Zinc in PDB 5k3q: Rhesus Macaques TRIM5ALPHA BBOX2 Domain

The structure of Rhesus Macaques TRIM5ALPHA BBOX2 Domain, PDB code: 5k3q was solved by J.K.Keown, D.C.Goldstone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.25 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	30.751, 54.556, 54.479, 90.00, 100.03, 90.00
R / Rfree (%)	17.7 / 22.9

The binding sites of Zinc atom in the Rhesus Macaques TRIM5ALPHA BBOX2 Domain (pdb code 5k3q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rhesus Macaques TRIM5ALPHA BBOX2 Domain, PDB code: 5k3q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Rhesus Macaques TRIM5ALPHA BBOX2 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rhesus Macaques TRIM5ALPHA BBOX2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:29.7 occ:1.00 SG A:CYS119 2.2 26.8 1.0 SG A:CYS116 2.3 23.1 1.0 ND1 A:HIS100 2.3 28.6 1.0 SG A:CYS97 2.4 30.3 1.0 CE1 A:HIS100 3.2 30.2 1.0 CG A:HIS100 3.3 30.4 1.0 CB A:CYS97 3.3 29.1 1.0 CB A:CYS119 3.4 25.3 1.0 CB A:CYS116 3.5 20.0 1.0 N A:CYS119 3.5 22.1 1.0 CB A:HIS100 3.6 32.7 1.0 CA A:CYS119 3.8 24.0 1.0 N A:CYS116 3.9 20.1 1.0 CA A:CYS116 4.1 17.1 1.0 N A:HIS100 4.3 36.3 1.0 NE2 A:HIS100 4.4 30.4 1.0 CD2 A:HIS100 4.4 30.2 1.0 C A:LEU118 4.4 22.3 1.0 CB A:ARG99 4.5 45.3 1.0 CA A:HIS100 4.6 35.4 1.0 C A:CYS116 4.6 16.9 1.0 O A:CYS116 4.6 18.5 1.0 CB A:LEU118 4.6 19.4 1.0 CA A:CYS97 4.8 30.8 1.0 CA A:LEU118 4.9 22.2 1.0 N A:LEU118 5.0 20.3 1.0

Zinc binding site 2 out of 8 in the Rhesus Macaques TRIM5ALPHA BBOX2 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rhesus Macaques TRIM5ALPHA BBOX2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:28.6 occ:1.00 SG A:CYS108 2.2 24.6 1.0 ND1 A:HIS125 2.2 22.6 1.0 OD2 A:ASP111 2.2 24.9 1.0 ND1 A:HIS128 2.3 35.3 1.0 CE1 A:HIS125 3.1 24.4 1.0 CG A:HIS128 3.2 34.7 1.0 CE1 A:HIS128 3.2 35.5 1.0 CG A:ASP111 3.2 23.8 1.0 CG A:HIS125 3.3 24.1 1.0 CB A:CYS108 3.4 20.0 1.0 CB A:HIS128 3.5 35.6 1.0 CB A:HIS125 3.7 29.0 1.0 CB A:ASP111 3.8 22.9 1.0 CA A:HIS125 4.1 33.4 1.0 OD1 A:ASP111 4.1 27.8 1.0 NE2 A:HIS128 4.2 38.0 1.0 CD2 A:HIS128 4.2 37.2 1.0 NE2 A:HIS125 4.3 24.4 1.0 N A:ASP111 4.3 24.3 1.0 CD2 A:HIS125 4.4 26.0 1.0 O A:GLU124 4.5 38.8 1.0 CB A:GLU110 4.5 35.0 1.0 CA A:ASP111 4.7 26.0 1.0 CA A:CYS108 4.7 21.0 1.0 CD1 A:ILE115 4.8 19.7 1.0

Zinc binding site 3 out of 8 in the Rhesus Macaques TRIM5ALPHA BBOX2 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rhesus Macaques TRIM5ALPHA BBOX2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:20.9 occ:1.00 ND1 B:HIS100 2.2 16.4 1.0 SG B:CYS116 2.3 19.3 1.0 SG B:CYS97 2.3 20.1 1.0 SG B:CYS119 2.3 22.7 1.0 CE1 B:HIS100 3.2 17.5 1.0 CG B:HIS100 3.2 17.7 1.0 CB B:CYS97 3.2 19.2 1.0 CB B:CYS116 3.4 19.8 1.0 CB B:HIS100 3.5 18.2 1.0 CB B:CYS119 3.6 22.1 1.0 N B:CYS119 3.6 18.2 1.0 N B:CYS116 3.9 16.9 1.0 CA B:CYS119 4.1 21.6 1.0 CA B:CYS116 4.1 17.3 1.0 N B:HIS100 4.3 16.8 1.0 NE2 B:HIS100 4.3 17.9 1.0 CD2 B:HIS100 4.4 18.8 1.0 O B:CYS116 4.5 16.4 1.0 C B:CYS116 4.5 16.9 1.0 CA B:HIS100 4.5 18.4 1.0 C B:LEU118 4.5 18.2 1.0 CB B:LEU118 4.6 19.1 1.0 CA B:CYS97 4.7 17.1 1.0 CB B:ARG99 4.7 17.5 1.0 N B:LEU118 4.9 17.2 1.0 CA B:LEU118 4.9 18.7 1.0

