Zinc in PDB 5k82: Crystal Structure of A Primate APOBEC3G N-Terminal Domain

The structure of Crystal Structure of A Primate APOBEC3G N-Terminal Domain, PDB code: 5k82 was solved by X.Xiao, S.-X.Li, H.Yang, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.30 / 2.91
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	152.395, 152.395, 79.778, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 25.1

The binding sites of Zinc atom in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain (pdb code 5k82). 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 A Primate APOBEC3G N-Terminal Domain, PDB code: 5k82:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain


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 A Primate APOBEC3G N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:93.0 occ:1.00 ND1 A:HIS65 1.8 1.0 1.0 SG A:CYS100 2.1 93.8 1.0 CE1 A:HIS65 2.6 0.6 1.0 SG A:CYS97 2.9 0.9 1.0 CG A:HIS65 2.9 0.2 1.0 CB A:CYS100 3.4 89.5 1.0 OE2 A:GLU67 3.4 0.0 1.0 CB A:HIS65 3.4 0.5 1.0 CB A:CYS97 3.4 87.3 1.0 NE2 A:HIS65 3.8 0.6 1.0 CD2 A:HIS65 3.9 0.4 1.0 CD A:GLU67 3.9 0.2 1.0 N A:CYS97 4.0 95.0 1.0 CB A:ALA62 4.1 0.8 1.0 CA A:CYS97 4.3 89.9 1.0 N A:CYS100 4.4 0.9 1.0 CA A:CYS100 4.5 98.6 1.0 OE1 A:GLU67 4.5 97.8 1.0 CG A:GLU67 4.5 95.2 1.0 CA A:ALA62 4.6 0.1 1.0 O A:ALA62 4.8 0.9 1.0 C A:CYS97 4.9 97.7 1.0 CA A:HIS65 4.9 0.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain


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 A Primate APOBEC3G N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:78.7 occ:1.00 ND1 B:HIS65 2.1 82.7 1.0 SG B:CYS100 2.3 71.6 1.0 SG B:CYS97 2.8 69.5 1.0 OE2 B:GLU67 2.9 91.9 1.0 CE1 B:HIS65 3.0 90.8 1.0 CB B:CYS97 3.1 66.2 1.0 CG B:HIS65 3.2 93.0 1.0 CB B:CYS100 3.3 71.5 1.0 CB B:HIS65 3.7 88.6 1.0 N B:CYS97 3.7 66.4 1.0 CD B:GLU67 3.8 84.4 1.0 CA B:CYS97 4.0 61.7 1.0 NE2 B:HIS65 4.2 99.2 1.0 CD2 B:HIS65 4.3 95.4 1.0 OE1 B:GLU67 4.4 84.3 1.0 CB B:ALA62 4.4 94.4 1.0 CA B:CYS100 4.5 73.5 1.0 N B:CYS100 4.6 79.2 1.0 CG B:GLU67 4.6 77.2 1.0 C B:CYS97 4.7 59.0 1.0 C B:PRO96 4.8 63.7 1.0 CA B:ALA62 4.9 0.7 1.0 O B:ALA62 5.0 0.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain


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 A Primate APOBEC3G N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:73.0 occ:1.00 ND1 C:HIS65 2.1 78.9 1.0 SG C:CYS100 2.3 76.3 1.0 SG C:CYS97 2.7 73.3 1.0 CE1 C:HIS65 2.9 85.1 1.0 CB C:CYS97 3.0 64.9 1.0 CB C:CYS100 3.2 75.3 1.0 CG C:HIS65 3.2 93.9 1.0 N C:CYS97 3.7 69.8 1.0 CB C:HIS65 3.7 86.0 1.0 OE1 C:GLU67 3.8 77.1 1.0 CA C:CYS97 3.9 58.0 1.0 NE2 C:HIS65 4.1 97.9 1.0 CD2 C:HIS65 4.3 98.4 1.0 CA C:CYS100 4.4 74.8 1.0 N C:CYS100 4.4 80.2 1.0 CD C:GLU67 4.5 84.9 1.0 OE2 C:GLU67 4.5 85.0 1.0 CB C:ALA62 4.6 98.3 1.0 C C:CYS97 4.6 59.7 1.0 C C:PRO96 4.9 60.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Primate APOBEC3G N-Terminal Domain


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 A Primate APOBEC3G N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:92.5 occ:1.00 ND1 D:HIS65 2.0 0.5 1.0 SG D:CYS100 2.1 91.6 1.0 SG D:CYS97 2.9 0.6 1.0 CE1 D:HIS65 2.9 0.5 1.0 CG D:HIS65 3.0 0.8 1.0 OE2 D:GLU67 3.3 0.0 1.0 CB D:CYS97 3.4 88.8 1.0 CB D:HIS65 3.4 0.3 1.0 CB D:CYS100 3.4 90.1 1.0 N D:CYS97 3.9 96.5 1.0 CD D:GLU67 3.9 0.8 1.0 NE2 D:HIS65 4.0 0.5 1.0 CD2 D:HIS65 4.0 0.4 1.0 CB D:ALA62 4.2 0.3 1.0 CA D:CYS97 4.2 92.7 1.0 O D:ALA62 4.4 1.0 1.0 N D:CYS100 4.5 0.8 1.0 OE1 D:GLU67 4.5 0.0 1.0 CA D:CYS100 4.5 0.4 1.0 CA D:ALA62 4.6 0.5 1.0 CG D:GLU67 4.7 92.1 1.0 C D:CYS97 4.8 98.3 1.0 CA D:HIS65 4.9 0.1 1.0 C D:ALA62 5.0 0.5 1.0

X.Xiao, S.X.Li, H.Yang, X.S.Chen. Crystal Structures of APOBEC3G N-Domain Alone and Its Complex with Dna. Nat Commun V. 7 12193 2016.
ISSN: ESSN 2041-1723
PubMed: 27480941
DOI: 10.1038/NCOMMS12193