Calcium in PDB 7s8d: Structure of Dna-Free Sgrai

The structure of Structure of Dna-Free Sgrai, PDB code: 7s8d was solved by N.C.Horton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.00 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.11, 72.379, 78.64, 90, 107.95, 90
R / Rfree (%)	20.2 / 24.6

The binding sites of Calcium atom in the Structure of Dna-Free Sgrai (pdb code 7s8d). 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 Dna-Free Sgrai, PDB code: 7s8d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Dna-Free Sgrai


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Dna-Free Sgrai within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:26.4 occ:0.62 O A:LEU150 2.2 21.0 1.0 OE2 A:GLU103 2.2 25.7 1.0 OD1 A:ASN149 2.4 21.5 1.0 O A:ASP188 2.4 16.9 1.0 O A:HOH601 2.5 24.2 1.0 O A:HOH714 3.0 27.8 1.0 C A:LEU150 3.2 17.0 1.0 N A:LEU150 3.3 17.3 1.0 C A:ASP188 3.4 16.9 1.0 CD A:GLU103 3.5 26.4 1.0 CG A:ASN149 3.6 25.7 1.0 CA A:ASP188 3.6 17.1 1.0 CA A:LEU150 3.8 17.2 1.0 CB A:ASP188 3.8 19.1 1.0 C A:ASN149 4.0 18.3 1.0 O A:HOH686 4.0 37.1 1.0 OE1 A:GLU103 4.2 38.4 1.0 O A:HOH546 4.3 20.3 1.0 N A:PRO151 4.3 20.7 1.0 CA A:ASN149 4.4 18.2 1.0 O A:HOH756 4.4 39.0 1.0 CB A:LEU150 4.4 12.1 1.0 ND2 A:ASN149 4.4 29.7 1.0 OD1 A:ASP188 4.5 23.9 1.0 CG A:GLU103 4.5 19.1 1.0 N A:LEU189 4.6 21.7 1.0 CG A:ASP188 4.6 22.2 1.0 CB A:ASN149 4.6 20.3 1.0 CA A:PRO151 4.7 25.5 1.0 O A:ASN149 4.8 18.5 1.0 C A:PRO151 4.8 23.8 1.0 O A:PRO151 4.9 22.8 1.0

Calcium binding site 2 out of 2 in the Structure of Dna-Free Sgrai


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Dna-Free Sgrai within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:31.3 occ:0.69 OD1 B:ASN149 2.4 26.4 1.0 O B:LEU150 2.4 20.8 1.0 O B:HOH598 2.5 25.7 1.0 OE2 B:GLU103 2.6 41.9 1.0 O B:HOH514 2.7 28.9 1.0 O B:ASP188 2.7 21.5 1.0 OE1 B:GLU103 2.9 36.7 1.0 CD B:GLU103 2.9 29.8 1.0 C B:ASP188 3.5 18.3 1.0 C B:LEU150 3.6 18.9 1.0 CG B:ASN149 3.6 28.0 1.0 N B:LEU150 3.7 19.1 1.0 CA B:ASP188 3.7 17.3 1.0 CB B:ASP188 3.8 19.7 1.0 CG B:GLU103 4.1 20.0 1.0 CA B:LEU150 4.2 22.5 1.0 ND2 B:ASN149 4.2 27.3 1.0 OD1 B:ASP188 4.3 24.1 1.0 C B:ASN149 4.4 23.1 1.0 CG B:ASP188 4.4 20.9 1.0 O B:HOH515 4.5 25.2 1.0 N B:PRO151 4.6 23.6 1.0 CA B:ASN149 4.7 16.0 1.0 CB B:ASN149 4.8 19.1 1.0 N B:LEU189 4.8 19.4 1.0 CB B:LEU150 4.8 22.6 1.0 CA B:PRO151 4.9 23.3 1.0 C B:PRO151 5.0 20.8 1.0

Z.Shan, N.Ghadirian, D.Lyumkis, N.C.Horton. Pretransition State and Apo Structures of the Filament-Forming Enzyme Sgrai Elucidate Mechanisms of Activation and Substrate Specificity. J.Biol.Chem. V. 298 01760 2022.
ISSN: ESSN 1083-351X
PubMed: 35202658
DOI: 10.1016/J.JBC.2022.101760