Calcium in PDB 7ygv: Crystal Structure of the CA2+-Bound EFHD1/Swiprosin-2

The structure of Crystal Structure of the CA2+-Bound EFHD1/Swiprosin-2, PDB code: 7ygv was solved by S.A.Mun, J.Park, J.Y.Kang, T.Park, M.Jin, J.Ynag, S.H.Eom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.72 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.251, 47.907, 63.434, 90, 90, 90
R / Rfree (%)	19.5 / 25.2

The structure of Crystal Structure of the CA2+-Bound EFHD1/Swiprosin-2 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the CA2+-Bound EFHD1/Swiprosin-2 (pdb code 7ygv). 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 the CA2+-Bound EFHD1/Swiprosin-2, PDB code: 7ygv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the CA2+-Bound EFHD1/Swiprosin-2


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 CA2+-Bound EFHD1/Swiprosin-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:35.9 occ:1.00 OD1 A:ASP104 2.2 39.6 1.0 O A:HOH312 2.3 44.1 1.0 O A:HOH309 2.3 36.0 1.0 OE2 A:GLU115 2.4 36.0 1.0 OD1 A:ASP108 2.5 44.0 1.0 O A:PHE110 2.5 35.7 1.0 OE1 A:GLU115 2.5 35.5 1.0 CD A:GLU115 2.8 34.9 1.0 CG A:ASP108 3.4 38.8 1.0 CG A:ASP104 3.4 40.7 1.0 C A:PHE110 3.6 34.0 1.0 OD2 A:ASP108 3.8 43.0 1.0 N A:GLY106 4.0 42.8 1.0 CA A:ASP104 4.1 36.5 1.0 OD2 A:ASP104 4.2 41.8 1.0 OD2 A:ASP112 4.2 39.4 1.0 N A:ASP108 4.2 44.9 1.0 CB A:ASP104 4.2 36.9 1.0 CG A:GLU115 4.3 29.6 1.0 N A:ARG107 4.3 43.1 1.0 CA A:GLY106 4.3 39.2 1.0 C A:ASP104 4.3 38.2 1.0 N A:PHE110 4.4 38.5 1.0 N A:ILE111 4.5 30.6 1.0 CB A:ASP108 4.5 38.7 1.0 CA A:PHE110 4.5 35.9 1.0 N A:ALA105 4.5 39.4 1.0 CA A:ILE111 4.5 30.9 1.0 C A:GLY106 4.6 41.7 1.0 N A:ASP112 4.7 30.2 1.0 CG A:ASP112 4.7 36.5 1.0 O A:ASP104 4.8 34.1 1.0 CB A:PHE110 4.8 37.9 1.0 CA A:ASP108 4.9 43.9 1.0 N A:GLY109 5.0 41.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the CA2+-Bound EFHD1/Swiprosin-2


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 CA2+-Bound EFHD1/Swiprosin-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:33.0 occ:1.00 O A:HOH302 2.2 50.7 1.0 OD1 A:ASP142 2.3 39.0 1.0 OD1 A:ASP140 2.3 33.5 1.0 OD1 A:ASP144 2.4 36.5 1.0 OE1 A:GLU151 2.5 34.0 1.0 O A:LYS146 2.5 37.8 1.0 OE2 A:GLU151 2.7 34.8 1.0 CD A:GLU151 2.9 34.3 1.0 CG A:ASP142 3.2 38.2 1.0 CG A:ASP144 3.3 34.3 1.0 OD2 A:ASP142 3.4 41.7 1.0 CG A:ASP140 3.6 34.3 1.0 OD2 A:ASP144 3.6 39.2 1.0 C A:LYS146 3.7 36.5 1.0 N A:SER148 4.2 32.8 1.0 N A:ASP144 4.3 28.3 1.0 N A:LYS146 4.4 33.6 1.0 OD2 A:ASP140 4.4 30.7 1.0 CA A:ASP140 4.4 33.2 1.0 CG A:GLU151 4.4 31.9 1.0 CA A:LEU147 4.4 33.0 1.0 CB A:ASP144 4.4 30.9 1.0 N A:ASP142 4.4 33.9 1.0 N A:LEU147 4.4 33.6 1.0 CB A:ASP142 4.5 29.5 1.0 CB A:ASP140 4.5 30.8 1.0 CA A:LYS146 4.6 33.8 1.0 N A:PHE143 4.7 36.7 1.0 C A:LEU147 4.7 31.6 1.0 OG A:SER148 4.8 35.5 1.0 C A:ASP140 4.8 32.8 1.0 CA A:ASP144 4.8 32.5 1.0 CA A:ASP142 4.8 30.8 1.0 N A:GLU141 4.8 34.3 1.0 C A:ASP142 4.9 34.3 1.0 CB A:SER148 4.9 31.8 1.0 N A:GLY145 4.9 31.5 1.0 CG A:LYS146 4.9 41.5 1.0

S.A.Mun, J.Park, J.Y.Kang, T.Park, M.Jin, J.Yang, S.H.Eom. Structural and Biochemical Insights Into Zn 2+ -Bound Ef-Hand Proteins, EFHD1 and EFHD2. Iucrj V. 10 233 2023.
ISSN: ESSN 2052-2525
PubMed: 36862489
DOI: 10.1107/S2052252523001501