Zinc in PDB 8i3x: Rice APIP6-Ring Homodimer

The structure of Rice APIP6-Ring Homodimer, PDB code: 8i3x was solved by Y.Zheng, X.Zhang, Y.Liu, J.Liu, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.64 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.239, 46.577, 83.182, 90, 90, 90
R / Rfree (%)	18.6 / 23.2

The binding sites of Zinc atom in the Rice APIP6-Ring Homodimer (pdb code 8i3x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Rice APIP6-Ring Homodimer, PDB code: 8i3x:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Rice APIP6-Ring Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rice APIP6-Ring Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:30.0 occ:1.00 CD2 A:HIS61 2.2 36.9 1.0 SG A:CYS64 2.4 31.2 1.0 SG A:CYS38 2.4 36.8 1.0 SG A:CYS35 2.4 34.4 1.0 CB A:CYS35 3.1 34.1 1.0 CG A:HIS61 3.1 31.9 1.0 CB A:CYS64 3.3 34.3 1.0 CB A:CYS38 3.3 40.9 1.0 NE2 A:HIS61 3.3 35.1 1.0 CB A:HIS61 3.5 26.8 1.0 N A:CYS38 3.8 35.8 1.0 NH2 A:ARG49 4.0 40.6 1.0 N A:HIS61 4.0 31.1 1.0 CA A:CYS38 4.1 36.3 1.0 NH1 A:ARG49 4.2 48.0 1.0 ND1 A:HIS61 4.3 37.6 1.0 CA A:HIS61 4.4 26.2 1.0 CE1 A:HIS61 4.4 32.5 1.0 CZ A:ARG49 4.4 41.8 1.0 CA A:CYS35 4.5 30.2 1.0 CB A:ILE37 4.6 30.0 1.0 CA A:CYS64 4.7 30.1 1.0 C A:ILE37 4.8 36.2 1.0 C A:CYS38 4.8 38.4 1.0 O A:CYS35 4.8 30.3 1.0 N A:LEU39 4.9 38.2 1.0 C A:CYS35 4.9 29.7 1.0 O A:HOH259 4.9 43.7 1.0

Zinc binding site 2 out of 4 in the Rice APIP6-Ring Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rice APIP6-Ring Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:30.0 occ:1.00 CD2 A:HIS58 2.1 34.3 1.0 SG A:CYS80 2.3 37.9 1.0 SG A:CYS56 2.3 34.7 1.0 SG A:CYS77 2.4 31.1 1.0 CB A:CYS77 3.1 30.8 1.0 CG A:HIS58 3.1 35.9 1.0 NE2 A:HIS58 3.1 46.6 1.0 CB A:CYS56 3.3 40.9 1.0 CB A:CYS80 3.4 39.6 1.0 CB A:HIS58 3.6 35.9 1.0 N A:CYS80 3.7 35.0 1.0 CA A:CYS80 4.2 37.8 1.0 ND1 A:HIS58 4.3 40.9 1.0 CE1 A:HIS58 4.3 36.0 1.0 O A:HOH248 4.4 48.9 1.0 CB A:ASN79 4.4 36.5 1.0 N A:HIS58 4.5 35.0 1.0 CA A:CYS77 4.5 26.8 1.0 CA A:CYS56 4.6 41.8 1.0 C A:ASN79 4.7 37.3 1.0 O A:HOH249 4.7 38.9 1.0 CA A:HIS58 4.7 28.6 1.0 C A:CYS56 4.8 40.1 1.0 C A:CYS80 4.9 38.1 1.0 CA A:ASN79 4.9 33.5 1.0 N A:ASN79 4.9 29.1 1.0 O A:CYS56 5.0 44.5 1.0

Zinc binding site 3 out of 4 in the Rice APIP6-Ring Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rice APIP6-Ring Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:30.0 occ:1.00 ND1 B:HIS61 2.3 38.0 1.0 SG B:CYS38 2.3 44.4 1.0 SG B:CYS35 2.4 43.1 1.0 SG B:CYS64 2.4 39.2 1.0 CB B:CYS35 3.1 46.0 1.0 CE1 B:HIS61 3.2 42.9 1.0 CG B:HIS61 3.3 35.5 1.0 CB B:CYS64 3.3 31.5 1.0 CB B:CYS38 3.3 46.8 1.0 CB B:HIS61 3.5 37.1 1.0 N B:CYS38 3.7 50.8 1.0 NH2 B:ARG49 3.9 43.9 1.0 N B:HIS61 4.0 34.3 1.0 CA B:CYS38 4.1 50.8 1.0 NH1 B:ARG49 4.3 48.4 1.0 NE2 B:HIS61 4.3 42.5 1.0 CD2 B:HIS61 4.4 34.8 1.0 CA B:HIS61 4.4 34.9 1.0 CZ B:ARG49 4.4 46.0 1.0 CA B:CYS35 4.5 44.8 1.0 CB B:ILE37 4.5 44.2 1.0 CA B:CYS64 4.7 31.2 1.0 C B:ILE37 4.7 52.7 1.0 O B:CYS35 4.8 49.0 1.0 C B:CYS38 4.9 48.7 1.0 C B:CYS35 4.9 49.3 1.0 N B:ILE37 5.0 45.2 1.0 CG2 B:ILE37 5.0 44.3 1.0 CA B:ILE37 5.0 48.4 1.0

Zinc binding site 4 out of 4 in the Rice APIP6-Ring Homodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rice APIP6-Ring Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:30.0 occ:1.00 ND1 B:HIS58 2.2 79.0 1.0 SG B:CYS80 2.4 61.0 1.0 SG B:CYS77 2.4 57.6 1.0 SG B:CYS56 2.5 57.3 1.0 CE1 B:HIS58 2.6 68.9 1.0 CG B:HIS58 2.6 56.8 1.0 NE2 B:HIS58 3.2 64.1 1.0 CD2 B:HIS58 3.2 65.5 1.0 CB B:CYS77 3.3 48.2 1.0 CB B:CYS80 3.4 64.3 1.0 CB B:HIS58 3.4 48.8 1.0 N B:CYS80 3.6 62.6 1.0 CB B:CYS56 3.7 60.8 1.0 CB B:ASN79 4.0 61.4 1.0 CA B:CYS80 4.1 64.2 1.0 N B:HIS58 4.4 44.8 1.0 CA B:HIS58 4.5 44.3 1.0 C B:ASN79 4.6 67.2 1.0 CA B:ASN79 4.7 60.9 1.0 N B:ASN79 4.7 56.3 1.0 CA B:CYS77 4.8 40.8 1.0 CA B:CYS56 4.9 54.1 1.0 C B:CYS80 4.9 59.2 1.0 C B:CYS56 4.9 46.5 1.0 CG B:ASN79 5.0 59.0 1.0 O B:CYS56 5.0 54.8 1.0

Y.Zheng, X.Zhang, Y.Liu, T.Zhu, X.Wu, Y.Ning, J.Liu, D.Wang. Crystal Structure of Rice APIP6 Reveals A New Dimerization Mode of Ring-Type E3 Ligases That Facilities the Construction of Its Working Model Phytopathol Res V. 5 2023.
DOI: 10.1186/S42483-023-00186-W