Calcium in PDB 1ezr: Crystal Structure of Nucleoside Hydrolase From Leishmania Major

All present enzymatic activity of Crystal Structure of Nucleoside Hydrolase From Leishmania Major:
3.2.2.1;

The structure of Crystal Structure of Nucleoside Hydrolase From Leishmania Major, PDB code: 1ezr was solved by W.Shi, V.L.Schramm, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.800, 79.200, 109.800, 90.00, 91.60, 90.00
R / Rfree (%)	20.3 / 25.5

The binding sites of Calcium atom in the Crystal Structure of Nucleoside Hydrolase From Leishmania Major (pdb code 1ezr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Nucleoside Hydrolase From Leishmania Major, PDB code: 1ezr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Nucleoside Hydrolase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Nucleoside Hydrolase From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:22.8 occ:1.00 O A:THR126 2.5 12.0 1.0 OD2 A:ASP241 2.7 17.6 1.0 OD1 A:ASP10 2.7 2.9 1.0 OD2 A:ASP15 2.8 26.6 1.0 OD1 A:ASP15 3.1 13.4 1.0 CG A:ASP15 3.3 26.5 1.0 OD1 A:ASP241 3.4 2.8 1.0 CG A:ASP241 3.4 12.8 1.0 CG A:ASP10 3.6 13.1 1.0 C A:THR126 3.7 15.5 1.0 OD2 A:ASP10 3.7 13.3 1.0 OD1 A:ASN168 4.1 28.4 1.0 ND2 A:ASN168 4.2 31.4 1.0 CA A:GLY127 4.3 27.3 1.0 OG1 A:THR126 4.4 31.0 1.0 N A:GLY127 4.4 27.2 1.0 CB A:THR126 4.4 16.8 1.0 CG A:ASN168 4.6 24.5 1.0 CA A:THR126 4.7 16.4 1.0 CB A:ASP15 4.8 19.1 1.0 CB A:ASP241 4.9 2.0 1.0 O A:ASP10 4.9 10.5 1.0 N A:ASP10 4.9 17.9 1.0 CB A:ASP14 4.9 28.2 1.0 N A:ASP15 5.0 13.9 1.0 CB A:ASP10 5.0 12.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Nucleoside Hydrolase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Nucleoside Hydrolase From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:35.1 occ:1.00 OD1 B:ASP10 2.6 31.9 1.0 O B:THR126 2.6 26.1 1.0 OD1 B:ASP15 2.8 29.7 1.0 OD2 B:ASP241 2.8 27.2 1.0 OD2 B:ASP15 2.9 18.6 1.0 CG B:ASP15 3.2 31.8 1.0 CG B:ASP10 3.5 35.9 1.0 OD1 B:ASP241 3.5 30.3 1.0 CG B:ASP241 3.5 30.5 1.0 OD2 B:ASP10 3.6 42.4 1.0 C B:THR126 3.8 23.1 1.0 OD1 B:ASN168 4.1 27.4 1.0 CA B:GLY127 4.4 25.1 1.0 ND2 B:ASN168 4.4 35.5 1.0 OG1 B:THR126 4.6 30.8 1.0 N B:GLY127 4.6 23.5 1.0 O B:ASP10 4.6 22.3 1.0 CB B:THR126 4.7 21.4 1.0 CB B:ASP15 4.7 27.2 1.0 CG B:ASN168 4.7 32.2 1.0 CA B:THR126 4.9 22.5 1.0 CB B:ASP10 4.9 33.6 1.0 N B:ASP10 4.9 28.7 1.0 CB B:ASP14 4.9 40.3 1.0 N B:ASP15 5.0 18.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Nucleoside Hydrolase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Nucleoside Hydrolase From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:42.9 occ:1.00 O C:THR126 2.4 31.1 1.0 OD1 C:ASP10 2.6 35.0 1.0 OD2 C:ASP241 2.7 38.9 1.0 OD2 C:ASP15 2.8 31.8 1.0 OD1 C:ASP15 3.0 33.2 1.0 CG C:ASP15 3.2 25.5 1.0 CG C:ASP241 3.5 38.0 1.0 CG C:ASP10 3.5 37.2 1.0 OD1 C:ASP241 3.5 28.8 1.0 C C:THR126 3.6 22.4 1.0 OD2 C:ASP10 3.6 28.4 1.0 OD1 C:ASN168 4.1 32.3 1.0 O C:HOH593 4.1 51.1 1.0 ND2 C:ASN168 4.1 23.8 1.0 CA C:GLY127 4.2 3.5 1.0 N C:GLY127 4.4 11.3 1.0 OG1 C:THR126 4.4 32.8 1.0 CB C:THR126 4.5 23.6 1.0 CG C:ASN168 4.6 22.9 1.0 CA C:THR126 4.7 21.4 1.0 O C:ASP10 4.7 26.5 1.0 CB C:ASP15 4.7 26.4 1.0 N C:ASP10 4.8 32.3 1.0 CB C:ASP10 4.9 33.4 1.0 CB C:ASP241 4.9 37.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Nucleoside Hydrolase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Nucleoside Hydrolase From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:33.1 occ:1.00 O D:THR126 2.5 8.1 1.0 OD1 D:ASP10 2.6 33.6 1.0 OD2 D:ASP241 2.6 16.8 1.0 OD2 D:ASP15 2.7 28.4 1.0 OD1 D:ASP15 2.8 45.0 1.0 CG D:ASP15 3.1 33.8 1.0 OD1 D:ASP241 3.3 23.5 1.0 CG D:ASP241 3.3 26.9 1.0 CG D:ASP10 3.5 29.3 1.0 C D:THR126 3.7 18.6 1.0 OD2 D:ASP10 3.8 30.4 1.0 OG1 D:THR126 4.3 7.6 1.0 OD1 D:ASN168 4.3 23.4 1.0 CB D:THR126 4.4 13.9 1.0 CA D:GLY127 4.4 30.0 1.0 ND2 D:ASN168 4.5 36.8 1.0 CB D:ASP15 4.5 33.1 1.0 N D:GLY127 4.5 23.2 1.0 O D:ASP10 4.6 31.1 1.0 CA D:THR126 4.7 19.0 1.0 N D:ASP10 4.8 25.4 1.0 N D:ASP15 4.8 28.6 1.0 CB D:ASP241 4.8 28.1 1.0 CG D:ASN168 4.9 27.5 1.0 CB D:ASP14 4.9 37.3 1.0 CB D:ASP10 4.9 24.3 1.0

W.Shi, V.L.Schramm, S.C.Almo. Nucleoside Hydrolase From Leishmania Major. Cloning, Expression, Catalytic Properties, Transition State Inhibitors, and the 2.5-A Crystal Structure. J.Biol.Chem. V. 274 21114 1999.
ISSN: ISSN 0021-9258
PubMed: 10409664
DOI: 10.1074/JBC.274.30.21114