Zinc in PDB 5eiu: Mini TRIM5 B-Box 2 Dimer C2 Crystal Form

The structure of Mini TRIM5 B-Box 2 Dimer C2 Crystal Form, PDB code: 5eiu was solved by J.M.Wagner, G.Doss, O.Pornillos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.48 / 1.91
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.662, 41.488, 111.301, 90.00, 99.06, 90.00
R / Rfree (%)	18.3 / 21.7

The binding sites of Zinc atom in the Mini TRIM5 B-Box 2 Dimer C2 Crystal Form (pdb code 5eiu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mini TRIM5 B-Box 2 Dimer C2 Crystal Form, PDB code: 5eiu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Mini TRIM5 B-Box 2 Dimer C2 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mini TRIM5 B-Box 2 Dimer C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:34.7 occ:1.00 ND1 A:HIS128 1.9 35.9 1.0 ND1 A:HIS125 2.0 47.6 1.0 OD2 A:ASP111 2.0 35.1 1.0 SG A:CYS108 2.3 35.2 1.0 HE1 A:HIS125 2.6 49.6 1.0 CE1 A:HIS125 2.6 41.3 1.0 CE1 A:HIS128 2.8 43.1 1.0 HE1 A:HIS128 2.9 51.8 1.0 CG A:ASP111 3.0 35.0 1.0 CG A:HIS128 3.1 45.0 1.0 HB2 A:ASP111 3.1 40.1 1.0 CG A:HIS125 3.2 47.5 1.0 CB A:CYS108 3.3 31.8 1.0 HB2 A:CYS108 3.3 38.2 1.0 HB3 A:HIS128 3.4 41.9 1.0 HB2 A:HIS128 3.4 41.9 1.0 HB3 A:CYS108 3.5 38.2 1.0 HA A:HIS125 3.5 62.6 1.0 CB A:HIS128 3.5 34.9 1.0 HB3 A:HIS125 3.6 53.1 1.0 CB A:ASP111 3.6 33.4 1.0 H A:ASP111 3.7 41.5 1.0 CB A:HIS125 3.8 44.2 1.0 NE2 A:HIS125 3.9 44.3 1.0 HB2 A:GLU110 3.9 59.3 1.0 NE2 A:HIS128 4.0 42.8 1.0 OD1 A:ASP111 4.0 48.1 1.0 CD2 A:HIS128 4.1 41.4 1.0 CA A:HIS125 4.1 52.2 1.0 CD2 A:HIS125 4.2 44.7 1.0 HB3 A:ASP111 4.2 40.1 1.0 N A:ASP111 4.3 34.5 1.0 O A:GLU124 4.4 62.3 1.0 HE2 A:HIS125 4.6 53.1 1.0 CA A:ASP111 4.6 33.6 1.0 H A:GLU110 4.7 39.4 1.0 CA A:CYS108 4.7 36.4 1.0 HE2 A:HIS128 4.7 51.3 1.0 HB2 A:HIS125 4.7 53.1 1.0 HD13 A:ILE115 4.8 46.7 1.0 CB A:GLU110 4.8 49.5 1.0 HG22 A:THR130 4.8 43.7 1.0 HA A:CYS108 4.9 43.7 1.0 HB3 A:GLU110 4.9 59.3 1.0 HD2 A:HIS128 5.0 49.6 1.0

