Zinc in PDB 7uu3: Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex

The structure of Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex, PDB code: 7uu3 was solved by H.J.Yang, S.-X.Li, X.-J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.70 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.709, 67.192, 79.624, 98.29, 108.72, 112.66
R / Rfree (%)	17 / 21

The binding sites of Zinc atom in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex (pdb code 7uu3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex, PDB code: 7uu3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:82.9 occ:1.00 ND1 A:HIS65 2.1 117.1 1.0 SG A:CYS97 2.3 101.2 1.0 SG A:CYS100 2.4 91.3 1.0 CE1 A:HIS65 3.0 112.8 1.0 CB A:CYS97 3.1 101.2 1.0 CG A:HIS65 3.1 112.2 1.0 CB A:CYS100 3.2 94.4 1.0 CB A:HIS65 3.5 106.7 1.0 N A:CYS97 3.6 95.8 1.0 OE2 A:GLU67 3.9 87.5 1.0 CA A:CYS97 3.9 100.3 1.0 OE1 A:GLU67 4.1 88.5 1.0 N A:CYS100 4.1 107.8 1.0 NE2 A:HIS65 4.1 113.0 1.0 CD A:GLU67 4.2 87.8 1.0 CD2 A:HIS65 4.2 113.6 1.0 CA A:CYS100 4.3 99.8 1.0 C A:CYS97 4.6 105.3 1.0 O A:ALA62 4.7 117.9 1.0 O A:CYS97 4.8 106.6 1.0 C A:PRO96 4.8 91.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:91.8 occ:1.00 ND1 A:HIS257 2.2 76.8 1.0 SG A:CYS290 2.3 77.5 1.0 SG A:CYS287 2.6 90.8 1.0 CE1 A:HIS257 3.0 80.2 1.0 CB A:CYS290 3.1 79.8 1.0 CG A:HIS257 3.1 75.2 1.0 CB A:CYS287 3.5 87.0 1.0 CB A:HIS257 3.5 74.7 1.0 N A:CYS287 3.6 79.2 1.0 NE2 A:HIS257 4.1 77.7 1.0 CA A:CYS287 4.1 83.4 1.0 CD2 A:HIS257 4.1 76.5 1.0 CA A:CYS290 4.3 81.9 1.0 N A:CYS290 4.4 86.4 1.0 C A:PRO286 4.6 76.5 1.0 CA A:PRO286 4.7 66.8 1.0 C A:CYS287 4.8 85.3 1.0 O A:CYS287 5.0 91.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:60.2 occ:1.00 ND1 B:HIS65 2.1 85.9 1.0 SG B:CYS97 2.2 61.3 1.0 SG B:CYS100 2.3 68.6 1.0 CE1 B:HIS65 3.0 75.7 1.0 CG B:HIS65 3.2 73.4 1.0 CB B:CYS100 3.2 67.4 1.0 CB B:CYS97 3.3 62.7 1.0 CB B:HIS65 3.5 69.2 1.0 N B:CYS97 3.8 60.7 1.0 N B:CYS100 4.0 70.7 1.0 OE2 B:GLU67 4.1 83.5 1.0 CA B:CYS97 4.1 60.7 1.0 NE2 B:HIS65 4.2 72.3 1.0 OE1 B:GLU67 4.2 80.8 1.0 CA B:CYS100 4.2 67.8 1.0 CD2 B:HIS65 4.2 72.2 1.0 CD B:GLU67 4.4 80.5 1.0 C B:CYS97 4.7 63.7 1.0 O B:CYS97 4.9 62.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:101.0 occ:1.00 SG B:CYS290 2.3 104.1 1.0 ND1 B:HIS257 2.3 113.7 1.0 SG B:CYS287 2.8 112.8 1.0 CG B:HIS257 3.1 111.3 1.0 CE1 B:HIS257 3.2 116.8 1.0 CB B:CYS290 3.4 108.3 1.0 CB B:CYS287 3.4 114.7 1.0 CB B:HIS257 3.4 105.9 1.0 N B:CYS287 3.7 107.5 1.0 CA B:CYS287 4.1 110.5 1.0 CD2 B:HIS257 4.2 113.3 1.0 NE2 B:HIS257 4.2 114.7 1.0 CA B:CYS290 4.6 112.5 1.0 N B:CYS290 4.7 116.9 1.0 C B:PRO286 4.8 108.2 1.0 CA B:PRO286 4.9 99.1 1.0 CA B:HIS257 4.9 97.1 1.0 C B:CYS287 5.0 111.2 1.0

H.Yang, K.Kim, S.Li, J.Pacheco, X.S.Chen. Structural Basis of Sequence-Specific Rna Recognition By the Antiviral Factor APOBEC3G. Nat Commun V. 13 7498 2022.
ISSN: ESSN 2041-1723
PubMed: 36470880
DOI: 10.1038/S41467-022-35201-9