Zinc in PDB 9b83: Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From Human GLI1 Gene

All present enzymatic activity of Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From Human GLI1 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 Human GLI1 Gene (pdb code 9b83). 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 Human GLI1 Gene, PDB code: 9b83:
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 Human GLI1 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 Human GLI1 Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:82.1 occ:1.00 O6 C:8AZ12 1.9 51.2 1.0 ND1 A:HIS910 2.3 66.0 1.0 SG A:CYS966 2.3 46.5 1.0 SG A:CYS1036 2.3 56.0 1.0 CE1 A:HIS910 2.4 59.6 1.0 CB A:CYS966 2.6 52.1 1.0 C6 C:8AZ12 2.8 40.1 1.0 C5 C:8AZ12 3.0 37.6 1.0 N A:CYS966 3.2 53.5 1.0 N7 C:8AZ12 3.4 49.3 1.0 N1 C:8AZ12 3.5 44.4 1.0 CA A:CYS966 3.5 49.5 1.0 CG A:HIS910 3.6 56.3 1.0 C4 C:8AZ12 3.7 39.8 1.0 CB A:CYS1036 3.7 46.1 1.0 NE2 A:HIS910 3.7 58.3 1.0 C2 C:8AZ12 4.1 45.7 1.0 N3 C:8AZ12 4.2 43.2 1.0 N8 C:8AZ12 4.2 47.3 1.0 CD2 A:HIS910 4.3 53.9 1.0 OE2 A:GLU912 4.3 64.9 1.0 N9 C:8AZ12 4.3 45.2 1.0 C A:PRO965 4.4 52.8 1.0 N A:CYS1036 4.5 46.2 1.0 CB A:HIS910 4.5 45.1 1.0 CE A:LYS1003 4.5 54.5 1.0 C A:CYS966 4.5 45.0 1.0 O A:CYS966 4.7 60.8 1.0 CA A:CYS1036 4.7 41.8 1.0 CA A:PRO965 4.8 41.9 1.0 CD A:GLU912 4.8 62.9 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From Human GLI1 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 Human GLI1 Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1303 b:116.0 occ:1.00 ND1 A:HIS1103 2.1 64.7 1.0 ND1 A:HIS988 2.1 79.1 1.0 SG A:CYS1082 2.3 79.7 1.0 SG A:CYS1081 2.3 79.2 1.0 CE1 A:HIS1103 2.6 58.1 1.0 CE1 A:HIS988 2.8 81.4 1.0 CG A:HIS988 3.2 78.4 1.0 CG A:HIS1103 3.3 59.2 1.0 CB A:CYS1081 3.6 65.6 1.0 N A:CYS1082 3.7 59.5 1.0 CB A:HIS988 3.7 78.4 1.0 CB A:CYS1082 3.8 72.4 1.0 NE2 A:HIS1103 3.8 54.8 1.0 C A:CYS1081 4.0 64.4 1.0 CA A:CYS1082 4.0 65.7 1.0 CB A:HIS1103 4.0 59.8 1.0 NE2 A:HIS988 4.0 79.5 1.0 O A:THR1077 4.1 76.7 1.0 CD2 A:HIS1103 4.2 59.0 1.0 CD2 A:HIS988 4.2 80.4 1.0 CA A:CYS1081 4.3 61.4 1.0 CA A:HIS1103 4.4 53.8 1.0 O A:CYS1081 4.6 74.7 1.0 CB A:THR1077 4.7 63.8 1.0 N A:CYS1081 4.7 63.2 1.0 C A:THR1077 4.8 67.9 1.0 CA A:THR1077 4.9 61.7 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From Human GLI1 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 Human GLI1 Gene within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:85.4 occ:1.00 CD2 B:HIS910 2.2 47.2 1.0 SG B:CYS1036 2.3 37.7 1.0 NE2 B:HIS910 2.3 46.4 1.0 SG B:CYS966 2.3 38.6 1.0 CG B:HIS910 3.1 44.3 1.0 CE1 B:HIS910 3.2 42.9 1.0 CB B:CYS966 3.5 35.2 1.0 ND1 B:HIS910 3.6 45.0 1.0 CB B:CYS1036 3.6 35.4 1.0 N B:CYS966 3.7 35.8 1.0 OE2 B:GLU912 3.8 35.9 1.0 CB B:HIS910 4.1 40.1 1.0 CA B:CYS966 4.2 32.1 1.0 CE B:LYS1003 4.3 47.4 1.0 NZ B:LYS1003 4.5 45.6 1.0 N B:CYS1036 4.6 37.8 1.0 CD B:GLU912 4.6 42.0 1.0 CA B:CYS1036 4.7 39.0 1.0 O B:GLU1008 4.8 57.7 1.0 C B:PRO965 4.8 36.6 1.0 CA B:PRO965 4.9 39.8 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of Human ADAR1 in Complex with Dsrna Derived From Human GLI1 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 Human GLI1 Gene within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1303 b:96.7 occ:1.00 ND1 B:HIS988 2.0 57.3 1.0 ND1 B:HIS1103 2.0 44.2 1.0 SG B:CYS1082 2.3 44.1 1.0 SG B:CYS1081 2.3 52.6 1.0 CE1 B:HIS988 2.5 54.9 1.0 CE1 B:HIS1103 2.6 42.0 1.0 CB B:CYS1081 2.8 46.3 1.0 CG B:HIS988 3.1 57.2 1.0 CG B:HIS1103 3.2 41.9 1.0 N B:CYS1082 3.3 37.6 1.0 NE2 B:HIS988 3.6 49.0 1.0 CB B:CYS1082 3.6 39.1 1.0 C B:CYS1081 3.6 40.5 1.0 CA B:CYS1082 3.7 39.3 1.0 NE2 B:HIS1103 3.7 43.7 1.0 CA B:CYS1081 3.8 42.2 1.0 CB B:HIS1103 3.9 42.5 1.0 CB B:HIS988 3.9 56.5 1.0 CD2 B:HIS988 3.9 54.9 1.0 O B:THR1077 4.0 44.7 1.0 CD2 B:HIS1103 4.0 44.1 1.0 CA B:HIS1103 4.3 47.1 1.0 O B:CYS1081 4.4 49.4 1.0 N B:CYS1081 4.5 48.2 1.0 CB B:THR1077 4.8 38.3 1.0 C B:THR1077 4.8 38.3 1.0 O B:ASN1102 4.9 35.0 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