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Calcium in PDB 2pc9: Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8

Enzymatic activity of Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8

All present enzymatic activity of Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8:
4.1.1.49;

Protein crystallography data

The structure of Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8, PDB code: 2pc9 was solved by M.Sugahara, 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) 39.91 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 109.695, 128.553, 178.991, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8 (pdb code 2pc9). 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 Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8, PDB code: 2pc9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2pc9

Go back to Calcium Binding Sites List in 2pc9
Calcium binding site 1 out of 4 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:Ca2001

b:43.7
occ:1.00
 O A:PHE133 2.4 28.8 1.0
O A:ARG130 2.8 29.4 1.0
O A:ASN131 2.9 21.5 1.0
O A:GLY267 3.0 27.2 1.0
O A:HOH3029 3.0 29.6 1.0
C A:ASN131 3.5 25.9 1.0
C A:PHE133 3.6 27.2 1.0
C A:GLY267 3.7 26.2 1.0
C A:ARG130 3.9 28.8 1.0
CA A:ASN131 3.9 26.3 1.0
CA A:GLY267 4.1 24.4 1.0
CA A:PRO323 4.3 22.9 1.0
N A:PHE133 4.3 26.0 1.0
CB A:PRO323 4.3 24.5 1.0
N A:ASN131 4.4 27.2 1.0
N A:MET132 4.5 27.3 1.0
C A:MET132 4.5 27.2 1.0
CA A:ILE134 4.5 27.9 1.0
N A:GLY268 4.6 24.3 1.0
N A:ILE134 4.6 28.0 1.0
CA A:PHE133 4.6 27.6 1.0
N A:LEU135 4.7 27.6 1.0
CG A:LEU135 4.7 32.3 1.0
O A:MET132 4.8 25.5 1.0
CA A:GLY268 4.9 23.9 1.0
N A:GLY267 5.0 25.7 1.0
CG A:PRO323 5.0 23.6 1.0

Calcium binding site 2 out of 4 in 2pc9

Go back to Calcium Binding Sites List in 2pc9
Calcium binding site 2 out of 4 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:Ca2002

b:81.2
occ:1.00
 O B:ASN131 2.7 47.1 1.0
O B:PHE133 2.8 55.8 1.0
O B:GLY267 2.9 48.4 1.0
O B:HOH3040 3.0 47.1 1.0
O B:ARG130 3.1 41.7 1.0
C B:ASN131 3.5 48.4 1.0
C B:GLY267 3.5 48.6 1.0
CA B:ASN131 3.9 47.6 1.0
C B:PHE133 3.9 55.1 1.0
CA B:GLY267 4.0 48.5 1.0
C B:ARG130 4.1 44.5 1.0
CB B:PRO323 4.4 42.9 1.0
N B:GLY268 4.4 48.2 1.0
O B:HOH3071 4.4 49.1 1.0
CA B:PRO323 4.4 43.5 1.0
N B:PHE133 4.5 54.3 1.0
N B:ASN131 4.5 46.3 1.0
N B:MET132 4.5 51.1 1.0
C B:MET132 4.7 53.4 1.0
CA B:ILE134 4.7 56.0 1.0
CA B:GLY268 4.7 49.4 1.0
N B:ILE134 4.8 55.4 1.0
CG B:PRO323 4.8 43.0 1.0
CA B:PHE133 4.8 54.5 1.0
N B:GLY267 4.9 48.8 1.0
O B:MET132 5.0 53.9 1.0

Calcium binding site 3 out of 4 in 2pc9

Go back to Calcium Binding Sites List in 2pc9
Calcium binding site 3 out of 4 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 3 of Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:57.2
occ:1.00
 O C:PHE133 2.6 39.0 1.0
O C:ARG130 2.8 36.8 1.0
O C:HOH3094 2.9 38.2 1.0
O C:ASN131 3.0 34.9 1.0
O C:GLY267 3.2 35.4 1.0
C C:ASN131 3.7 36.7 1.0
C C:GLY267 3.7 34.6 1.0
C C:PHE133 3.8 38.2 1.0
C C:ARG130 4.0 35.2 1.0
CA C:ASN131 4.0 36.4 1.0
CB C:PRO323 4.0 39.5 1.0
CA C:GLY267 4.1 33.4 1.0
N C:ASN131 4.5 35.6 1.0
CA C:PRO323 4.5 40.4 1.0
N C:PHE133 4.5 39.2 1.0
CA C:ILE134 4.5 36.4 1.0
N C:GLY268 4.6 34.1 1.0
N C:ILE134 4.6 36.4 1.0
N C:MET132 4.7 36.8 1.0
CA C:PHE133 4.7 38.5 1.0
C C:MET132 4.8 38.9 1.0
N C:LEU135 4.8 37.9 1.0
CG C:LEU135 4.9 38.8 1.0
CA C:GLY268 5.0 34.2 1.0

Calcium binding site 4 out of 4 in 2pc9

Go back to Calcium Binding Sites List in 2pc9
Calcium binding site 4 out of 4 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 4 of Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2004

b:46.7
occ:1.00
 O D:PHE133 2.6 29.6 1.0
O D:ASN131 2.7 23.7 1.0
O D:ARG130 2.8 27.7 1.0
O D:HOH3233 3.0 38.9 1.0
O D:GLY267 3.2 29.0 1.0
O D:HOH3033 3.3 33.5 1.0
C D:ASN131 3.4 25.7 1.0
C D:GLY267 3.7 29.0 1.0
CA D:ASN131 3.7 24.9 1.0
C D:PHE133 3.8 29.9 1.0
C D:ARG130 3.9 27.4 1.0
CB D:PRO323 4.0 28.2 1.0
O D:HOH3164 4.1 61.5 1.0
CA D:GLY267 4.2 28.1 1.0
N D:ASN131 4.3 26.0 1.0
CA D:PRO323 4.4 27.6 1.0
N D:PHE133 4.4 28.3 1.0
N D:MET132 4.4 26.2 1.0
N D:GLY268 4.4 30.3 1.0
C D:MET132 4.6 28.9 1.0
CA D:PHE133 4.7 29.0 1.0
CA D:ILE134 4.7 29.7 1.0
N D:ILE134 4.7 29.8 1.0
CA D:GLY268 4.8 31.3 1.0
CG D:LEU135 4.8 35.0 1.0
N D:LEU135 4.9 30.4 1.0
CA D:MET132 5.0 28.4 1.0
N D:GLY267 5.0 28.8 1.0

Reference:

M.Sugahara, N.Kunishima. Crystal Structure of Atp-Dependent Phosphoenolpyruvate Carboxykinase From Thermus Thermophilus HB8 To Be Published.
Page generated: Tue Jul 8 07:40:20 2025

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