Zinc binding site 4 out of 8 in the Rhesus Macaques TRIM5ALPHA BBOX2 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rhesus Macaques TRIM5ALPHA BBOX2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:40.6 occ:1.00 SG B:CYS108 2.1 35.5 1.0 OD2 B:ASP111 2.1 29.9 1.0 ND1 B:HIS125 2.2 39.1 1.0 ND1 B:HIS128 2.4 51.4 1.0 CG B:HIS125 3.0 41.5 1.0 CG B:ASP111 3.1 25.4 1.0 CE1 B:HIS128 3.1 54.5 1.0 CB B:HIS125 3.2 45.8 1.0 CE1 B:HIS125 3.2 37.1 1.0 CG B:HIS128 3.3 51.7 1.0 CB B:CYS108 3.4 31.3 1.0 CB B:ASP111 3.6 24.1 1.0 CB B:HIS128 3.7 48.8 1.0 CA B:HIS125 3.9 47.9 1.0 NE2 B:HIS128 4.1 58.0 1.0 OD1 B:ASP111 4.1 32.2 1.0 CD2 B:HIS125 4.1 41.1 1.0 CD2 B:HIS128 4.2 54.5 1.0 NE2 B:HIS125 4.2 38.9 1.0 N B:ASP111 4.2 35.0 1.0 CA B:ASP111 4.6 32.2 1.0 CA B:CYS108 4.7 30.8 1.0 N B:HIS125 4.7 50.2 1.0 O B:GLU124 4.8 46.7 1.0 CB B:GLU110 4.9 43.6 1.0

Zinc binding site 5 out of 8 in the Rhesus Macaques TRIM5ALPHA BBOX2 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rhesus Macaques TRIM5ALPHA BBOX2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:23.3 occ:1.00 SG C:CYS108 2.2 22.1 1.0 OD2 C:ASP111 2.2 25.8 1.0 ND1 C:HIS125 2.3 20.9 1.0 ND1 C:HIS128 2.3 27.4 1.0 CG C:ASP111 2.6 24.7 1.0 OD1 C:ASP111 3.0 32.6 1.0 CE1 C:HIS128 3.2 29.1 1.0 CG C:HIS128 3.3 24.5 1.0 CE1 C:HIS125 3.3 20.5 1.0 CG C:HIS125 3.3 22.5 1.0 CB C:CYS108 3.4 16.4 1.0 CB C:ASP111 3.5 23.9 1.0 CB C:HIS128 3.6 20.8 1.0 CB C:HIS125 3.6 22.5 1.0 CA C:HIS125 4.0 22.1 1.0 N C:ASP111 4.2 22.6 1.0 NE2 C:HIS128 4.3 29.8 1.0 CD2 C:HIS128 4.3 27.1 1.0 NE2 C:HIS125 4.4 22.6 1.0 O C:GLU124 4.4 30.2 1.0 CD2 C:HIS125 4.5 23.1 1.0 CA C:ASP111 4.5 23.2 1.0 CA C:CYS108 4.7 18.6 1.0 CB C:GLU110 4.8 27.8 1.0 N C:HIS125 4.9 21.1 1.0 CD1 C:ILE115 4.9 21.0 1.0 C C:HIS125 5.0 22.2 1.0 O C:HIS125 5.0 20.8 1.0

