Calcium in PDB 3fz0: Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)

All present enzymatic activity of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh):
3.2.2.1;

The structure of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh), PDB code: 3fz0 was solved by A.Vandemeulebroucke, C.Minici, I.Bruno, L.Muzzolini, P.Tornaghi, D.W.Parkin, V.L.Schramm, W.Versees, J.Steyaert, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	124.690, 116.040, 204.760, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.4

The binding sites of Calcium atom in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh) (pdb code 3fz0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh), PDB code: 3fz0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:63.8 occ:1.00 O A:HOH402 2.3 43.7 1.0 O A:LEU131 2.4 61.9 1.0 OD2 A:ASP280 2.5 64.9 1.0 O A:HOH386 2.5 38.5 1.0 OD1 A:ASP11 2.5 66.5 1.0 OD2 A:ASP16 2.6 62.6 1.0 OD1 A:ASP16 2.6 65.9 1.0 CG A:ASP16 2.9 63.0 1.0 CG A:ASP280 3.4 65.4 1.0 C A:LEU131 3.6 61.5 1.0 OD1 A:ASP280 3.6 67.3 1.0 CG A:ASP11 3.6 65.9 1.0 OD2 A:ASP11 4.1 65.6 1.0 O4 A:BTB401 4.3 50.3 1.0 CB A:LEU131 4.3 60.4 1.0 OD1 A:ASP15 4.4 64.7 1.0 CB A:ASP16 4.4 61.5 1.0 CA A:GLY132 4.5 62.0 1.0 C4 A:BTB401 4.5 55.4 1.0 CA A:LEU131 4.5 61.1 1.0 N A:GLY132 4.5 61.5 1.0 O3 A:BTB401 4.5 52.0 1.0 ND2 A:ASN179 4.6 58.4 1.0 OD1 A:ASN179 4.6 63.2 1.0 OD2 A:ASP15 4.6 63.1 1.0 N A:ASP11 4.6 64.8 1.0 CB A:ASP280 4.8 63.9 1.0 CG A:ASP15 4.8 64.4 1.0 CB A:ASP11 4.9 65.5 1.0 N A:ASP16 4.9 62.3 1.0

Calcium binding site 2 out of 4 in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:62.4 occ:1.00 O B:LEU131 2.3 62.3 1.0 O B:HOH410 2.3 33.9 1.0 OD2 B:ASP280 2.4 65.5 1.0 OD1 B:ASP11 2.4 66.2 1.0 O B:HOH409 2.4 28.7 1.0 OD2 B:ASP16 2.5 63.3 1.0 OD1 B:ASP16 2.6 65.6 1.0 O B:HOH408 2.7 45.1 1.0 CG B:ASP16 2.9 62.9 1.0 CG B:ASP280 3.4 65.4 1.0 C B:LEU131 3.5 61.5 1.0 OD1 B:ASP280 3.6 66.7 1.0 CG B:ASP11 3.6 65.6 1.0 O4 B:BTB401 3.9 51.3 1.0 OD2 B:ASP11 4.1 65.1 1.0 O B:HOH364 4.1 54.5 1.0 CB B:LEU131 4.2 60.4 1.0 O3 B:BTB401 4.2 50.7 1.0 CB B:ASP16 4.4 61.4 1.0 CA B:GLY132 4.4 61.7 1.0 N B:GLY132 4.4 61.3 1.0 CA B:LEU131 4.4 60.8 1.0 OD1 B:ASP15 4.5 64.4 1.0 N B:ASP11 4.6 64.7 1.0 ND2 B:ASN179 4.6 59.0 1.0 OD1 B:ASN179 4.7 63.4 1.0 CB B:ASP280 4.7 63.9 1.0 OD2 B:ASP15 4.8 63.8 1.0 CB B:ASP11 4.8 65.2 1.0 N B:ASP16 4.9 62.0 1.0 CG B:ASP15 5.0 64.6 1.0 CA B:ASP16 5.0 61.5 1.0 OG1 B:THR10 5.0 63.1 1.0

