Zinc in PDB 9b89: Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene in the Pre-Editing State

All present enzymatic activity of Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From HT2C Gene in the Pre-Editing State:
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 in the Pre-Editing State (pdb code 9b89). 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 in the Pre-Editing State, PDB code: 9b89:
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 in the Pre-Editing State


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 in the Pre-Editing State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:91.4 occ:1.00 ND1 A:HIS910 2.3 63.3 1.0 SG A:CYS966 2.3 65.2 1.0 SG A:CYS1036 2.3 67.5 1.0 CE1 A:HIS910 2.3 63.3 1.0 CB A:CYS966 2.6 65.2 1.0 N A:CYS966 3.2 65.2 1.0 CA A:CYS966 3.5 65.2 1.0 NE2 A:HIS910 3.6 63.3 1.0 CG A:HIS910 3.6 63.3 1.0 CB A:CYS1036 3.7 67.5 1.0 CD2 A:HIS910 4.2 63.3 1.0 OE2 A:GLU912 4.3 55.7 1.0 C A:PRO965 4.4 67.7 1.0 N A:CYS1036 4.5 67.5 1.0 C A:CYS966 4.5 65.2 1.0 CE A:LYS1003 4.5 77.3 1.0 CB A:HIS910 4.5 63.3 1.0 O A:CYS966 4.7 65.2 1.0 CA A:CYS1036 4.7 67.5 1.0 CD A:GLU912 4.8 55.7 1.0 CA A:PRO965 4.8 67.7 1.0 OE1 A:GLU912 5.0 55.7 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 in the Pre-Editing State


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 in the Pre-Editing State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1303 b:93.2 occ:1.00 ND1 A:HIS988 2.1 80.5 1.0 ND1 A:HIS1103 2.1 83.1 1.0 SG A:CYS1081 2.3 67.0 1.0 SG A:CYS1082 2.3 65.6 1.0 CE1 A:HIS1103 2.6 83.1 1.0 CE1 A:HIS988 2.8 80.5 1.0 CG A:HIS988 3.2 80.5 1.0 CG A:HIS1103 3.3 83.1 1.0 CB A:CYS1081 3.6 67.0 1.0 N A:CYS1082 3.7 65.6 1.0 CB A:HIS988 3.7 80.5 1.0 CB A:CYS1082 3.8 65.6 1.0 NE2 A:HIS1103 3.8 83.1 1.0 C A:CYS1081 4.0 67.0 1.0 CA A:CYS1082 4.0 65.6 1.0 NE2 A:HIS988 4.0 80.5 1.0 CB A:HIS1103 4.0 83.1 1.0 O A:THR1077 4.1 69.5 1.0 CD2 A:HIS1103 4.2 83.1 1.0 CD2 A:HIS988 4.2 80.5 1.0 CA A:CYS1081 4.3 67.0 1.0 CA A:HIS1103 4.5 83.1 1.0 O A:CYS1081 4.6 67.0 1.0 CB A:THR1077 4.7 69.5 1.0 N A:CYS1081 4.7 67.0 1.0 C A:THR1077 4.8 69.5 1.0 CA A:THR1077 4.9 69.5 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 in the Pre-Editing State


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 in the Pre-Editing State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:64.3 occ:1.00 CD2 B:HIS910 2.3 67.6 1.0 SG B:CYS1036 2.3 76.0 1.0 SG B:CYS966 2.3 73.4 1.0 NE2 B:HIS910 2.3 67.6 1.0 CG B:HIS910 3.2 67.6 1.0 CE1 B:HIS910 3.2 67.6 1.0 CB B:CYS966 3.4 73.4 1.0 N B:CYS966 3.6 73.4 1.0 CB B:CYS1036 3.6 76.0 1.0 ND1 B:HIS910 3.7 67.6 1.0 OE2 B:GLU912 3.9 67.7 1.0 CA B:CYS966 4.2 73.4 1.0 CB B:HIS910 4.3 67.6 1.0 CE B:LYS1003 4.3 84.6 1.0 NZ B:LYS1003 4.5 84.6 1.0 N B:CYS1036 4.6 76.0 1.0 CD B:GLU912 4.7 67.7 1.0 C B:PRO965 4.7 64.3 1.0 CA B:CYS1036 4.7 76.0 1.0 O B:GLU1008 4.8 75.2 1.0 CA B:PRO965 4.8 64.3 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 in the Pre-Editing State


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 in the Pre-Editing State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1303 b:98.7 occ:1.00 ND1 B:HIS988 2.0 89.7 1.0 ND1 B:HIS1103 2.0 74.2 1.0 SG B:CYS1082 2.3 88.5 1.0 SG B:CYS1081 2.3 85.5 1.0 CE1 B:HIS988 2.5 89.7 1.0 CE1 B:HIS1103 2.5 74.2 1.0 CB B:CYS1081 2.8 85.5 1.0 CG B:HIS988 3.1 89.7 1.0 CG B:HIS1103 3.2 74.2 1.0 N B:CYS1082 3.3 88.5 1.0 CB B:CYS1082 3.6 88.5 1.0 NE2 B:HIS988 3.6 89.7 1.0 C B:CYS1081 3.6 85.5 1.0 CA B:CYS1082 3.7 88.5 1.0 NE2 B:HIS1103 3.7 74.2 1.0 CA B:CYS1081 3.8 85.5 1.0 CB B:HIS988 3.9 89.7 1.0 CD2 B:HIS988 3.9 89.7 1.0 CB B:HIS1103 3.9 74.2 1.0 O B:THR1077 3.9 85.2 1.0 CD2 B:HIS1103 4.1 74.2 1.0 CA B:HIS1103 4.3 74.2 1.0 O B:CYS1081 4.4 85.5 1.0 N B:CYS1081 4.5 85.5 1.0 CB B:THR1077 4.7 85.2 1.0 C B:THR1077 4.8 85.2 1.0 CA B:THR1077 5.0 85.2 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