Calcium in PDB 3mkm: Crystal Structure of the E. Coli Pyrimidine Nucleoside Hydrolase Yeik (Apo-Form)

All present enzymatic activity of Crystal Structure of the E. Coli Pyrimidine Nucleoside Hydrolase Yeik (Apo-Form):
3.2.2.8;

The structure of Crystal Structure of the E. Coli Pyrimidine Nucleoside Hydrolase Yeik (Apo-Form), PDB code: 3mkm was solved by G.Garau, A.Fornili, B.Giabbai, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.91 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.601, 85.231, 90.060, 66.65, 79.39, 85.30
R / Rfree (%)	18.5 / 22.3

The binding sites of Calcium atom in the Crystal Structure of the E. Coli Pyrimidine Nucleoside Hydrolase Yeik (Apo-Form) (pdb code 3mkm). 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 (Apo-Form), PDB code: 3mkm:
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 (Apo-Form)


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 (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:14.7 occ:1.00 O A:VAL124 2.3 15.2 1.0 OD1 A:ASP16 2.4 13.5 1.0 O A:HOH320 2.4 15.4 1.0 OD1 A:ASP11 2.4 14.7 1.0 OD2 A:ASP240 2.5 15.9 1.0 OD2 A:ASP16 2.6 14.7 1.0 O A:HOH405 2.6 16.8 1.0 O A:HOH361 2.7 20.4 1.0 CG A:ASP16 2.8 16.2 1.0 CG A:ASP240 3.5 17.1 1.0 C A:VAL124 3.5 15.3 1.0 CG A:ASP11 3.5 15.2 1.0 ND2 A:ASN40 3.7 16.8 1.0 OD1 A:ASP240 3.8 17.0 1.0 OD2 A:ASP11 3.9 15.0 1.0 CA A:GLY125 4.2 15.6 1.0 N A:GLY125 4.2 15.5 1.0 CB A:ASP16 4.3 16.7 1.0 OD1 A:ASP15 4.4 16.2 1.0 N A:ASP11 4.5 15.8 1.0 O A:HOH556 4.5 21.1 1.0 OD1 A:ASN166 4.5 12.0 1.0 O A:ASP11 4.6 15.8 1.0 CB A:VAL124 4.6 15.3 1.0 CG2 A:VAL124 4.6 14.7 1.0 ND2 A:ASN166 4.6 11.5 1.0 CA A:VAL124 4.6 15.0 1.0 O A:HOH423 4.6 16.9 1.0 CG A:ASN40 4.7 17.2 1.0 OD2 A:ASP15 4.8 16.1 1.0 CB A:ASP240 4.8 16.9 1.0 N A:ASP16 4.8 17.0 1.0 CB A:ASP11 4.8 15.3 1.0 C A:ASP11 4.9 16.1 1.0 CA A:ASP16 4.9 16.6 1.0 CG A:ASP15 4.9 16.9 1.0 OD1 A:ASN40 5.0 18.0 1.0 CA A:ASP11 5.0 15.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the E. Coli Pyrimidine Nucleoside Hydrolase Yeik (Apo-Form)


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 (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:14.8 occ:1.00 OD1 B:ASP11 2.4 16.1 1.0 O B:VAL124 2.4 16.3 1.0 OD1 B:ASP16 2.4 14.9 1.0 O B:HOH318 2.4 13.9 1.0 O B:HOH500 2.5 12.2 1.0 OD2 B:ASP240 2.5 17.8 1.0 OD2 B:ASP16 2.5 17.0 1.0 O B:HOH332 2.7 9.8 1.0 CG B:ASP16 2.8 18.2 1.0 CG B:ASP240 3.5 19.0 1.0 CG B:ASP11 3.5 17.4 1.0 C B:VAL124 3.5 16.2 1.0 ND2 B:ASN40 3.6 20.0 1.0 OD1 B:ASP240 3.8 18.6 1.0 OD2 B:ASP11 4.0 16.9 1.0 CA B:GLY125 4.2 16.4 1.0 N B:GLY125 4.2 16.1 1.0 CB B:ASP16 4.3 19.2 1.0 N B:ASP11 4.5 17.2 1.0 OD1 B:ASN166 4.5 12.3 1.0 O B:ASP11 4.6 18.2 1.0 CB B:VAL124 4.6 16.4 1.0 ND2 B:ASN166 4.6 13.1 1.0 CG2 B:VAL124 4.6 15.4 1.0 CA B:VAL124 4.6 15.8 1.0 CG B:ASN40 4.7 20.9 1.0 O B:HOH434 4.7 40.0 1.0 CB B:ASP11 4.8 17.3 1.0 N B:ASP16 4.8 20.3 1.0 C B:ASP11 4.8 18.2 1.0 CB B:ASP240 4.9 18.5 1.0 CA B:ASP16 4.9 19.4 1.0 CA B:ASP11 4.9 17.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the E. Coli Pyrimidine Nucleoside Hydrolase Yeik (Apo-Form)


