Calcium in PDB 8db6: Adenosine/Guanosine Nucleoside Hydrolase

The structure of Adenosine/Guanosine Nucleoside Hydrolase, PDB code: 8db6 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)	29.65 / 2.02
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.596, 75.115, 85.209, 76.16, 81.49, 88.15
R / Rfree (%)	20.4 / 23.7

The binding sites of Calcium atom in the Adenosine/Guanosine Nucleoside Hydrolase (pdb code 8db6). 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, PDB code: 8db6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:32.0 occ:1.00 O B:LEU125 2.3 28.5 1.0 OD2 B:ASP239 2.4 27.6 1.0 OD1 B:ASP13 2.4 31.3 1.0 OD1 B:ASP8 2.5 32.2 1.0 O3 B:GOL401 2.6 47.2 1.0 OD2 B:ASP13 2.7 30.4 1.0 CG B:ASP13 2.8 33.1 1.0 O2 B:GOL401 2.9 45.6 1.0 C3 B:GOL401 3.3 48.1 1.0 CG B:ASP239 3.4 32.3 1.0 C B:LEU125 3.6 33.0 1.0 CG B:ASP8 3.6 35.2 1.0 C2 B:GOL401 3.7 55.3 1.0 OD1 B:ASP239 3.7 32.6 1.0 OD1 B:ASN37 3.8 48.2 1.0 OD2 B:ASP8 4.0 33.9 1.0 CB B:LEU125 4.2 30.0 1.0 CB B:ASP13 4.3 30.5 1.0 OD1 B:ASP12 4.3 31.2 1.0 CA B:LEU125 4.4 31.5 1.0 OD1 B:ASN168 4.5 33.0 1.0 N B:ALA126 4.5 29.4 1.0 CA B:ALA126 4.5 30.2 1.0 ND2 B:ASN168 4.6 30.8 1.0 N B:ASP8 4.7 28.2 1.0 CB B:ASP239 4.7 30.1 1.0 C1 B:GOL401 4.8 63.7 1.0 OD2 B:ASP12 4.8 33.7 1.0 CB B:ALA126 4.8 29.9 1.0 N B:ASP13 4.8 32.1 1.0 CG B:ASN37 4.9 45.0 1.0 CA B:ASP13 4.9 31.9 1.0 CG B:ASP12 4.9 32.9 1.0 CB B:ASP8 4.9 32.6 1.0 O B:ASP8 5.0 34.0 1.0

Calcium binding site 2 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:127.4 occ:1.00 O3 A:GOL401 2.1 47.9 1.0 O A:LEU125 2.4 28.3 1.0 O2 A:GOL401 2.5 27.5 1.0 OD1 A:ASP8 2.5 30.2 1.0 OD2 A:ASP239 2.6 24.2 1.0 OD1 A:ASP13 2.7 41.5 1.0 OD2 A:ASP13 2.9 34.0 1.0 CG A:ASP13 3.1 33.1 1.0 C3 A:GOL401 3.2 60.4 1.0 C2 A:GOL401 3.2 56.3 1.0 CG A:ASP239 3.5 33.9 1.0 CG A:ASP8 3.6 33.7 1.0 C A:LEU125 3.6 29.9 1.0 OD1 A:ASP239 3.6 33.6 1.0 ND2 A:ASN37 3.9 38.7 1.0 OD2 A:ASP8 3.9 36.0 1.0 CB A:LEU125 4.3 29.8 1.0 CA A:ALA126 4.4 29.3 1.0 OD1 A:ASN168 4.4 33.8 1.0 N A:ALA126 4.5 29.1 1.0 CA A:LEU125 4.5 30.6 1.0 ND2 A:ASN168 4.5 28.8 1.0 OD1 A:ASP12 4.5 31.1 1.0 CB A:ASP13 4.5 33.4 1.0 C1 A:GOL401 4.6 62.7 1.0 N A:ASP8 4.7 27.1 1.0 CB A:ALA126 4.8 26.6 1.0 CG A:ASN37 4.9 42.8 1.0 CG A:ASN168 4.9 31.9 1.0 CB A:ASP8 4.9 29.6 1.0 CB A:ASP239 4.9 26.1 1.0

