Calcium in PDB 2hd9: Crystal Structure of PH1033 From Pyrococcus Horikoshii OT3

The structure of Crystal Structure of PH1033 From Pyrococcus Horikoshii OT3, PDB code: 2hd9 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)	31.96 / 1.35
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	39.891, 39.891, 168.481, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 23.4

The binding sites of Calcium atom in the Crystal Structure of PH1033 From Pyrococcus Horikoshii OT3 (pdb code 2hd9). 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 PH1033 From Pyrococcus Horikoshii OT3, PDB code: 2hd9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of PH1033 From Pyrococcus Horikoshii OT3


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 PH1033 From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:12.0 occ:1.00 O1 A:CIT1001 2.3 15.6 1.0 O1 A:CIT1002 2.4 15.8 1.0 O7 A:CIT1001 2.4 11.8 1.0 OE1 A:GLU86 2.4 12.3 1.0 O A:HOH3023 2.5 21.6 1.0 O7 A:CIT1002 2.5 14.4 1.0 O A:HOH3007 2.6 13.5 1.0 C1 A:CIT1002 3.2 17.3 1.0 CA A:CA2002 3.2 16.2 1.0 C1 A:CIT1001 3.3 15.6 1.0 C3 A:CIT1001 3.5 12.1 1.0 C3 A:CIT1002 3.5 15.0 1.0 CD A:GLU86 3.6 11.0 1.0 C2 A:CIT1001 3.7 13.8 1.0 C2 A:CIT1002 3.7 15.5 1.0 O5 A:CIT1002 3.8 13.0 1.0 C6 A:CIT1002 3.9 15.1 1.0 O5 A:CIT1001 4.0 13.8 1.0 C6 A:CIT1001 4.1 14.6 1.0 O A:HOH3060 4.2 23.7 1.0 CB A:GLU86 4.2 10.8 1.0 O2 A:CIT1002 4.2 17.7 1.0 O A:HOH3066 4.2 26.1 1.0 O A:HOH3005 4.3 14.3 1.0 CG A:GLU86 4.3 12.2 1.0 O2 A:CIT1001 4.4 17.2 1.0 O A:HOH3002 4.5 11.2 1.0 OE2 A:GLU86 4.5 11.7 1.0 C4 A:CIT1001 4.7 12.3 1.0 O3 A:CIT1001 4.8 12.4 1.0 CA A:GLU86 4.8 12.3 1.0 C4 A:CIT1002 4.8 14.4 1.0 O3 A:CIT1002 4.9 13.6 1.0 O6 A:CIT1002 4.9 15.0 1.0 CB A:PRO25 4.9 11.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of PH1033 From Pyrococcus Horikoshii OT3


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 PH1033 From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:16.2 occ:1.00 O7 A:CIT1001 1.9 11.8 1.0 O3 A:CIT1001 1.9 12.4 1.0 O7 A:CIT1002 1.9 14.4 1.0 O3 A:CIT1002 1.9 13.6 1.0 O5 A:CIT1002 2.0 13.0 1.0 O5 A:CIT1001 2.0 13.8 1.0 C3 A:CIT1002 2.7 15.0 1.0 C6 A:CIT1002 2.7 15.1 1.0 C3 A:CIT1001 2.7 12.1 1.0 C6 A:CIT1001 2.7 14.6 1.0 C5 A:CIT1001 2.9 13.8 1.0 C5 A:CIT1002 2.9 15.0 1.0 CA A:CA2001 3.2 12.0 1.0 C4 A:CIT1001 3.3 12.3 1.0 C4 A:CIT1002 3.3 14.4 1.0 O A:HOH3066 3.9 26.1 1.0 O6 A:CIT1002 3.9 15.0 1.0 O6 A:CIT1001 3.9 16.6 1.0 O1 A:CIT1002 4.0 15.8 1.0 O1 A:CIT1001 4.0 15.6 1.0 C2 A:CIT1002 4.0 15.5 1.0 O4 A:CIT1001 4.0 13.5 1.0 C2 A:CIT1001 4.0 13.8 1.0 O4 A:CIT1002 4.1 15.6 1.0 CA A:GLY84 4.2 14.8 1.0 CB A:GLU86 4.4 10.8 1.0 C1 A:CIT1002 4.5 17.3 1.0 C1 A:CIT1001 4.5 15.6 1.0 O A:HOH3023 4.6 21.6 1.0 N A:LYS85 4.7 13.6 1.0 OE1 A:GLU86 4.7 12.3 1.0 N A:GLU86 4.7 13.0 1.0 N A:GLY84 4.9 15.5 1.0 C A:GLY84 5.0 13.9 1.0

M.Sugahara, Y.Asada, Y.Morikawa, Y.Kageyama, N.Kunishima. Nucleant-Mediated Protein Crystallization with the Application of Microporous Synthetic Zeolites. Acta Crystallogr.,Sect.D V. 64 686 2008.
ISSN: ISSN 0907-4449
PubMed: 18560157
DOI: 10.1107/S0907444908009980