Calcium in PDB 1j3b: Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8

The structure of Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8, PDB code: 1j3b was solved by M.Sugahara, M.Miyano, N.Kunishima, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.10 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.702, 129.910, 173.391, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 22.6

The binding sites of Calcium atom in the Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8 (pdb code 1j3b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8, PDB code: 1j3b:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8


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 Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:30.3 occ:1.00 O A:PHE133 2.6 26.9 1.0 O A:ASN131 2.7 28.2 1.0 O A:ARG130 2.8 23.4 1.0 O A:HOH3030 2.9 31.7 1.0 O A:GLY267 3.1 25.7 1.0 C A:ASN131 3.4 27.6 1.0 C A:GLY267 3.6 26.5 1.0 C A:PHE133 3.8 27.4 1.0 CA A:ASN131 3.8 26.1 1.0 C A:ARG130 3.9 24.5 1.0 CB A:PRO323 4.0 31.0 1.0 CA A:GLY267 4.1 26.0 1.0 O A:HOH3022 4.1 36.4 1.0 N A:ASN131 4.3 24.9 1.0 N A:PHE133 4.4 27.4 1.0 CA A:PRO323 4.4 29.8 1.0 N A:MET132 4.5 27.2 1.0 N A:GLY268 4.5 26.3 1.0 C A:MET132 4.6 28.4 1.0 CA A:PHE133 4.6 27.1 1.0 CA A:ILE134 4.7 26.4 1.0 N A:ILE134 4.7 26.8 1.0 N A:LEU135 4.8 26.6 1.0 CA A:GLY268 4.9 28.6 1.0 N A:GLY267 4.9 25.4 1.0 CG A:LEU135 5.0 33.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8


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 Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:31.8 occ:1.00 O B:PHE133 2.6 28.8 1.0 O B:ASN131 2.8 24.4 1.0 O B:ARG130 2.8 26.3 1.0 O B:HOH3104 3.0 30.5 1.0 O B:GLY267 3.0 30.1 1.0 C B:ASN131 3.5 24.6 1.0 C B:GLY267 3.6 29.0 1.0 C B:PHE133 3.8 29.3 1.0 CA B:ASN131 3.8 25.8 1.0 C B:ARG130 3.9 26.2 1.0 O B:HOH3069 4.0 38.0 1.0 CB B:PRO323 4.0 27.6 1.0 CA B:GLY267 4.1 27.6 1.0 CA B:PRO323 4.3 28.0 1.0 N B:ASN131 4.4 24.9 1.0 N B:PHE133 4.4 26.2 1.0 N B:MET132 4.5 23.8 1.0 N B:GLY268 4.5 29.6 1.0 CA B:ILE134 4.6 29.9 1.0 C B:MET132 4.6 26.5 1.0 N B:ILE134 4.7 28.3 1.0 CA B:PHE133 4.7 27.9 1.0 N B:LEU135 4.9 30.6 1.0 CA B:GLY268 4.9 30.8 1.0 N B:GLY267 5.0 26.4 1.0

M.Sugahara, N.Ohshima, Y.Ukita, M.Sugahara, N.Kunishima. Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8 Showing the Structural Basis of Induced Fit and Thermostability. Acta Crystallogr.,Sect.D V. 61 1500 2005.
ISSN: ISSN 0907-4449
PubMed: 16239727
DOI: 10.1107/S090744490502651X