Zinc in PDB 6yxe: Structure of the TRIM69 Ring Domain

All present enzymatic activity of Structure of the TRIM69 Ring Domain:
2.3.2.27;

The structure of Structure of the TRIM69 Ring Domain, PDB code: 6yxe 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)	65.46 / 2.10
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	109.965, 109.965, 90.135, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 24

The binding sites of Zinc atom in the Structure of the TRIM69 Ring Domain (pdb code 6yxe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the TRIM69 Ring Domain, PDB code: 6yxe:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the TRIM69 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the TRIM69 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:36.2 occ:1.00 SG A:CYS64 2.2 35.9 1.0 SG A:CYS44 2.3 38.4 1.0 SG A:CYS61 2.3 32.8 1.0 SG A:CYS41 2.4 35.5 1.0 CB A:CYS41 3.0 34.3 1.0 CB A:CYS61 3.2 31.6 1.0 CB A:CYS44 3.3 40.8 1.0 CB A:CYS64 3.3 34.7 1.0 N A:CYS44 3.8 41.0 1.0 N A:CYS61 3.9 30.5 1.0 CA A:CYS44 4.1 42.5 1.0 CA A:CYS61 4.1 31.0 1.0 CA A:CYS41 4.5 33.6 1.0 CA A:CYS64 4.7 35.2 1.0 CB A:LEU43 4.8 40.5 1.0 C A:LEU43 4.8 42.1 1.0 C A:CYS41 4.9 36.0 1.0 O A:CYS41 5.0 37.2 1.0 C A:CYS44 5.0 43.3 1.0

Zinc binding site 2 out of 4 in the Structure of the TRIM69 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the TRIM69 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:50.5 occ:1.00 ND1 A:HIS58 2.0 46.3 1.0 SG A:CYS56 2.3 46.6 1.0 SG A:CYS78 2.3 50.1 1.0 SG A:CYS81 2.3 61.2 1.0 CE1 A:HIS58 3.0 48.1 1.0 CG A:HIS58 3.0 43.6 1.0 CB A:CYS78 3.1 54.3 1.0 CB A:CYS56 3.3 51.4 1.0 CB A:HIS58 3.4 41.1 1.0 CB A:CYS81 3.5 63.6 1.0 N A:CYS81 3.8 62.5 1.0 NE2 A:HIS58 4.1 45.8 1.0 CD2 A:HIS58 4.2 43.5 1.0 CA A:CYS81 4.2 65.7 1.0 N A:HIS58 4.3 40.6 1.0 CB A:GLU80 4.5 63.1 1.0 CA A:HIS58 4.5 39.2 1.0 CA A:CYS78 4.6 55.0 1.0 CA A:CYS56 4.6 52.0 1.0 C A:CYS56 4.8 49.2 1.0 C A:GLU80 4.9 63.6 1.0 O A:CYS56 4.9 51.3 1.0 C A:CYS81 4.9 68.8 1.0

Zinc binding site 3 out of 4 in the Structure of the TRIM69 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the TRIM69 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:57.7 occ:1.00 SG B:CYS64 2.3 51.9 1.0 SG B:CYS61 2.3 53.7 1.0 SG B:CYS44 2.3 63.6 1.0 SG B:CYS41 2.3 51.2 1.0 CB B:CYS41 3.0 55.8 1.0 CB B:CYS61 3.2 50.2 1.0 CB B:CYS64 3.3 47.5 1.0 CB B:CYS44 3.3 63.5 1.0 N B:CYS44 3.8 58.4 1.0 N B:CYS61 3.9 44.2 1.0 CA B:CYS61 4.1 46.9 1.0 CA B:CYS44 4.2 62.6 1.0 CA B:CYS41 4.4 56.2 1.0 CA B:CYS64 4.7 47.4 1.0 CB B:LEU43 4.7 50.3 1.0 C B:LEU43 4.9 57.6 1.0 C B:CYS41 4.9 57.0 1.0 O B:CYS41 4.9 59.3 1.0

Zinc binding site 4 out of 4 in the Structure of the TRIM69 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the TRIM69 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:35.1 occ:1.00 ND1 B:HIS58 2.0 40.3 1.0 SG B:CYS81 2.3 34.5 1.0 SG B:CYS78 2.3 34.1 1.0 SG B:CYS56 2.3 35.0 1.0 CE1 B:HIS58 3.0 41.1 1.0 CG B:HIS58 3.1 38.9 1.0 CB B:CYS78 3.1 35.4 1.0 CB B:CYS56 3.3 38.1 1.0 CB B:CYS81 3.4 36.3 1.0 CB B:HIS58 3.5 37.5 1.0 N B:CYS81 3.7 36.9 1.0 NE2 B:HIS58 4.1 40.9 1.0 CA B:CYS81 4.1 37.2 1.0 CD2 B:HIS58 4.2 40.7 1.0 N B:HIS58 4.4 36.4 1.0 CB B:GLU80 4.5 40.8 1.0 CA B:CYS78 4.6 36.6 1.0 CA B:HIS58 4.6 36.3 1.0 CA B:CYS56 4.6 37.9 1.0 C B:GLU80 4.8 39.0 1.0 C B:CYS56 4.8 38.2 1.0 C B:CYS81 4.8 37.2 1.0 N B:LYS82 5.0 36.4 1.0 O B:CYS56 5.0 40.0 1.0 N B:GLU80 5.0 37.8 1.0 CA B:GLU80 5.0 39.6 1.0

J.R.Keown, J.Yang, M.M.Black, D.C.Goldstone. The Ring Domain of TRIM69 Promotes Higher-Order Assembly. Acta Crystallogr D Struct V. 76 954 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 33021497
DOI: 10.1107/S2059798320010499