Calcium binding site 3 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:38.3 occ:1.00 O C:LEU125 2.3 37.4 1.0 OD1 C:ASP8 2.4 38.5 1.0 OD2 C:ASP239 2.4 39.3 1.0 OD1 C:ASP13 2.4 38.2 1.0 O1 C:GOL401 2.5 45.1 1.0 O2 C:GOL401 2.5 46.0 1.0 C2 C:GOL401 2.6 67.4 1.0 OD2 C:ASP13 2.7 35.9 1.0 CG C:ASP13 2.9 40.6 1.0 C1 C:GOL401 2.9 69.8 1.0 CG C:ASP239 3.4 40.9 1.0 CG C:ASP8 3.5 41.3 1.0 C C:LEU125 3.6 38.5 1.0 ND2 C:ASN37 3.6 44.4 1.0 OD1 C:ASP239 3.7 39.6 1.0 OD2 C:ASP8 3.9 43.1 1.0 C3 C:GOL401 4.1 53.9 1.0 CB C:LEU125 4.2 37.5 1.0 CB C:ASP13 4.3 37.4 1.0 OD1 C:ASP12 4.4 40.3 1.0 CA C:ALA126 4.4 39.3 1.0 CA C:LEU125 4.5 39.0 1.0 N C:ALA126 4.5 36.8 1.0 OD1 C:ASN168 4.6 39.0 1.0 N C:ASP8 4.6 39.0 1.0 ND2 C:ASN168 4.6 39.6 1.0 CG C:ASN37 4.7 46.4 1.0 CB C:ASP239 4.7 34.8 1.0 CB C:ASP8 4.8 38.2 1.0 CB C:ALA126 4.8 39.1 1.0 N C:ASP13 4.8 33.9 1.0 CA C:ASP13 4.9 37.7 1.0 OD2 C:ASP12 4.9 38.2 1.0 C C:ASP8 5.0 43.2 1.0

Calcium binding site 4 out of 4 in the Adenosine/Guanosine Nucleoside Hydrolase


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:54.4 occ:1.00 O D:LEU125 2.3 45.5 1.0 O D:HOH541 2.4 47.7 1.0 OD2 D:ASP239 2.4 49.1 1.0 O D:HOH522 2.4 47.7 1.0 OD1 D:ASP8 2.5 46.0 1.0 O D:HOH505 2.6 51.7 1.0 OD1 D:ASP13 2.6 47.0 1.0 OD2 D:ASP13 2.7 40.0 1.0 CG D:ASP13 2.9 43.7 1.0 CG D:ASP239 3.4 51.5 1.0 C D:LEU125 3.5 42.9 1.0 CG D:ASP8 3.5 44.0 1.0 OD1 D:ASP239 3.7 53.7 1.0 ND2 D:ASN37 3.7 50.9 1.0 OD2 D:ASP8 3.8 43.8 1.0 CB D:LEU125 4.2 44.2 1.0 CB D:ASP13 4.4 41.4 1.0 CA D:LEU125 4.4 44.4 1.0 N D:ALA126 4.4 43.4 1.0 CA D:ALA126 4.4 42.6 1.0 ND2 D:ASN168 4.5 48.9 1.0 OD1 D:ASN168 4.5 47.6 1.0 OD1 D:ASP12 4.6 51.0 1.0 OD2 D:ASP12 4.6 53.2 1.0 N D:ASP8 4.7 35.8 1.0 CB D:ALA126 4.7 38.9 1.0 CB D:ASP239 4.8 49.3 1.0 CG D:ASN37 4.8 48.9 1.0 CB D:ASP8 4.8 41.3 1.0 CA D:ASP13 4.9 42.7 1.0 N D:ASP13 4.9 42.3 1.0 CG D:ASP12 4.9 52.9 1.0 CG D:ASN168 5.0 50.5 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