Calcium in PDB 1jn9: Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene

All present enzymatic activity of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene:
3.5.1.1;

The structure of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene, PDB code: 1jn9 was solved by D.Borek, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.941, 70.425, 148.862, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 23.2

The structure of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene (pdb code 1jn9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene, PDB code: 1jn9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:23.9 occ:1.00 O A:HOH487 2.2 29.7 1.0 O A:HOH414 2.3 36.0 1.0 O A:SER117 2.3 17.3 1.0 O A:HOH415 2.3 25.9 1.0 O A:HOH416 2.4 21.2 1.0 O A:MET114 2.4 16.1 1.0 O A:HOH413 2.5 14.1 1.0 C A:SER117 3.5 15.3 1.0 C A:MET114 3.6 16.1 1.0 CA A:PRO118 4.0 15.5 1.0 N A:PRO118 4.2 15.3 1.0 O A:HOH460 4.3 29.9 1.0 N A:SER117 4.3 15.2 1.0 O A:VAL113 4.4 15.7 1.0 N A:GLU115 4.4 15.8 1.0 CA A:GLU115 4.4 15.5 1.0 C A:GLU115 4.5 14.9 1.0 CA A:MET114 4.6 15.6 1.0 CA A:SER117 4.6 15.6 1.0 C A:PRO118 4.6 15.2 1.0 O A:GLU115 4.7 14.2 1.0 N A:GLN116 4.8 14.8 1.0 N A:HIS119 4.9 14.6 1.0 O A:HIS119 4.9 15.0 1.0 O A:HOH417 5.0 13.3 1.0 NZ A:LYS93 5.0 19.2 0.5 O A:HOH449 5.0 18.9 1.0

Calcium binding site 2 out of 3 in the Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:25.8 occ:1.00 O A:HOH470 2.1 21.4 1.0 O A:HOH469 2.3 22.1 1.0 O A:HOH468 2.3 20.7 1.0 OD2 A:ASP51 2.3 20.9 1.0 O A:HOH467 2.4 28.8 1.0 OD1 A:ASP51 2.8 14.7 1.0 CG A:ASP51 2.9 15.4 1.0 O A:HOH472 3.9 38.4 1.0 O A:HOH471 4.2 32.1 1.0 O A:HOH474 4.2 29.5 1.0 NH2 A:ARG111 4.3 20.6 1.0 O A:HOH454 4.4 26.9 1.0 CB A:ASP51 4.4 15.0 1.0 O A:HOH444 4.4 26.0 1.0 O A:HOH515 4.6 37.2 1.0 O A:HOH473 4.9 36.0 1.0

Calcium binding site 3 out of 3 in the Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca409 b:41.9 occ:1.00 O B:HOH453 2.3 40.8 1.0 O B:HOH454 2.5 39.7 1.0 OD1 B:ASP304 2.6 24.2 1.0 OD2 B:ASP304 2.8 24.3 1.0 CG B:ASP304 3.1 21.8 1.0 CB B:ASP304 4.6 20.1 1.0 N B:THR305 4.8 19.1 1.0 O B:HOH455 4.8 28.4 1.0

K.Michalska, D.Borek, A.Hernandez-Santoyo, M.Jaskolski. Crystal Packing of Plant-Type L-Asparaginase From Escherichia Coli. Acta Crystallogr.,Sect.D V. 64 309 2008.
ISSN: ISSN 0907-4449
PubMed: 18323626
DOI: 10.1107/S0907444907068072