Zinc in PDB 9b84: Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene

All present enzymatic activity of Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene:
3.5.4.37;

The binding sites of Zinc atom in the Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene (pdb code 9b84). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene, PDB code: 9b84:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:61.5 occ:1.00 SG A:CYS1036 2.3 21.9 1.0 ND1 A:HIS910 2.3 14.6 1.0 SG A:CYS966 2.3 34.6 1.0 CE1 A:HIS910 2.8 19.8 1.0 CG A:HIS910 3.1 8.3 1.0 O6 F:8AZ6 3.4 13.3 1.0 NZ A:LYS1003 3.6 23.8 1.0 NE2 A:HIS910 3.7 19.9 1.0 OE2 A:GLU912 3.7 23.0 1.0 CB A:HIS910 3.8 9.3 1.0 CD2 A:HIS910 3.9 11.5 1.0 CD A:LYS1003 3.9 16.7 1.0 CB A:CYS966 3.9 31.1 1.0 CB A:CYS1036 4.0 25.6 1.0 CD1 A:ILE913 4.0 7.2 1.0 C6 F:8AZ6 4.3 20.0 1.0 CE A:LYS1003 4.4 13.9 1.0 C5 F:8AZ6 4.5 20.0 1.0 N1 F:8AZ6 4.5 20.0 1.0 N A:CYS1036 4.6 26.0 1.0 CA A:CYS1036 4.7 19.4 1.0 C4 F:8AZ6 4.7 20.0 1.0 C2 F:8AZ6 4.8 20.0 1.0 N A:CYS966 4.8 26.7 1.0 N3 F:8AZ6 4.9 20.0 1.0 CD A:GLU912 4.9 19.5 1.0 N7 F:8AZ6 5.0 20.0 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1303 b:49.8 occ:1.00 ND1 A:HIS988 2.1 28.7 1.0 ND1 A:HIS1103 2.2 27.8 1.0 SG A:CYS1082 2.3 26.8 1.0 SG A:CYS1081 2.3 54.4 1.0 CG A:HIS988 2.5 30.1 1.0 CB A:HIS988 2.8 37.4 1.0 CG A:HIS1103 3.0 32.8 1.0 CE1 A:HIS988 3.1 25.4 1.0 CB A:HIS1103 3.2 38.2 1.0 CE1 A:HIS1103 3.2 29.0 1.0 CD2 A:HIS988 3.5 31.4 1.0 NE2 A:HIS988 3.8 27.3 1.0 CB A:CYS1081 3.8 31.5 1.0 CB A:CYS1082 3.9 33.1 1.0 O A:THR1077 4.0 43.4 1.0 CD2 A:HIS1103 4.1 33.1 1.0 CA A:HIS1103 4.2 37.5 1.0 NE2 A:HIS1103 4.2 26.5 1.0 CA A:HIS988 4.3 35.6 1.0 CB A:THR1077 4.4 33.1 1.0 C A:CYS1081 4.5 20.9 1.0 N A:CYS1082 4.6 19.5 1.0 C A:THR1077 4.6 35.3 1.0 CA A:CYS1081 4.7 27.0 1.0 CA A:CYS1082 4.8 28.4 1.0 CG2 A:THR1077 4.8 33.7 1.0 CA A:THR1077 4.8 32.3 1.0 O A:CYS1081 4.9 28.7 1.0 CD A:PRO990 5.0 43.2 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:91.1 occ:1.00 SG B:CYS966 2.3 3.8 1.0 ND1 B:HIS910 2.3 33.5 1.0 SG B:CYS1036 2.3 30.2 1.0 CE1 B:HIS910 2.3 32.0 1.0 CB B:CYS966 2.8 20.8 1.0 NE2 B:HIS910 3.5 20.0 1.0 CG B:HIS910 3.6 20.9 1.0 CB B:CYS1036 3.7 14.7 1.0 N B:CYS966 3.7 23.3 1.0 CA B:CYS966 3.9 23.3 1.0 CD2 B:HIS910 4.1 24.9 1.0 CB B:HIS910 4.5 22.7 1.0 O B:GLU1008 4.6 34.1 1.0 N B:CYS1036 4.6 24.5 1.0 CA B:CYS1036 4.8 5.4 1.0 C B:CYS966 4.8 15.6 1.0 OE2 B:GLU912 4.9 27.2 1.0 NZ B:LYS1003 5.0 20.4 1.0 C B:PRO965 5.0 24.7 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1303 b:72.2 occ:1.00 ND1 B:HIS988 2.0 37.3 1.0 ND1 B:HIS1103 2.1 29.1 1.0 SG B:CYS1082 2.3 44.4 1.0 SG B:CYS1081 2.3 37.2 1.0 CE1 B:HIS988 2.7 33.7 1.0 CE1 B:HIS1103 2.8 29.5 1.0 CB B:CYS1081 2.9 32.5 1.0 CG B:HIS1103 3.2 24.0 1.0 CG B:HIS988 3.3 36.9 1.0 N B:CYS1082 3.5 33.3 1.0 CB B:CYS1082 3.6 29.4 1.0 CB B:HIS1103 3.8 19.0 1.0 CA B:CYS1082 3.9 33.1 1.0 C B:CYS1081 3.9 31.4 1.0 NE2 B:HIS988 3.9 32.7 1.0 CB B:HIS988 3.9 37.0 1.0 CA B:CYS1081 4.0 30.3 1.0 NE2 B:HIS1103 4.0 31.9 1.0 O B:THR1077 4.0 39.8 1.0 CA B:HIS1103 4.2 22.8 1.0 CD2 B:HIS1103 4.2 26.8 1.0 CD2 B:HIS988 4.2 38.0 1.0 CB B:THR1077 4.4 30.2 1.0 O B:CYS1081 4.7 32.3 1.0 CA B:THR1077 4.7 24.8 1.0 N B:CYS1081 4.7 24.5 1.0 C B:THR1077 4.7 29.9 1.0 C B:HIS1103 4.9 20.3 1.0

X.Deng, L.Sun, M.Zhang, R.Basavaraj, J.Wang, Y.L.Weng, Y.Gao. Biochemical Profiling and Structural Basis of ADAR1-Mediated Rna Editing Mol.Cell 2025.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2025.02.017