Calcium in PDB 1q8f: Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik

All present enzymatic activity of Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik:
3.2.2.8;

The structure of Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik, PDB code: 1q8f was solved by B.Giabbai, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.83 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.808, 85.707, 90.678, 112.95, 101.95, 85.92
R / Rfree (%)	15.3 / 17

The binding sites of Calcium atom in the Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik (pdb code 1q8f). 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 the E.Coli Pyrimidine Nucleoside Hydrolase Yeik, PDB code: 1q8f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik


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 the E.Coli Pyrimidine Nucleoside Hydrolase Yeik within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:13.2 occ:1.00 OD2 A:ASP240 2.3 9.8 1.0 O A:VAL124 2.4 9.1 1.0 OD1 A:ASP11 2.5 10.3 1.0 O A:HOH3022 2.5 11.2 1.0 OD1 A:ASP16 2.5 10.7 1.0 OD2 A:ASP16 2.5 10.9 1.0 O A:HOH3026 2.5 12.2 1.0 O3 A:GOL3001 2.6 13.9 1.0 CG A:ASP16 2.9 10.3 1.0 CG A:ASP240 3.4 9.9 1.0 C A:VAL124 3.5 9.3 1.0 CG A:ASP11 3.6 11.4 1.0 OD1 A:ASP240 3.6 9.7 1.0 C3 A:GOL3001 3.8 20.0 1.0 OD1 A:ASN40 3.8 13.4 1.0 OD2 A:ASP11 3.9 11.1 1.0 CA A:GLY125 4.2 9.7 1.0 N A:GLY125 4.3 9.5 1.0 CB A:ASP16 4.3 10.2 1.0 O2 A:GOL3001 4.4 22.9 1.0 OD1 A:ASN166 4.4 9.4 1.0 CG2 A:VAL124 4.5 9.9 1.0 ND2 A:ASN166 4.5 8.7 1.0 CB A:VAL124 4.5 9.7 1.0 OD1 A:ASP15 4.5 13.2 1.0 N A:ASP11 4.6 10.3 1.0 OD2 A:ASP15 4.6 13.2 1.0 C2 A:GOL3001 4.6 19.5 1.0 CA A:VAL124 4.6 9.7 1.0 O A:ASP11 4.6 11.4 1.0 CG A:ASN40 4.7 11.9 1.0 CB A:ASP240 4.7 8.2 1.0 N A:ASP16 4.8 10.6 1.0 CB A:ASP11 4.9 11.0 1.0 CG A:ASP15 4.9 12.9 1.0 CA A:ASP16 4.9 10.4 1.0 C A:ASP11 4.9 11.4 1.0 CG A:ASN166 4.9 10.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik


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 the E.Coli Pyrimidine Nucleoside Hydrolase Yeik within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:19.4 occ:1.00 OD2 B:ASP240 2.3 12.6 1.0 O B:VAL124 2.4 12.7 1.0 O B:HOH3041 2.5 18.9 1.0 OD2 B:ASP16 2.5 12.7 1.0 OD1 B:ASP11 2.5 11.8 1.0 O3 B:GOL3002 2.5 18.8 1.0 OD1 B:ASP16 2.6 13.7 1.0 O B:HOH3028 2.6 17.1 1.0 CG B:ASP16 2.9 12.2 1.0 CG B:ASP240 3.3 12.1 1.0 C B:VAL124 3.5 11.6 1.0 OD1 B:ASP240 3.6 14.3 1.0 CG B:ASP11 3.6 12.9 1.0 C3 B:GOL3002 3.7 24.1 1.0 OD1 B:ASN40 3.8 17.2 1.0 OD2 B:ASP11 3.9 12.8 1.0 CA B:GLY125 4.2 11.6 1.0 N B:GLY125 4.2 11.6 1.0 CB B:ASP16 4.3 11.5 1.0 O2 B:GOL3002 4.4 26.1 1.0 OD1 B:ASN166 4.4 13.1 1.0 OD1 B:ASP15 4.5 14.7 1.0 ND2 B:ASN166 4.5 11.3 1.0 CG2 B:VAL124 4.6 11.0 1.0 N B:ASP11 4.6 12.3 1.0 OD2 B:ASP15 4.6 14.6 1.0 CB B:VAL124 4.6 11.0 1.0 C2 B:GOL3002 4.6 24.3 1.0 O B:ASP11 4.6 12.5 1.0 CA B:VAL124 4.6 11.4 1.0 CG B:ASN40 4.7 13.3 1.0 N B:ASP16 4.7 12.7 1.0 CB B:ASP240 4.7 11.7 1.0 CG B:ASP15 4.8 15.2 1.0 CA B:ASP16 4.9 12.1 1.0 CB B:ASP11 4.9 12.2 1.0 CG B:ASN166 4.9 11.3 1.0 C B:ASP11 4.9 12.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik


