Zinc in PDB 6voy: Cryo-Em Structure of Htlv-1 Instasome

The structure of Cryo-Em Structure of Htlv-1 Instasome also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Htlv-1 Instasome (pdb code 6voy). 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 Htlv-1 Instasome, PDB code: 6voy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of Htlv-1 Instasome


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 Htlv-1 Instasome within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.0 occ:1.00 ND1 A:HIS10 2.0 90.9 1.0 NE2 A:HIS6 2.0 93.8 1.0 CB A:CYS33 2.1 0.8 1.0 SG A:CYS36 2.2 99.4 1.0 SG A:CYS33 2.2 0.8 1.0 CE1 A:HIS10 2.2 90.9 1.0 CE1 A:HIS6 2.9 93.8 1.0 CD2 A:HIS6 3.1 93.8 1.0 CG A:HIS10 3.3 90.9 1.0 CA A:CYS33 3.5 0.8 1.0 NE2 A:HIS10 3.5 90.9 1.0 CB A:CYS36 3.6 99.4 1.0 N A:CYS36 3.8 99.4 1.0 ND1 A:HIS6 4.1 93.8 1.0 CD2 A:HIS10 4.1 90.9 1.0 CG A:HIS6 4.2 93.8 1.0 C A:CYS33 4.2 0.8 1.0 CB A:HIS10 4.2 90.9 1.0 O A:CYS33 4.3 0.8 1.0 CA A:CYS36 4.3 99.4 1.0 N A:CYS33 4.5 0.8 1.0 CB A:ALA35 4.6 0.4 1.0 O A:HIS6 4.9 93.8 1.0 C A:ALA35 4.9 0.4 1.0 CA A:HIS10 4.9 90.9 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of Htlv-1 Instasome


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 Htlv-1 Instasome within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:0.6 occ:1.00 NE2 B:HIS10 1.7 0.1 1.0 NE2 B:HIS6 1.9 0.7 1.0 CD2 B:HIS10 2.0 0.1 1.0 SG B:CYS33 2.2 0.4 1.0 SG B:CYS36 2.4 0.9 1.0 CD2 B:HIS6 2.7 0.7 1.0 CE1 B:HIS10 2.8 0.1 1.0 CE1 B:HIS6 3.0 0.7 1.0 CG B:HIS10 3.1 0.1 1.0 CB B:CYS36 3.5 0.9 1.0 ND1 B:HIS10 3.5 0.1 1.0 CB B:CYS33 3.5 0.4 1.0 O B:SER32 3.7 0.5 1.0 CG B:HIS6 3.9 0.7 1.0 ND1 B:HIS6 4.0 0.7 1.0 CB B:HIS10 4.4 0.1 1.0 C B:SER32 4.6 0.5 1.0 O B:ILE29 4.7 0.9 1.0 N B:CYS36 4.7 0.9 1.0 CA B:CYS36 4.7 0.9 1.0 OG B:SER32 4.7 0.5 1.0 CA B:CYS33 4.7 0.4 1.0 N B:CYS33 5.0 0.4 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of Htlv-1 Instasome


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 Htlv-1 Instasome within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:0.8 occ:1.00 NE2 C:HIS6 2.0 98.1 1.0 ND1 C:HIS10 2.0 91.5 1.0 CE1 C:HIS6 2.1 98.1 1.0 CB C:CYS36 2.1 95.5 1.0 SG C:CYS33 2.1 0.3 1.0 SG C:CYS36 2.4 95.5 1.0 CE1 C:HIS10 3.0 91.5 1.0 CG C:HIS10 3.1 91.5 1.0 CB C:CYS33 3.1 0.3 1.0 CD2 C:HIS6 3.4 98.1 1.0 ND1 C:HIS6 3.4 98.1 1.0 CB C:HIS10 3.5 91.5 1.0 CA C:CYS36 3.6 95.5 1.0 CG C:HIS6 4.0 98.1 1.0 CA C:HIS10 4.0 91.5 1.0 NE2 C:HIS10 4.1 91.5 1.0 N C:CYS36 4.2 95.5 1.0 CD2 C:HIS10 4.2 91.5 1.0 O C:CYS33 4.4 0.3 1.0 CA C:CYS33 4.5 0.3 1.0 C C:CYS36 4.6 95.5 1.0 NZ A:LYS168 4.7 68.2 1.0 C C:CYS33 4.9 0.3 1.0 C C:HIS10 4.9 91.5 1.0 CD2 C:LEU30 4.9 0.9 1.0 O C:HIS6 4.9 98.1 1.0 O C:CYS36 5.0 95.5 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of Htlv-1 Instasome


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 Htlv-1 Instasome within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.1 occ:1.00 CD2 D:HIS10 1.9 0.8 1.0 NE2 D:HIS10 2.0 0.8 1.0 NE2 D:HIS6 2.1 0.6 1.0 SG D:CYS36 2.4 0.2 1.0 SG D:CYS33 2.4 0.4 1.0 CE1 D:HIS6 2.5 0.6 1.0 CB D:CYS33 3.0 0.4 1.0 CG D:HIS10 3.2 0.8 1.0 CE1 D:HIS10 3.3 0.8 1.0 CD2 D:HIS6 3.4 0.6 1.0 O D:CYS33 3.6 0.4 1.0 CB D:CYS36 3.6 0.2 1.0 ND1 D:HIS10 3.8 0.8 1.0 ND1 D:HIS6 3.8 0.6 1.0 O D:SER32 4.2 0.1 1.0 CA D:CYS33 4.2 0.4 1.0 CG D:HIS6 4.2 0.6 1.0 CB D:HIS10 4.3 0.8 1.0 C D:CYS33 4.3 0.4 1.0 CA D:HIS10 4.6 0.8 1.0 C D:SER32 5.0 0.1 1.0

V.Bhatt, K.Shi, D.J.Salamango, N.H.Moeller, K.K.Pandey, S.Bera, T.E.Bohl, F.Kurniawan, K.Orellana, W.Zhang, D.P.Grandgenett, R.S.Harris, A.C.Sundborger-Lunna, H.Aihara. Structural Basis of Host Protein Hijacking in Human T-Cell Leukemia Virus Integration. Nat Commun V. 11 3121 2020.
ISSN: ESSN 2041-1723
PubMed: 32561747
DOI: 10.1038/S41467-020-16963-6