Zinc in PDB 7ygy: Crystal Structure of the ZN2+-Bound EFHD2/Swiprosin-1

The structure of Crystal Structure of the ZN2+-Bound EFHD2/Swiprosin-1, PDB code: 7ygy 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)	46.45 / 2.60
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	92.9, 92.9, 92.9, 90, 90, 90
R / Rfree (%)	22.9 / 26

The binding sites of Zinc atom in the Crystal Structure of the ZN2+-Bound EFHD2/Swiprosin-1 (pdb code 7ygy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the ZN2+-Bound EFHD2/Swiprosin-1, PDB code: 7ygy:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the ZN2+-Bound EFHD2/Swiprosin-1


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 EFHD2/Swiprosin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:94.3 occ:1.00 O A:HOH302 2.1 70.8 1.0 OD1 A:ASP145 2.1 80.1 1.0 OD1 A:ASP141 2.3 78.0 1.0 OD1 A:ASP143 2.4 82.8 1.0 OE2 A:GLU152 2.5 75.7 1.0 O A:LYS147 2.5 76.4 1.0 OE1 A:GLU152 2.5 70.4 1.0 CD A:GLU152 2.8 71.5 1.0 CG A:ASP145 3.2 80.5 1.0 CG A:ASP143 3.3 84.5 1.0 CG A:ASP141 3.3 78.2 1.0 C A:LYS147 3.6 73.2 1.0 OD2 A:ASP143 3.7 87.1 1.0 OD2 A:ASP145 3.7 88.7 1.0 CA A:ASP141 4.1 71.2 1.0 CB A:ASP141 4.1 67.3 1.0 N A:ASP145 4.1 77.9 1.0 OD2 A:ASP141 4.2 84.3 1.0 CG A:GLU152 4.2 67.3 1.0 N A:LYS147 4.3 75.7 1.0 CA A:LEU148 4.3 68.9 1.0 N A:SER149 4.3 66.9 1.0 N A:ASP143 4.3 76.9 1.0 CB A:ASP145 4.4 81.4 1.0 N A:LEU148 4.4 66.1 1.0 CA A:LYS147 4.5 72.9 1.0 C A:ASP141 4.6 75.2 1.0 N A:PHE144 4.6 80.1 1.0 CB A:ASP143 4.6 78.0 1.0 N A:SER146 4.6 79.9 1.0 N A:GLU142 4.6 74.2 1.0 CA A:ASP145 4.6 80.0 1.0 C A:ASP143 4.7 74.8 1.0 CA A:ASP143 4.7 76.6 1.0 C A:LEU148 4.8 67.3 1.0 C A:ASP145 4.8 81.1 1.0 CB A:GLU152 4.9 64.5 1.0 CD2 A:LEU148 4.9 64.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the ZN2+-Bound EFHD2/Swiprosin-1


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 EFHD2/Swiprosin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:75.0 occ:1.00 NE2 A:HIS130 2.3 73.6 1.0 NZ A:LYS134 2.5 77.6 1.0 CE A:LYS134 2.9 68.7 1.0 CD2 A:HIS130 3.0 65.7 1.0 CE1 A:HIS130 3.2 79.3 1.0 CD A:LYS134 4.0 84.8 1.0 CG A:HIS130 4.0 68.3 1.0 ND1 A:HIS130 4.1 88.6 1.0 CG A:LYS134 4.6 79.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the ZN2+-Bound EFHD2/Swiprosin-1


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 EFHD2/Swiprosin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:97.2 occ:1.00 OE1 A:GLU116 2.0 83.2 1.0 O A:HOH303 2.0 76.1 1.0 O A:HOH301 2.0 86.5 1.0 O A:PHE111 2.1 70.0 1.0 OD1 A:ASP105 2.2 80.0 1.0 OD1 A:ASP109 2.4 87.5 1.0 CD A:GLU116 2.7 80.9 1.0 OE2 A:GLU116 2.8 83.4 1.0 CG A:ASP105 3.2 79.0 1.0 C A:PHE111 3.2 69.6 1.0 CG A:ASP109 3.4 80.9 1.0 OD2 A:ASP109 3.8 78.3 1.0 OD2 A:ASP105 4.0 78.2 1.0 CA A:ILE112 4.1 63.6 1.0 CB A:ASP105 4.1 70.1 1.0 N A:ILE112 4.1 63.9 1.0 CA A:ASP105 4.1 73.0 1.0 CG A:GLU116 4.1 73.1 1.0 N A:PHE111 4.2 74.3 1.0 CA A:PHE111 4.2 74.5 1.0 N A:ASP113 4.3 58.5 1.0 N A:ASP109 4.4 76.9 1.0 OD1 A:ASP113 4.4 81.3 1.0 C A:ASP105 4.5 78.3 1.0 N A:GLY107 4.6 81.5 1.0 CG A:ASP113 4.6 80.0 1.0 CB A:ASP109 4.6 78.6 1.0 N A:ALA106 4.6 75.4 1.0 C A:ILE112 4.7 62.4 1.0 CB A:PHE111 4.7 72.0 1.0 N A:ARG108 4.7 81.6 1.0 CB A:GLU116 4.8 70.7 1.0 OD2 A:ASP113 4.9 77.3 1.0 CA A:ASP109 4.9 76.4 1.0 CA A:GLY107 4.9 82.5 1.0 C A:ASP109 5.0 81.2 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