Calcium in PDB 9g8k: Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with CA2+ and Etidronate

The structure of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with CA2+ and Etidronate, PDB code: 9g8k was solved by K.Vidilaseris, J.Liu, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.22 / 3.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.742, 111.663, 105.199, 90, 106.67, 90
R / Rfree (%)	26.9 / 29.4

The structure of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with CA2+ and Etidronate also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

The binding sites of Calcium atom in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with CA2+ and Etidronate (pdb code 9g8k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with CA2+ and Etidronate, PDB code: 9g8k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with CA2+ and Etidronate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with CA2+ and Etidronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca806 b:89.9 occ:1.00 O A:HOH901 2.3 87.2 1.0 O14 A:911801 2.5 112.1 1.0 NZ A:LYS695 2.9 80.3 1.0 HO14 A:911801 3.0 136.1 1.0 OD1 A:ASP692 3.2 82.7 1.0 OD1 A:ASP660 3.3 110.3 1.0 O2 A:911801 3.3 104.8 1.0 CE A:LYS695 3.5 81.5 1.0 O9 A:911801 3.6 105.2 1.0 C7 A:911801 3.6 131.3 1.0 CG A:ASP660 3.6 86.7 1.0 HO5 A:911801 3.7 165.8 1.0 O5 A:911801 3.8 136.8 1.0 P1 A:911801 3.8 148.3 1.0 CG A:ASP692 4.1 88.3 1.0 OD2 A:ASP660 4.1 84.0 1.0 CB A:ASP660 4.2 73.2 1.0 P8 A:911801 4.3 145.3 1.0 O A:HOH902 4.3 61.6 1.0 OD2 A:ASP692 4.3 108.0 1.0 OD1 A:ASP688 4.4 80.4 1.0 OD2 A:ASP688 4.7 106.1 1.0 OD2 A:ASP696 4.7 95.1 1.0 C16 A:911801 4.8 115.8 1.0 CD A:LYS695 4.9 70.0 1.0 MG A:MG802 4.9 85.3 1.0 CG A:ASP688 5.0 83.0 1.0

Calcium binding site 2 out of 2 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with CA2+ and Etidronate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with CA2+ and Etidronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca809 b:98.3 occ:1.00 OD1 B:ASP660 2.6 117.2 1.0 O14 B:911801 2.7 122.6 1.0 MG B:MG805 2.8 92.7 1.0 HO14 B:911801 2.8 148.8 1.0 OD1 B:ASP692 3.0 117.2 1.0 HO5 B:911801 3.2 166.3 1.0 CG B:ASP660 3.4 109.8 1.0 OD2 B:ASP692 3.5 140.4 1.0 OD2 B:ASP688 3.6 118.3 1.0 CG B:ASP692 3.6 122.7 1.0 OD1 B:ASP688 3.6 111.0 1.0 CG B:ASP688 3.8 111.6 1.0 O2 B:911801 3.8 120.7 1.0 CB B:ASP660 3.8 98.4 1.0 O5 B:911801 3.9 137.2 1.0 C7 B:911801 3.9 134.1 1.0 O9 B:911801 4.1 147.2 1.0 P1 B:911801 4.2 158.8 1.0 NZ B:LYS695 4.2 80.6 1.0 OD2 B:ASP660 4.2 106.0 1.0 CA B:ASP660 4.7 92.2 1.0 P8 B:911801 4.7 158.6 1.0 CB B:ASP688 4.8 111.8 1.0

J.Liu, A.Shah, Y.Ma, K.Hardman, N.G.Johansson, O.Ribeiro, A.Brookfield, A.Bowen, J.Yli-Kauhaluoma, H.Xhaard, L.J.Jeuken, A.Goldman, C.Pliotas, K.Vidilaseris. Conformational Dynamics and Asymmetry in Multimodal Inhibition of Membrane-Bound Pyrophosphatases Elife 2024.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.102288.1