Zinc in PDB 8h0i: Cryo-Em Structure of APOBEC3G-Vif Complex

The structure of Cryo-Em Structure of APOBEC3G-Vif Complex also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of APOBEC3G-Vif Complex (pdb code 8h0i). 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 APOBEC3G-Vif Complex, PDB code: 8h0i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of APOBEC3G-Vif Complex


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 APOBEC3G-Vif Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:57.5 occ:1.00 ND1 A:HIS53 2.3 28.9 1.0 SG A:CYS87 2.3 29.6 1.0 SG A:CYS84 2.3 28.5 1.0 CL A:CL403 2.3 35.6 1.0 CE1 A:HIS53 3.0 28.9 1.0 CB A:CYS87 3.1 29.6 1.0 CG A:HIS53 3.4 28.9 1.0 CB A:CYS84 3.4 28.5 1.0 N A:CYS84 3.5 28.5 1.0 OE1 A:GLU55 3.8 22.6 1.0 CB A:HIS53 3.8 28.9 1.0 CA A:CYS84 4.0 28.5 1.0 NE2 A:HIS53 4.2 28.9 1.0 N A:CYS87 4.3 29.6 1.0 CD A:GLU55 4.3 22.6 1.0 CA A:CYS87 4.3 29.6 1.0 CD2 A:HIS53 4.3 28.9 1.0 OE2 A:GLU55 4.4 22.6 1.0 C A:PRO83 4.5 20.1 1.0 CA A:PRO83 4.6 20.1 1.0 C A:CYS84 4.7 28.5 1.0 N4 X:C9 4.7 60.1 1.0 O A:CYS84 4.8 28.5 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of APOBEC3G-Vif Complex


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 APOBEC3G-Vif Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:202.7 occ:1.00 ND1 A:HIS240 2.0 140.3 1.0 SG A:CYS274 2.3 145.8 1.0 SG A:CYS271 2.3 152.4 1.0 CE1 A:HIS240 2.9 140.3 1.0 CG A:HIS240 3.0 140.3 1.0 CB A:HIS240 3.4 140.3 1.0 CB A:CYS271 3.4 152.4 1.0 CB A:CYS274 3.5 145.8 1.0 NE2 A:HIS240 4.0 140.3 1.0 CD2 A:HIS240 4.1 140.3 1.0 N A:CYS274 4.2 145.8 1.0 CA A:CYS274 4.4 145.8 1.0 CA A:CYS271 4.6 152.4 1.0 N A:CYS271 4.6 152.4 1.0 OE1 A:GLU242 4.6 119.9 1.0 CA A:HIS240 4.6 140.3 1.0 N A:HIS240 4.6 140.3 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of APOBEC3G-Vif Complex


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 APOBEC3G-Vif Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:58.5 occ:1.00 ND1 B:HIS53 2.3 28.8 1.0 SG B:CYS84 2.3 28.9 1.0 SG B:CYS87 2.3 29.5 1.0 CL B:CL403 2.3 36.6 1.0 CE1 B:HIS53 3.0 28.8 1.0 CB B:CYS87 3.1 29.5 1.0 CG B:HIS53 3.4 28.8 1.0 CB B:CYS84 3.4 28.9 1.0 N B:CYS84 3.5 28.9 1.0 OE1 B:GLU55 3.8 22.4 1.0 CB B:HIS53 3.8 28.8 1.0 CA B:CYS84 4.0 28.9 1.0 NE2 B:HIS53 4.2 28.8 1.0 N B:CYS87 4.3 29.5 1.0 CD B:GLU55 4.3 22.4 1.0 CA B:CYS87 4.3 29.5 1.0 CD2 B:HIS53 4.3 28.8 1.0 OE2 B:GLU55 4.4 22.4 1.0 C B:PRO83 4.5 19.4 1.0 CA B:PRO83 4.6 19.4 1.0 C B:CYS84 4.7 28.9 1.0 N4 Y:C9 4.7 60.2 1.0 O B:CYS84 4.8 28.9 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of APOBEC3G-Vif Complex


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 APOBEC3G-Vif Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:200.8 occ:1.00 ND1 B:HIS240 2.0 140.2 1.0 SG B:CYS271 2.3 151.3 1.0 SG B:CYS274 2.3 144.8 1.0 CE1 B:HIS240 2.9 140.2 1.0 CG B:HIS240 3.0 140.2 1.0 CB B:CYS271 3.4 151.3 1.0 CB B:HIS240 3.4 140.2 1.0 CB B:CYS274 3.5 144.8 1.0 NE2 B:HIS240 4.0 140.2 1.0 CD2 B:HIS240 4.1 140.2 1.0 N B:CYS274 4.2 144.8 1.0 CA B:CYS274 4.4 144.8 1.0 CA B:CYS271 4.6 151.3 1.0 N B:CYS271 4.6 151.3 1.0 OE1 B:GLU242 4.7 119.7 1.0 CA B:HIS240 4.7 140.2 1.0 N B:HIS240 4.7 140.2 1.0

T.Kouno, S.Shibata, M.Shigematsu, J.Hyun, T.G.Kim, H.Matsuo, M.Wolf. Structural Insights Into Rna Bridging Between Hiv-1 Vif and Antiviral Factor APOBEC3G. Nat Commun V. 14 4037 2023.
ISSN: ESSN 2041-1723
PubMed: 37419875
DOI: 10.1038/S41467-023-39796-5