Zinc in PDB 5w9a: The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B

All present enzymatic activity of The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B:
2.3.2.27;

The structure of The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B, PDB code: 5w9a was solved by J.R.Keown, D.C.Goldstone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.91 / 2.74
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.014, 115.319, 174.164, 90.00, 90.00, 90.00
R / Rfree (%)	26 / 27.4

The binding sites of Zinc atom in the The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B (pdb code 5w9a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B, PDB code: 5w9a:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.1 occ:1.00 SG A:CYS116 2.4 0.7 1.0 SG A:CYS97 2.4 0.0 1.0 SG A:CYS119 2.5 0.4 1.0 ND1 A:HIS100 3.1 0.9 1.0 CB A:CYS97 3.2 94.5 1.0 CB A:CYS116 3.2 0.8 1.0 N A:CYS116 3.6 0.0 1.0 CB A:HIS100 3.7 0.8 1.0 CG A:HIS100 3.8 0.1 1.0 CB A:CYS119 4.0 0.9 1.0 CA A:CYS116 4.0 98.1 1.0 CE1 A:HIS100 4.1 0.3 1.0 N A:HIS100 4.2 0.1 1.0 N A:CYS119 4.4 0.4 1.0 CA A:HIS100 4.5 0.6 1.0 C A:ILE115 4.6 0.8 1.0 CA A:CYS97 4.6 0.7 1.0 C A:CYS116 4.7 97.8 1.0 CA A:CYS119 4.7 0.4 1.0 CB A:ARG99 4.8 0.2 1.0 NH1 A:ARG99 4.9 0.8 1.0 CA A:ILE115 4.9 89.8 1.0 O A:CYS116 4.9 0.7 1.0 CD2 A:HIS100 5.0 0.2 1.0 CB A:ILE115 5.0 95.4 1.0

Zinc binding site 2 out of 4 in the The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:0.2 occ:1.00 OD2 A:ASP111 2.0 0.7 1.0 ND1 A:HIS125 2.3 0.4 1.0 SG A:CYS108 2.4 0.1 1.0 ND1 A:HIS128 2.7 0.1 1.0 CG A:ASP111 2.9 0.5 1.0 CG A:HIS125 3.0 0.2 1.0 CB A:HIS125 3.1 0.4 1.0 CE1 A:HIS125 3.4 0.1 1.0 CB A:CYS108 3.4 98.2 1.0 CB A:ASP111 3.4 0.8 1.0 CE1 A:HIS128 3.5 0.7 1.0 CA A:HIS125 3.8 0.5 1.0 CG A:HIS128 3.8 0.8 1.0 OD1 A:ASP111 3.9 0.5 1.0 CB A:HIS128 4.1 0.7 1.0 CD2 A:HIS125 4.2 0.9 1.0 NE2 A:HIS125 4.3 0.5 1.0 N A:ASP111 4.4 96.9 1.0 CA A:ASP111 4.5 98.1 1.0 O A:HIS125 4.5 0.4 1.0 C A:HIS125 4.6 0.2 1.0 NE2 A:HIS128 4.7 0.6 1.0 CD1 A:ILE115 4.8 94.4 1.0 CA A:CYS108 4.8 97.0 1.0 CD2 A:HIS128 4.8 0.9 1.0 O A:GLU124 4.8 0.3 1.0 N A:HIS125 4.9 0.7 1.0

Zinc binding site 3 out of 4 in the The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:75.8 occ:1.00 SG B:CYS116 2.4 98.8 1.0 ND1 B:HIS100 2.5 89.3 1.0 SG B:CYS119 2.6 82.8 1.0 SG B:CYS97 2.6 87.5 1.0 CB B:HIS100 3.1 92.1 1.0 CG B:HIS100 3.1 93.1 1.0 CB B:CYS97 3.3 83.8 1.0 CB B:CYS116 3.6 84.5 1.0 CE1 B:HIS100 3.7 87.9 1.0 N B:HIS100 3.7 95.2 1.0 CA B:HIS100 4.0 85.8 1.0 CB B:CYS119 4.1 86.8 1.0 N B:CYS116 4.2 71.4 1.0 N B:CYS119 4.3 93.0 1.0 CD2 B:HIS100 4.3 92.6 1.0 CA B:CYS116 4.4 72.1 1.0 NE2 B:HIS100 4.6 92.7 1.0 CB B:ARG99 4.6 0.3 1.0 N B:GLY101 4.7 90.7 1.0 CA B:CYS119 4.7 91.6 1.0 C B:ARG99 4.7 95.0 1.0 CB B:LEU118 4.8 74.2 1.0 C B:HIS100 4.8 83.1 1.0 CA B:CYS97 4.8 89.5 1.0

Zinc binding site 4 out of 4 in the The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of the TRIM5ALPHA Bbox- Coiled Coil in Complex LC3B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:84.3 occ:1.00 OD2 B:ASP111 2.1 0.1 1.0 ND1 B:HIS128 2.2 0.1 1.0 SG B:CYS108 2.4 71.9 1.0 ND1 B:HIS125 2.5 94.2 1.0 CG B:ASP111 3.0 0.8 1.0 CE1 B:HIS128 3.1 0.6 1.0 CB B:HIS125 3.1 88.3 1.0 CG B:HIS125 3.2 85.9 1.0 CG B:HIS128 3.3 99.7 1.0 CA B:HIS125 3.6 95.0 1.0 CB B:CYS108 3.6 73.8 1.0 CE1 B:HIS125 3.6 0.8 1.0 CB B:HIS128 3.7 81.7 1.0 CB B:ASP111 3.7 89.4 1.0 OD1 B:ASP111 3.8 0.3 1.0 NE2 B:HIS128 4.3 0.1 1.0 N B:ASP111 4.3 77.1 1.0 O B:HIS125 4.4 88.0 1.0 CD2 B:HIS128 4.4 1.0 1.0 C B:HIS125 4.4 94.4 1.0 CD2 B:HIS125 4.4 88.7 1.0 NE2 B:HIS125 4.6 92.0 1.0 O B:GLU124 4.6 85.2 1.0 CA B:ASP111 4.6 74.1 1.0 N B:HIS125 4.7 0.8 1.0 CB B:GLU110 4.9 93.0 1.0 CA B:CYS108 5.0 68.3 1.0

J.R.Keown, M.M.Black, A.Ferron, M.Yap, M.J.Barnett, F.G.Pearce, J.P.Stoye, D.C.Goldstone. A Helical LC3-Interacting Region Mediates the Interaction Between the Retroviral Restriction Factor TRIM5 Alpha and Mammalian Autophagy-Related ATG8 Proteins. J. Biol. Chem. V. 293 18378 2018.
ISSN: ESSN 1083-351X
PubMed: 30282803
DOI: 10.1074/JBC.RA118.004202