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 (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:19.0 occ:1.00 O C:HOH504 2.3 19.1 1.0 O C:VAL124 2.4 20.0 1.0 OD1 C:ASP16 2.5 19.8 1.0 OD1 C:ASP11 2.5 20.8 1.0 OD2 C:ASP240 2.5 22.6 1.0 O C:HOH358 2.5 17.1 1.0 OD2 C:ASP16 2.6 21.5 1.0 O C:HOH335 2.6 8.4 1.0 CG C:ASP16 2.8 22.8 1.0 CG C:ASP240 3.5 23.5 1.0 C C:VAL124 3.6 20.2 1.0 ND2 C:ASN40 3.6 24.3 1.0 CG C:ASP11 3.6 21.5 1.0 OD1 C:ASP240 3.7 23.1 1.0 OD2 C:ASP11 4.0 20.9 1.0 CA C:GLY125 4.3 20.1 1.0 CB C:ASP16 4.3 24.2 1.0 N C:GLY125 4.3 20.1 1.0 OD1 C:ASN166 4.5 16.1 1.0 O C:ASP11 4.5 22.6 1.0 O C:HOH413 4.6 25.2 1.0 N C:ASP11 4.6 21.6 1.0 ND2 C:ASN166 4.6 16.8 1.0 CG2 C:VAL124 4.6 20.1 1.0 CG C:ASN40 4.6 24.7 1.0 CB C:VAL124 4.7 20.9 1.0 CA C:VAL124 4.7 19.9 1.0 O C:HOH558 4.8 28.8 1.0 N C:ASP16 4.8 25.5 1.0 CB C:ASP240 4.8 23.5 1.0 OD1 C:ASP15 4.8 35.2 1.0 CA C:ASP16 4.9 24.4 1.0 C C:ASP11 4.9 22.7 1.0 CB C:ASP11 4.9 21.4 1.0 OD1 C:ASN40 5.0 25.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the E. Coli Pyrimidine Nucleoside Hydrolase Yeik (Apo-Form)


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 (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:22.2 occ:1.00 O D:VAL124 2.3 20.8 1.0 O D:HOH331 2.4 17.6 1.0 OD2 D:ASP240 2.4 22.2 1.0 OD1 D:ASP11 2.5 21.5 1.0 O D:HOH510 2.5 20.4 1.0 OD1 D:ASP16 2.5 20.0 1.0 OD2 D:ASP16 2.6 22.2 1.0 O D:HOH438 2.8 36.4 1.0 CG D:ASP16 2.9 23.3 1.0 CG D:ASP240 3.4 22.9 1.0 C D:VAL124 3.5 20.8 1.0 CG D:ASP11 3.6 22.4 1.0 OD1 D:ASP240 3.6 22.2 1.0 ND2 D:ASN40 3.7 24.2 1.0 OD2 D:ASP11 4.0 21.9 1.0 CA D:GLY125 4.2 21.4 1.0 N D:GLY125 4.2 21.0 1.0 CB D:ASP16 4.4 24.6 1.0 OD1 D:ASN166 4.4 17.0 1.0 OD1 D:ASP15 4.4 28.2 1.0 ND2 D:ASN166 4.5 16.9 1.0 CB D:VAL124 4.5 21.1 1.0 CG2 D:VAL124 4.6 20.7 1.0 N D:ASP11 4.6 23.0 1.0 CA D:VAL124 4.6 20.5 1.0 O D:ASP11 4.7 23.9 1.0 O D:HOH402 4.7 17.4 1.0 CG D:ASN40 4.7 24.7 1.0 CB D:ASP240 4.7 22.8 1.0 OD2 D:ASP15 4.8 31.5 1.0 N D:ASP16 4.8 25.2 1.0 CA D:ASP16 4.9 24.3 1.0 CG D:ASP15 4.9 27.8 1.0 CB D:ASP11 4.9 22.7 1.0 CG D:ASN166 4.9 19.4 1.0 C D:ASP11 5.0 24.1 1.0 OD1 D:ASN40 5.0 25.5 1.0

A.Fornili, B.Giabbai, G.Garau, M.Degano. Energy Landscapes Associated with Macromolecular Conformational Changes From Endpoint Structures J.Am.Chem.Soc. V. 132 17570 2010.
ISSN: ISSN 0002-7863
PubMed: 21082835
DOI: 10.1021/JA107640U