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 the E.Coli Pyrimidine Nucleoside Hydrolase Yeik within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2003 b:11.9 occ:1.00 O C:VAL124 2.4 8.6 1.0 OD2 C:ASP240 2.4 9.1 1.0 OD2 C:ASP16 2.5 9.7 1.0 O C:HOH3047 2.5 12.9 1.0 OD1 C:ASP11 2.5 9.1 1.0 OD1 C:ASP16 2.5 10.6 1.0 O C:HOH3027 2.5 10.7 1.0 O3 C:GOL3003 2.7 12.5 1.0 CG C:ASP16 2.9 9.2 1.0 CG C:ASP240 3.4 9.0 1.0 C C:VAL124 3.5 8.3 1.0 CG C:ASP11 3.6 11.1 1.0 OD1 C:ASP240 3.7 8.5 1.0 OD1 C:ASN40 3.7 13.4 1.0 C3 C:GOL3003 3.8 19.0 1.0 OD2 C:ASP11 4.0 9.5 1.0 CA C:GLY125 4.2 8.1 1.0 N C:GLY125 4.3 8.8 1.0 CB C:ASP16 4.3 9.0 1.0 O2 C:GOL3003 4.3 21.4 1.0 OD1 C:ASN166 4.4 9.4 1.0 OD1 C:ASP15 4.5 11.9 1.0 CB C:VAL124 4.5 8.2 1.0 ND2 C:ASN166 4.5 8.0 1.0 CG2 C:VAL124 4.5 8.8 1.0 N C:ASP11 4.6 8.3 1.0 O C:ASP11 4.6 9.3 1.0 C2 C:GOL3003 4.6 18.3 1.0 CA C:VAL124 4.6 8.0 1.0 CG C:ASN40 4.7 10.2 1.0 OD2 C:ASP15 4.7 11.7 1.0 N C:ASP16 4.7 10.0 1.0 CB C:ASP240 4.8 8.7 1.0 CA C:ASP16 4.9 9.7 1.0 CG C:ASP15 4.9 12.1 1.0 CB C:ASP11 4.9 9.5 1.0 C C:ASP11 4.9 9.6 1.0 CG C:ASN166 4.9 8.3 1.0 ND2 C:ASN40 5.0 7.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the E.Coli Pyrimidine Nucleoside Hydrolase Yeik


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 the E.Coli Pyrimidine Nucleoside Hydrolase Yeik within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2004 b:11.9 occ:1.00 O D:VAL124 2.4 7.4 1.0 O D:HOH3039 2.4 11.4 1.0 OD2 D:ASP240 2.4 8.3 1.0 OD1 D:ASP11 2.5 11.3 1.0 OD2 D:ASP16 2.5 8.7 1.0 O D:HOH3023 2.5 10.1 1.0 OD1 D:ASP16 2.5 10.0 1.0 O3 D:GOL3004 2.7 12.7 1.0 CG D:ASP16 2.9 8.7 1.0 CG D:ASP240 3.4 8.7 1.0 C D:VAL124 3.6 8.0 1.0 CG D:ASP11 3.6 11.3 1.0 OD1 D:ASP240 3.7 8.1 1.0 OD1 D:ASN40 3.7 12.5 1.0 C3 D:GOL3004 3.8 18.6 1.0 OD2 D:ASP11 3.9 10.6 1.0 CA D:GLY125 4.3 7.2 1.0 N D:GLY125 4.3 7.5 1.0 CB D:ASP16 4.3 8.4 1.0 O2 D:GOL3004 4.4 20.7 1.0 OD1 D:ASP15 4.4 10.6 1.0 OD1 D:ASN166 4.5 9.0 1.0 CG2 D:VAL124 4.5 8.8 1.0 CB D:VAL124 4.5 6.8 1.0 N D:ASP11 4.5 8.3 1.0 ND2 D:ASN166 4.6 8.2 1.0 O D:ASP11 4.6 9.1 1.0 OD2 D:ASP15 4.6 10.6 1.0 C2 D:GOL3004 4.6 17.8 1.0 CA D:VAL124 4.6 7.7 1.0 CG D:ASN40 4.7 9.6 1.0 CB D:ASP240 4.7 8.2 1.0 N D:ASP16 4.8 9.3 1.0 CG D:ASP15 4.8 12.0 1.0 CB D:ASP11 4.9 9.0 1.0 CA D:ASP16 4.9 8.8 1.0 C D:ASP11 4.9 9.0 1.0 ND2 D:ASN40 5.0 6.1 1.0 CG D:ASN166 5.0 8.4 1.0

B.Giabbai, M.Degano. Crystal Structure to 1.7 A of the Escherichia Coli Pyrimidine Nucleoside Hydrolase Yeik, A Novel Candidate For Cancer Gene Therapy. Structure V. 12 739 2004.
ISSN: ISSN 0969-2126
PubMed: 15130467
DOI: 10.1016/J.STR.2004.03.018