Zinc binding site 6 out of 8 in the Rhesus Macaques TRIM5ALPHA BBOX2 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rhesus Macaques TRIM5ALPHA BBOX2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:26.6 occ:1.00 ND1 C:HIS100 2.2 32.6 1.0 SG C:CYS116 2.3 22.2 1.0 SG C:CYS119 2.3 24.1 1.0 SG C:CYS97 2.3 29.3 1.0 CE1 C:HIS100 3.0 37.5 1.0 CB C:CYS97 3.3 27.7 1.0 CG C:HIS100 3.3 32.5 1.0 N C:CYS119 3.4 22.1 1.0 CB C:CYS116 3.4 19.3 1.0 CB C:CYS119 3.5 20.8 1.0 CA C:CYS119 3.8 22.1 1.0 CB C:HIS100 3.8 33.5 1.0 N C:CYS116 3.8 17.8 1.0 CA C:CYS116 4.1 17.9 1.0 NE2 C:HIS100 4.2 32.3 1.0 N C:HIS100 4.2 34.3 1.0 C C:LEU118 4.3 22.9 1.0 CD2 C:HIS100 4.3 32.3 1.0 CB C:ARG99 4.4 40.4 1.0 C C:CYS116 4.4 18.6 1.0 O C:CYS116 4.5 18.9 1.0 CB C:LEU118 4.6 24.0 1.0 CA C:HIS100 4.7 35.2 1.0 CD C:ARG99 4.7 48.3 1.0 CA C:CYS97 4.7 30.6 1.0 CA C:LEU118 4.8 24.1 1.0 N C:LEU118 4.8 21.5 1.0

Zinc binding site 7 out of 8 in the Rhesus Macaques TRIM5ALPHA BBOX2 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rhesus Macaques TRIM5ALPHA BBOX2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:22.4 occ:1.00 SG D:CYS108 2.2 22.6 1.0 OD2 D:ASP111 2.2 20.8 1.0 ND1 D:HIS128 2.2 22.7 1.0 ND1 D:HIS125 2.3 24.2 1.0 CE1 D:HIS128 3.0 25.2 1.0 CE1 D:HIS125 3.2 25.4 1.0 CG D:ASP111 3.2 21.1 1.0 CG D:HIS125 3.3 25.4 1.0 CG D:HIS128 3.3 24.7 1.0 CB D:CYS108 3.3 19.5 1.0 CB D:HIS125 3.6 25.9 1.0 CB D:ASP111 3.7 20.5 1.0 CB D:HIS128 3.7 26.4 1.0 CA D:HIS125 4.0 29.7 1.0 N D:ASP111 4.1 20.7 1.0 NE2 D:HIS128 4.2 26.2 1.0 OD1 D:ASP111 4.3 24.1 1.0 NE2 D:HIS125 4.3 26.8 1.0 CD2 D:HIS128 4.3 26.9 1.0 CD2 D:HIS125 4.4 27.3 1.0 O D:HOH323 4.4 30.6 1.0 O D:GLU124 4.5 33.1 1.0 CA D:ASP111 4.5 22.2 1.0 CB D:GLU110 4.6 25.4 1.0 CA D:CYS108 4.7 18.0 1.0 N D:HIS125 4.9 30.4 1.0 C D:GLU110 5.0 21.8 1.0 C D:HIS125 5.0 31.0 1.0

Zinc binding site 8 out of 8 in the Rhesus Macaques TRIM5ALPHA BBOX2 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rhesus Macaques TRIM5ALPHA BBOX2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:20.4 occ:1.00 SG D:CYS116 2.2 19.1 1.0 ND1 D:HIS100 2.3 22.9 1.0 SG D:CYS119 2.3 19.9 1.0 SG D:CYS97 2.4 20.7 1.0 CE1 D:HIS100 3.2 25.1 1.0 CG D:HIS100 3.2 21.2 1.0 CB D:CYS97 3.3 19.6 1.0 CB D:CYS116 3.4 17.9 1.0 CB D:HIS100 3.5 19.3 1.0 CB D:CYS119 3.5 20.3 1.0 N D:CYS119 3.5 20.1 1.0 N D:CYS116 3.8 17.1 1.0 CA D:CYS119 4.0 20.2 1.0 CA D:CYS116 4.1 18.1 1.0 N D:HIS100 4.2 18.7 1.0 NE2 D:HIS100 4.3 24.2 1.0 O D:HOH329 4.4 37.2 1.0 CD2 D:HIS100 4.4 24.5 1.0 CA D:HIS100 4.5 19.5 1.0 C D:CYS116 4.5 18.7 1.0 C D:LEU118 4.5 21.4 1.0 O D:CYS116 4.5 18.5 1.0 CB D:ARG99 4.5 23.3 1.0 CB D:LEU118 4.7 19.3 1.0 CA D:CYS97 4.7 17.4 1.0 N D:LEU118 4.9 20.4 1.0 CA D:LEU118 4.9 20.6 1.0 CD D:ARG99 5.0 33.8 1.0

J.R.Keown, D.C.Goldstone. Crystal Structure of the TRIM5 Alpha BBOX2 Domain From Rhesus Macaques Describes A Plastic Oligomerisation Interface. J.Struct.Biol. V. 195 282 2016.
ISSN: ESSN 1095-8657
PubMed: 27402535
DOI: 10.1016/J.JSB.2016.07.004