ASP239 3.2 47.9 1.0 OD1 A:ASP239 3.5 48.7 1.0 ND2 A:ASN37 3.6 46.8 1.0 CG A:ASP239 3.7 48.9 1.0 C A:LEU125 3.8 46.9 1.0 ND2 A:ASN168 3.9 48.7 1.0 OD1 A:ASN168 3.9 47.5 1.0 OD1 A:ASP12 4.2 47.9 1.0 CG A:ASN168 4.3 48.2 1.0 CB A:LEU125 4.5 47.1 1.0 CA A:ALA126 4.6 46.2 1.0 N A:ALA126 4.6 46.6 1.0 CG A:ASN37 4.6 46.3 1.0 O A:ASP8 4.6 45.7 1.0 CB A:ASP8 4.7 44.8 1.0 OD2 A:ASP12 4.7 48.4 1.0 CA A:LEU125 4.7 46.8 1.0 CB A:ASP13 4.7 47.3 1.0 OD1 A:ASN37 4.8 46.2 1.0 CG A:ASP12 4.8 48.1 1.0

Calcium binding site 2 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase Bound to 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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:52.4 occ:1.00 O14 B:R1Y401 2.2 54.3 1.0 O13 B:R1Y401 2.3 54.5 1.0 OD1 B:ASP8 2.3 51.8 1.0 OD1 B:ASP13 2.5 54.7 1.0 OD2 B:ASP239 2.6 52.8 1.0 O B:LEU125 2.8 51.9 1.0 OD2 B:ASP13 2.8 52.1 1.0 ND2 B:ASN37 3.0 53.7 1.0 CG B:ASP13 3.0 50.5 1.0 C07 B:R1Y401 3.2 55.7 1.0 CG B:ASP8 3.3 52.2 1.0 C08 B:R1Y401 3.3 56.0 1.0 CG B:ASP239 3.5 52.5 1.0 OD2 B:ASP8 3.6 53.1 1.0 OD1 B:ASP239 3.7 54.3 1.0 C B:LEU125 3.9 50.6 1.0 CG B:ASN37 4.1 54.5 1.0 ND2 B:ASN168 4.1 55.9 1.0 C06 B:R1Y401 4.2 57.7 1.0 OD1 B:ASP12 4.3 52.5 1.0 OD1 B:ASN168 4.4 56.5 1.0 CA B:ALA126 4.4 51.3 1.0 OD2 B:ASP12 4.5 53.0 1.0 OD1 B:ASN37 4.5 55.7 1.0 CB B:ASP13 4.5 52.2 1.0 C09 B:R1Y401 4.5 58.4 1.0 N B:ALA126 4.6 51.1 1.0 O B:ASP8 4.6 51.9 1.0 CB B:ASP8 4.6 51.1 1.0 N B:ASP8 4.7 49.9 1.0 CB B:LEU125 4.7 50.0 1.0 CG B:ASN168 4.7 56.7 1.0 CG B:ASP12 4.7 52.6 1.0 CB B:ALA126 4.8 50.7 1.0 C B:ASP8 4.8 51.2 1.0 CA B:LEU125 4.8 50.5 1.0 CB B:ASP239 4.9 53.0 1.0 O10 B:R1Y401 4.9 59.3 1.0 CA B:ASP8 5.0 50.8 1.0

Calcium binding site 3 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase Bound to 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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:50.6 occ:1.00 O14 C:R1Y401 2.1 54.2 1.0 O C:LEU125 2.6 48.6 1.0 OD1 C:ASP8 2.7 49.8 1.0 OD1 C:ASP13 3.0 50.5 1.0 O13 C:R1Y401 3.0 54.4 1.0 C07 C:R1Y401 3.2 54.0 1.0 OD1 C:ASN37 3.3 55.4 1.0 OD2 C:ASP239 3.4 49.6 1.0 OD1 C:ASP12 3.5 52.0 1.0 C08 C:R1Y401 3.6 53.6 1.0 CG C:ASP8 3.6 50.5 1.0 OD2 C:ASP13 3.6 49.9 1.0 CG C:ASP13 3.7 50.7 1.0 OD2 C:ASP8 3.7 51.5 1.0 C C:LEU125 3.8 47.7 1.0 OD1 C:ASP239 3.8 49.3 1.0 OD1 C:ASN168 3.9 51.6 1.0 CG C:ASP239 4.0 49.8 1.0 CG C:ASN37 4.3 56.5 1.0 CA C:ALA126 4.3 48.2 1.0 C09 C:R1Y401 4.3 54.2 1.0 ND2 C:ASN168 4.4 52.5 1.0 CG C:ASP12 4.5 52.5 1.0 N C:ALA126 4.5 47.4 1.0 C06 C:R1Y401 4.5 56.1 1.0 CG C:ASN168 4.6 51.7 1.0 OD2 C:ASP12 4.6 54.2 1.0 ND2 C:ASN37 4.6 57.1 1.0 CB C:ALA126 4.7 47.2 1.0 CB C:LEU125 4.9 46.6 1.0 CA C:LEU125 4.9 46.4 1.0

Calcium binding site 4 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase Bound to 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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:51.6 occ:1.00 O14 D:R1Y401 2.2 54.7 1.0 O13 D:R1Y401 2.3 55.5 1.0 OD2 D:ASP239 2.4 51.6 1.0 O D:LEU125 2.5 51.3 1.0 OD2 D:ASP13 2.5 51.0 1.0 OD1 D:ASP8 2.5 50.6 1.0 OD1 D:ASP13 2.6 52.5 1.0 CG D:ASP13 2.8 51.3 1.0 C07 D:R1Y401 3.2 56.3 1.0 C08 D:R1Y401 3.2 56.6 1.0 CG D:ASP239 3.4 51.9 1.0 C D:LEU125 3.5 50.7 1.0 CG D:ASP8 3.5 51.0 1.0 OD1 D:ASP239 3.6 52.5 1.0 OD2 D:ASP8 3.7 51.9 1.0 ND2 D:ASN37 4.0 52.5 1.0 CB D:LEU125 4.0 50.0 1.0 ND2 D:ASN168 4.1 54.5 1.0 CA D:LEU125 4.2 50.0 1.0 CB D:ASP13 4.3 51.7 1.0 OD1 D:ASN168 4.3 55.9 1.0 N D:ALA126 4.5 50.9 1.0 C09 D:R1Y401 4.5 58.9 1.0 C06 D:R1Y401 4.5 58.2 1.0 OD1 D:ASP12 4.5 52.4 1.0 CA D:ALA126 4.7 54.6 1.0 CG D:ASN168 4.7 55.9 1.0 OD1 D:ASN37 4.7 54.5 1.0 CB D:ASP239 4.7 51.7 1.0 CG D:ASN37 4.8 53.2 1.0 CA D:ASP13 4.8 51.8 1.0 N D:ASP13 4.8 51.5 1.0 O D:ASP8 4.8 51.5 1.0 OD2 D:ASP12 4.8 52.3 1.0 N D:ASP8 4.9 49.0 1.0 CB D:ASP8 4.9 50.3 1.0 CE D:MET151 5.0 56.9 1.0 O10 D:R1Y401 5.0 59.8 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