Calcium binding site 3 out of 4 in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca400 b:61.1 occ:1.00 O C:HOH410 2.3 43.2 1.0 OD1 C:ASP11 2.3 66.2 1.0 O C:LEU131 2.4 61.8 1.0 O C:HOH411 2.5 42.4 1.0 OD2 C:ASP16 2.5 63.2 1.0 OD2 C:ASP280 2.5 64.9 1.0 OD1 C:ASP16 2.6 65.7 1.0 O C:HOH407 2.6 45.1 1.0 CG C:ASP16 2.9 62.8 1.0 CG C:ASP11 3.5 65.9 1.0 CG C:ASP280 3.5 65.2 1.0 C C:LEU131 3.6 61.5 1.0 OD1 C:ASP280 3.7 67.1 1.0 OD2 C:ASP11 3.9 65.5 1.0 O4 C:BTB401 4.0 47.6 1.0 O3 C:BTB401 4.3 48.0 1.0 CB C:ASP16 4.3 61.7 1.0 CB C:LEU131 4.3 60.6 1.0 OD1 C:ASP15 4.4 64.5 1.0 CA C:GLY132 4.5 62.0 1.0 N C:ASP11 4.5 64.9 1.0 N C:GLY132 4.5 61.5 1.0 CA C:LEU131 4.6 61.1 1.0 ND2 C:ASN179 4.6 58.8 1.0 CB C:ASP11 4.7 65.5 1.0 OD1 C:ASN179 4.8 63.7 1.0 OD2 C:ASP15 4.8 63.2 1.0 CB C:ASP280 4.9 63.7 1.0 N C:ASP16 4.9 61.9 1.0 CA C:ASP16 4.9 61.6 1.0 CG C:ASP15 4.9 64.3 1.0 CA C:ASP11 4.9 65.7 1.0 OG1 C:THR10 5.0 63.1 1.0

Calcium binding site 4 out of 4 in the Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Inosine-Guanosine Nucleoside Hydrolase (Ig-Nh) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca400 b:60.2 occ:1.00 O D:HOH385 2.3 41.2 1.0 O D:LEU131 2.4 62.0 1.0 O D:HOH384 2.4 45.1 1.0 OD2 D:ASP280 2.4 65.0 1.0 OD2 D:ASP16 2.4 62.6 1.0 OD1 D:ASP11 2.5 66.5 1.0 OD1 D:ASP16 2.5 65.9 1.0 CG D:ASP16 2.8 62.8 1.0 CG D:ASP280 3.4 65.3 1.0 CG D:ASP11 3.6 65.8 1.0 C D:LEU131 3.6 61.6 1.0 OD1 D:ASP280 3.7 67.5 1.0 O3 D:BTB401 3.8 61.1 1.0 OD2 D:ASP11 4.0 65.8 1.0 CB D:LEU131 4.2 60.5 1.0 CB D:ASP16 4.3 61.6 1.0 OD1 D:ASP15 4.3 64.7 1.0 CA D:GLY132 4.5 61.9 1.0 CA D:LEU131 4.5 61.1 1.0 N D:GLY132 4.5 61.8 1.0 O1 D:BTB401 4.5 57.3 1.0 N D:ASP11 4.6 65.1 1.0 OD2 D:ASP15 4.7 63.4 1.0 OD1 D:ASN179 4.7 63.4 1.0 ND2 D:ASN179 4.8 59.0 1.0 CB D:ASP280 4.8 63.8 1.0 N D:ASP16 4.8 61.9 1.0 CB D:ASP11 4.8 65.2 1.0 CA D:ASP16 4.9 61.5 1.0 CG D:ASP15 4.9 64.4 1.0 OG1 D:THR10 5.0 63.2 1.0

A.Vandemeulebroucke, C.Minici, I.Bruno, L.Muzzolini, P.Tornaghi, D.W.Parkin, W.Versees, J.Steyaert, M.Degano. Structure and Mechanism of the 6-Oxopurine Nucleosidase From Trypanosoma Brucei Brucei Biochemistry V. 49 8999 2010.
ISSN: ISSN 0006-2960
PubMed: 20825170
DOI: 10.1021/BI100697D