Calcium in PDB 8db8: Adenosine/Guanosine Nucleoside Hydrolase Bound to Imh

The structure of Adenosine/Guanosine Nucleoside Hydrolase Bound to Imh, PDB code: 8db8 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)	37.38 / 2.21
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.025, 76.48, 86.636, 75.48, 81.67, 86.5
R / Rfree (%)	22.1 / 26.6

The binding sites of Calcium atom in the Adenosine/Guanosine Nucleoside Hydrolase Bound to Imh (pdb code 8db8). 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 Imh, PDB code: 8db8:
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 Imh


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 Imh within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:34.9 occ:1.00 O B:LEU125 2.4 35.7 1.0 O3' B:IMH401 2.4 36.8 1.0 O2' B:IMH401 2.4 27.8 1.0 OD2 B:ASP13 2.4 30.3 1.0 OD2 B:ASP239 2.4 31.5 1.0 O B:HOH518 2.4 32.3 1.0 OD1 B:ASP8 2.5 31.4 1.0 OD1 B:ASP13 2.7 33.9 1.0 CG B:ASP13 2.9 30.3 1.0 CG B:ASP239 3.4 29.1 1.0 C3' B:IMH401 3.5 38.6 1.0 C2' B:IMH401 3.5 34.0 1.0 ND2 B:ASN37 3.5 33.8 1.0 CG B:ASP8 3.6 32.8 1.0 C B:LEU125 3.6 28.4 1.0 OD1 B:ASP239 3.6 30.2 1.0 OD2 B:ASP8 3.9 27.8 1.0 OD1 B:ASP12 4.3 31.7 1.0 CB B:ASP13 4.3 33.1 1.0 ND2 B:ASN168 4.3 30.4 1.0 CB B:LEU125 4.3 30.6 1.0 CA B:ALA126 4.5 29.4 1.0 N B:ALA126 4.5 28.0 1.0 OD1 B:ASN168 4.5 34.2 1.0 C1' B:IMH401 4.5 38.7 1.0 CG B:ASN37 4.5 37.7 1.0 CA B:LEU125 4.6 29.1 1.0 C4' B:IMH401 4.6 37.7 1.0 N B:ASP8 4.7 30.3 1.0 CB B:ALA126 4.7 31.1 1.0 CB B:ASP239 4.7 29.9 1.0 N4' B:IMH401 4.8 37.5 1.0 OD2 B:ASP12 4.8 25.6 1.0 OD1 B:ASN37 4.9 40.3 1.0 O B:ASP8 4.9 20.2 1.0 CG B:ASN168 4.9 29.5 1.0 CG B:ASP12 4.9 31.7 1.0 CB B:ASP8 4.9 32.2 1.0 CA B:ASP13 4.9 26.9 1.0 N B:ASP13 4.9 24.5 1.0

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


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 Imh within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:54.5 occ:1.00 OD1 A:ASP8 2.4 25.1 1.0 O A:LEU125 2.5 27.6 1.0 OD2 A:ASP13 2.5 35.4 1.0 OD2 A:ASP239 2.6 27.9 1.0 O A:HOH503 2.7 32.3 1.0 O A:HOH548 2.7 34.6 1.0 OD1 A:ASP13 2.8 28.0 1.0 CG A:ASP13 3.0 35.4 1.0 CG A:ASP8 3.3 29.8 1.0 OD2 A:ASP8 3.5 36.4 1.0 CG A:ASP239 3.6 33.1 1.0 C A:LEU125 3.7 31.7 1.0 OD1 A:ASP239 3.8 31.3 1.0 OD1 A:ASP12 4.2 32.2 1.0 CB A:LEU125 4.4 28.3 1.0 OD1 A:ASN168 4.4 27.2 1.0 CB A:ASP13 4.5 29.7 1.0 CA A:ALA126 4.5 32.4 1.0 N A:ALA126 4.5 30.8 1.0 CA A:LEU125 4.6 33.3 1.0 N A:ASP8 4.7 27.5 1.0 CB A:ASP8 4.7 25.8 1.0 OD2 A:ASP12 4.8 34.2 1.0 ND2 A:ASN168 4.8 24.4 1.0 CB A:ALA126 4.8 28.2 1.0 CG A:ASP12 4.9 30.6 1.0 CB A:ASP239 4.9 28.3 1.0 O A:ASP8 5.0 26.8 1.0

