Zinc in PDB 7clt: Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein

The structure of Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein, PDB code: 7clt was solved by S.A.Mun, J.Park, K.R.Park, Y.Lee, J.Y.Kang, T.Park, M.Jin, J.Yang, C.D.Jun, S.H.Eom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.60 / 2.07
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.77, 47.556, 87.199, 90, 90, 90
R / Rfree (%)	20.9 / 22.9

The structure of Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein (pdb code 7clt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein, PDB code: 7clt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:21.4 occ:1.00 NE2 A:HIS157 1.9 23.9 1.0 OE1 A:GLU163 2.1 23.7 1.0 OE2 A:GLU163 2.7 25.6 1.0 CD A:GLU163 2.7 23.9 1.0 CE1 A:HIS157 2.8 26.1 1.0 CD2 A:HIS157 3.0 21.5 1.0 ND1 A:HIS157 4.0 26.7 1.0 CG A:HIS157 4.1 25.8 1.0 CG A:GLU163 4.2 24.5 1.0 CB A:ALA161 4.6 27.6 1.0 CG A:LYS158 4.9 21.5 1.0 CB A:GLU163 4.9 23.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:26.7 occ:1.00 OD1 A:ASP142 2.0 21.9 1.0 OD1 A:ASP144 2.0 20.7 1.0 O A:HOH420 2.2 12.7 1.0 CG A:ASP142 2.8 23.4 1.0 CG A:ASP144 3.0 20.9 1.0 OD2 A:ASP142 3.0 21.3 1.0 OD2 A:ASP144 3.4 17.0 1.0 CA A:CA302 3.6 19.1 1.0 CE2 A:PHE110 4.2 29.1 1.0 CB A:ASP142 4.2 18.6 1.0 CB A:ASP144 4.3 17.2 1.0 CE A:LYS146 4.5 26.3 1.0 O A:HOH413 4.6 25.2 1.0 CD2 A:PHE110 4.8 22.5 1.0 CG A:LYS146 4.8 19.1 1.0 CZ A:PHE110 4.8 25.3 1.0 O A:LYS146 4.9 15.3 1.0 OE1 A:GLU151 4.9 16.5 1.0 CB A:SER148 5.0 22.8 1.0

S.A.Mun, J.Park, K.R.Park, Y.Lee, J.Y.Kang, T.Park, M.Jin, J.Yang, C.D.Jun, S.H.Eom. Structural and Biochemical Characterization of EFHD1/Swiprosin-2, An Actin-Binding Protein in Mitochondria Front Cell Dev Biol 2020.
ISSN: ESSN 2296-634X
DOI: 10.3389/FCELL.2020.628222