Calcium in PDB 6vpq: Crystal Structure of the C-Terminal Domain of Denr

The structure of Crystal Structure of the C-Terminal Domain of Denr, PDB code: 6vpq was solved by I.B.Lomakin, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.67 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.670, 47.260, 95.500, 90.00, 106.29, 90.00
R / Rfree (%)	17.8 / 24.7

The structure of Crystal Structure of the C-Terminal Domain of Denr also contains other interesting chemical elements:

Magnesium

(Mg)

23 atoms

The binding sites of Calcium atom in the Crystal Structure of the C-Terminal Domain of Denr (pdb code 6vpq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the C-Terminal Domain of Denr, PDB code: 6vpq:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca208 b:90.9 occ:1.00 O B:GLU180 2.5 35.2 1.0 O B:HOH318 3.2 57.1 1.0 OE1 B:GLU180 3.5 51.8 0.6 C B:GLU180 3.6 37.9 1.0 O B:HOH366 3.8 56.9 1.0 O B:HOH380 3.9 64.2 1.0 CA B:GLU180 4.0 40.7 0.6 CA B:GLU180 4.0 41.3 0.5 CD B:GLU180 4.3 46.0 0.6 CG B:PRO183 4.4 42.1 1.0 CB B:GLU180 4.6 43.9 0.6 O B:HOH342 4.6 39.3 1.0 CD B:PRO183 4.6 30.5 1.0 CB B:GLU180 4.7 45.9 0.5 N B:LYS181 4.8 31.2 1.0 O B:GLN179 4.8 39.2 1.0 CB B:PRO183 4.8 36.9 1.0 OE2 B:GLU180 4.8 53.2 0.6

Calcium binding site 2 out of 3 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca206 b:95.5 occ:1.00 O A:HOH378 2.7 29.8 0.6 O C:HOH340 2.7 48.7 1.0 O C:HOH359 3.0 44.5 1.0 O C:HOH384 3.1 59.4 1.0 OE2 C:GLU163 3.2 43.6 1.0 CA C:GLY160 3.7 42.3 1.0 CD C:GLU163 3.9 45.5 1.0 O C:HOH312 3.9 64.7 1.0 NH1 A:ARG130 4.0 34.2 1.0 CB C:GLU163 4.1 37.4 1.0 O C:HOH370 4.1 48.7 1.0 N C:GLU161 4.4 42.4 1.0 C C:GLY160 4.5 43.3 1.0 OE1 C:GLU163 4.5 39.3 1.0 O C:THR159 4.6 42.9 1.0 CG C:GLU163 4.6 37.9 1.0 N C:GLY160 4.7 38.0 1.0 O C:HOH335 4.8 38.1 1.0 CZ A:ARG130 4.8 37.7 1.0 C C:THR159 5.0 43.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca204 b:95.5 occ:1.00 O D:HOH305 2.4 45.4 0.4 O D:HOH330 2.4 73.9 1.0 O D:HOH305 2.7 46.7 0.6 O D:HOH308 4.0 62.6 1.0 O D:HOH316 4.6 42.9 1.0 OD1 D:ASP187 4.8 62.5 1.0 OD2 D:ASP187 5.0 76.9 1.0

I.B.Lomakin, S.De, J.Wang, A.Borkar, T.A.Steitz. Crystal Structure of the C-Terminal Domain of Denr. Comp.Stuct.Biol.J 2020.
DOI: 10.1016/J.CSBJ.2020.03.009