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


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 Imh within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:69.2 occ:1.00 O C:HOH525 2.4 34.8 1.0 OD2 C:ASP239 2.4 30.2 1.0 OD1 C:ASP13 2.4 41.9 1.0 O C:HOH532 2.4 30.8 1.0 O C:LEU125 2.4 35.5 1.0 OD1 C:ASP8 2.5 31.9 1.0 OD2 C:ASP13 2.6 35.3 1.0 CG C:ASP13 2.8 37.8 1.0 O C:HOH507 2.8 34.7 1.0 CG C:ASP239 3.4 34.2 1.0 CG C:ASP8 3.6 37.1 1.0 C C:LEU125 3.6 32.8 1.0 OD1 C:ASP239 3.6 30.1 1.0 ND2 C:ASN37 3.7 47.5 1.0 OD2 C:ASP8 3.9 44.8 1.0 O C:HOH533 3.9 32.1 1.0 CB C:LEU125 4.1 31.9 1.0 OD1 C:ASP12 4.2 35.1 1.0 CB C:ASP13 4.3 32.9 1.0 CA C:LEU125 4.5 33.2 1.0 N C:ALA126 4.5 36.6 1.0 O C:HOH546 4.5 38.4 1.0 CA C:ALA126 4.5 34.4 1.0 OD1 C:ASN168 4.6 32.3 1.0 N C:ASP8 4.7 36.0 1.0 CG C:ASN37 4.7 51.0 1.0 CB C:ASP239 4.7 28.4 1.0 ND2 C:ASN168 4.7 31.6 1.0 N C:ASP13 4.8 27.0 1.0 CA C:ASP13 4.8 30.6 1.0 CB C:ALA126 4.9 34.8 1.0 O C:ASP8 4.9 30.7 1.0 CB C:ASP8 4.9 35.5 1.0 OD2 C:ASP12 4.9 36.7 1.0 CG C:ASP12 4.9 28.2 1.0 C C:ASP8 5.0 31.1 1.0

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


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 Imh within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:61.9 occ:1.00 O D:LEU125 2.3 41.0 1.0 O2' D:IMH401 2.3 52.7 1.0 OD1 D:ASP8 2.3 43.6 1.0 OD1 D:ASP13 2.6 42.6 1.0 OD2 D:ASP13 2.6 36.3 1.0 O3' D:IMH401 2.7 46.7 1.0 OD2 D:ASP239 2.7 34.8 1.0 CG D:ASP13 3.0 42.3 1.0 CG D:ASP8 3.3 40.4 1.0 OD1 D:ASP239 3.4 44.1 1.0 CG D:ASP239 3.4 43.0 1.0 ND2 D:ASN37 3.4 41.9 1.0 OD2 D:ASP8 3.5 46.6 1.0 C2' D:IMH401 3.5 50.0 1.0 C D:LEU125 3.6 43.2 1.0 C3' D:IMH401 3.7 50.1 1.0 OD1 D:ASP12 4.2 38.7 1.0 CB D:LEU125 4.2 38.8 1.0 CG D:ASN37 4.3 45.1 1.0 ND2 D:ASN168 4.4 44.6 1.0 CA D:LEU125 4.4 40.4 1.0 CB D:ASP13 4.4 41.1 1.0 C1' D:IMH401 4.4 56.1 1.0 OD1 D:ASN37 4.5 50.6 1.0 CA D:ALA126 4.5 38.5 1.0 N D:ALA126 4.5 41.0 1.0 OD1 D:ASN168 4.5 47.1 1.0 N D:ASP8 4.6 37.8 1.0 C4' D:IMH401 4.7 46.7 1.0 CB D:ASP8 4.7 37.5 1.0 OD2 D:ASP12 4.7 45.0 1.0 N4' D:IMH401 4.7 55.5 1.0 O D:ASP8 4.8 38.5 1.0 CB D:ALA126 4.8 39.5 1.0 CG D:ASP12 4.8 43.7 1.0 CB D:ASP239 4.9 42.8 1.0 C D:ASP8 4.9 40.4 1.0 CG D:ASN168 5.0 43.9 1.0 N D:ASP13 5.0 33.1 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