Zinc in PDB 7ygw: Crystal Structure of the ZN2+-Bound EFHD1/Swiprosin-2

The structure of Crystal Structure of the ZN2+-Bound EFHD1/Swiprosin-2, PDB code: 7ygw was solved by S.A.Mun, J.Park, J.Y.Kang, T.Park, M.Jin, J.Yang, S.H.Eom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.96 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.959, 47.393, 63.399, 90, 90, 90
R / Rfree (%)	19.8 / 21.1

The binding sites of Zinc atom in the Crystal Structure of the ZN2+-Bound EFHD1/Swiprosin-2 (pdb code 7ygw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the ZN2+-Bound EFHD1/Swiprosin-2, PDB code: 7ygw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the ZN2+-Bound EFHD1/Swiprosin-2


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 ZN2+-Bound EFHD1/Swiprosin-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:20.0 occ:0.57 OD1 A:ASP104 2.2 25.0 1.0 O A:PHE110 2.2 17.7 1.0 OD1 A:ASP108 2.3 25.2 1.0 O A:HOH306 2.4 26.2 1.0 OE1 A:GLU115 2.4 20.3 1.0 O A:HOH317 2.4 26.0 1.0 OE2 A:GLU115 2.6 23.2 1.0 CD A:GLU115 2.8 19.3 1.0 CG A:ASP108 3.2 27.1 1.0 CG A:ASP104 3.3 23.0 1.0 C A:PHE110 3.3 20.1 1.0 OD2 A:ASP108 3.6 28.5 1.0 N A:PHE110 4.0 21.3 1.0 OD2 A:ASP104 4.1 22.9 1.0 CA A:PHE110 4.2 21.1 1.0 CA A:ASP104 4.2 20.6 1.0 CB A:ASP104 4.2 19.5 1.0 OD2 A:ASP112 4.2 27.2 1.0 N A:ILE111 4.2 16.6 1.0 N A:ASP108 4.3 28.3 1.0 N A:GLY106 4.3 28.4 1.0 CA A:ILE111 4.3 14.8 1.0 CG A:GLU115 4.3 16.9 1.0 CB A:ASP108 4.4 26.6 1.0 N A:ASP112 4.4 15.8 1.0 C A:ASP104 4.5 25.3 1.0 CB A:PHE110 4.5 19.6 1.0 CA A:GLY106 4.5 29.8 1.0 N A:ARG107 4.5 30.7 1.0 CG A:ASP112 4.7 24.6 1.0 C A:GLY106 4.7 30.5 1.0 N A:ALA105 4.7 26.3 1.0 CA A:ASP108 4.8 27.1 1.0 C A:ILE111 4.9 17.2 1.0 N A:GLY109 4.9 25.7 1.0 O A:ASP104 5.0 27.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the ZN2+-Bound EFHD1/Swiprosin-2


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 ZN2+-Bound EFHD1/Swiprosin-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:16.9 occ:0.60 OD1 A:ASP140 2.1 18.7 1.0 O A:LYS146 2.3 16.0 1.0 OD1 A:ASP144 2.3 20.2 1.0 OD1 A:ASP142 2.3 21.0 1.0 OE1 A:GLU151 2.4 14.5 1.0 O A:HOH301 2.4 22.7 1.0 OE2 A:GLU151 2.7 18.5 1.0 CD A:GLU151 2.9 18.3 1.0 CG A:ASP142 3.3 24.0 1.0 CG A:ASP144 3.3 21.1 1.0 CG A:ASP140 3.3 16.4 1.0 C A:LYS146 3.5 14.1 1.0 OD2 A:ASP142 3.6 24.5 1.0 OD2 A:ASP144 3.7 23.3 1.0 OD2 A:ASP140 4.1 20.9 1.0 N A:LYS146 4.1 14.0 1.0 CA A:ASP140 4.2 17.1 1.0 N A:ASP144 4.2 18.2 1.0 N A:SER148 4.3 12.9 1.0 CB A:ASP140 4.3 17.8 1.0 N A:LEU147 4.4 12.6 1.0 CG A:GLU151 4.4 16.0 1.0 CA A:LEU147 4.4 12.1 1.0 CA A:LYS146 4.4 15.5 1.0 N A:ASP142 4.4 18.3 1.0 CB A:ASP144 4.5 19.7 1.0 C A:ASP140 4.6 18.0 1.0 CB A:ASP142 4.6 18.5 1.0 N A:PHE143 4.7 17.6 1.0 N A:GLU141 4.7 15.1 1.0 N A:GLY145 4.7 17.6 1.0 C A:LEU147 4.7 13.8 1.0 CA A:ASP144 4.7 17.3 1.0 CG A:LYS146 4.8 25.0 1.0 C A:ASP142 4.8 22.4 1.0 CA A:ASP142 4.9 19.2 1.0 C A:ASP144 4.9 20.4 1.0 OG A:SER148 5.0 16.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the ZN2+-Bound EFHD1/Swiprosin-2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the ZN2+-Bound EFHD1/Swiprosin-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:26.9 occ:0.30 O A:HOH331 2.2 31.9 1.0 ND1 A:HIS129 2.3 14.5 1.0 CE1 A:HIS129 3.1 18.5 1.0 CG A:HIS129 3.3 17.8 1.0 CB A:HIS129 3.7 14.2 1.0 NZ A:LYS117 4.0 33.9 1.0 NE2 A:HIS129 4.2 16.5 1.0 CD A:LYS117 4.4 27.2 1.0 CD2 A:HIS129 4.4 16.3 1.0 CA A:HIS129 4.4 15.5 1.0 CD2 A:LEU113 4.7 26.3 1.0 CE A:LYS117 4.8 35.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the ZN2+-Bound EFHD1/Swiprosin-2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the ZN2+-Bound EFHD1/Swiprosin-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:16.2 occ:0.62 NZ A:LYS133 1.8 26.7 1.0 NE2 A:HIS129 2.1 16.5 1.0 CE A:LYS133 2.6 22.4 1.0 CE1 A:HIS129 3.0 18.5 1.0 CD2 A:HIS129 3.1 16.3 1.0 CD A:LYS133 3.8 26.9 1.0 ND1 A:HIS129 4.1 14.5 1.0 CG A:HIS129 4.2 17.8 1.0 CG A:LYS133 4.5 24.9 1.0 CD2 A:LEU113 4.9 26.3 1.0 CD2 A:LEU130 4.9 20.6 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