Zinc binding site 2 out of 4 in the Mini TRIM5 B-Box 2 Dimer C2 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mini TRIM5 B-Box 2 Dimer C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:38.3 occ:1.00 ND1 A:HIS100 2.0 37.0 1.0 SG A:CYS119 2.3 43.1 1.0 SG A:CYS97 2.3 44.8 1.0 SG A:CYS116 2.4 38.1 1.0 H A:CYS119 2.9 43.4 1.0 CE1 A:HIS100 2.9 45.2 1.0 HB2 A:HIS100 2.9 49.9 1.0 HE1 A:HIS100 3.1 54.2 1.0 CG A:HIS100 3.1 43.0 1.0 HB2 A:CYS97 3.2 47.1 1.0 H A:CYS116 3.2 47.2 1.0 CB A:CYS97 3.3 39.3 1.0 HB3 A:CYS116 3.4 43.4 1.0 HB3 A:CYS97 3.5 47.1 1.0 CB A:CYS116 3.5 36.2 1.0 N A:CYS119 3.5 36.1 1.0 CB A:CYS119 3.5 32.1 1.0 CB A:HIS100 3.5 41.6 1.0 H A:HIS100 3.5 56.9 1.0 HB2 A:CYS119 3.7 38.5 1.0 HB2 A:LEU118 3.8 47.4 1.0 N A:CYS116 3.9 39.4 1.0 HB3 A:ARG99 3.9 63.6 1.0 CA A:CYS119 4.0 34.5 1.0 NE2 A:HIS100 4.1 45.0 1.0 HA A:CYS119 4.1 41.4 1.0 N A:HIS100 4.1 47.4 1.0 CA A:CYS116 4.2 37.1 1.0 CD2 A:HIS100 4.2 41.6 1.0 HB3 A:HIS100 4.2 49.9 1.0 HB2 A:CYS116 4.3 43.4 1.0 HB3 A:CYS119 4.3 38.5 1.0 H A:LEU118 4.3 44.9 1.0 H A:ARG99 4.4 59.5 1.0 CA A:HIS100 4.5 44.3 1.0 C A:LEU118 4.5 46.5 1.0 C A:CYS116 4.6 35.0 1.0 CB A:LEU118 4.6 39.5 1.0 O A:CYS116 4.6 31.3 1.0 HB2 A:GLU102 4.6 48.2 1.0 CA A:CYS97 4.7 42.8 1.0 HB A:ILE115 4.7 47.4 1.0 HB3 A:LEU118 4.8 47.4 1.0 N A:LEU118 4.8 37.4 1.0 HA A:ILE115 4.8 36.8 1.0 HA A:CYS97 4.8 51.3 1.0 HE2 A:HIS100 4.9 54.0 1.0 HG2 A:ARG99 4.9 75.7 1.0 CB A:ARG99 4.9 53.0 1.0 CA A:LEU118 4.9 36.3 1.0 H A:GLU102 4.9 47.6 1.0 HD23 A:LEU104 4.9 42.5 1.0 HD21 A:LEU104 4.9 42.5 1.0 C A:ILE115 5.0 30.5 1.0

Zinc binding site 3 out of 4 in the Mini TRIM5 B-Box 2 Dimer C2 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mini TRIM5 B-Box 2 Dimer C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:35.4 occ:1.00 ND1 D:HIS125 2.0 31.1 1.0 ND1 D:HIS128 2.0 31.4 1.0 OD2 D:ASP111 2.0 37.8 1.0 SG D:CYS108 2.3 33.6 1.0 CE1 D:HIS125 2.8 32.0 1.0 HE1 D:HIS125 2.9 38.4 1.0 CE1 D:HIS128 2.9 43.7 1.0 HE1 D:HIS128 3.1 52.4 1.0 CG D:HIS128 3.1 31.4 1.0 CG D:ASP111 3.1 50.5 1.0 CG D:HIS125 3.1 31.6 1.0 HB2 D:ASP111 3.2 40.8 1.0 HA D:HIS125 3.2 42.1 1.0 HB3 D:HIS125 3.3 38.1 1.0 HB3 D:HIS128 3.3 40.7 1.0 HB2 D:HIS128 3.4 40.7 1.0 CB D:CYS108 3.4 29.8 1.0 HB2 D:CYS108 3.4 35.8 1.0 CB D:HIS128 3.5 33.9 1.0 HB3 D:CYS108 3.6 35.8 1.0 CB D:HIS125 3.6 31.8 1.0 H D:ASP111 3.6 41.0 1.0 CB D:ASP111 3.7 34.0 1.0 HB2 D:GLU110 3.9 43.9 1.0 CA D:HIS125 3.9 35.1 1.0 NE2 D:HIS125 4.0 36.1 1.0 NE2 D:HIS128 4.1 35.2 1.0 OD1 D:ASP111 4.1 49.8 1.0 CD2 D:HIS128 4.2 35.2 1.0 CD2 D:HIS125 4.2 31.9 1.0 N D:ASP111 4.2 34.2 1.0 O D:GLU124 4.4 42.6 1.0 HB3 D:ASP111 4.4 40.8 1.0 HD13 D:ILE115 4.4 37.2 1.0 HB2 D:HIS125 4.5 38.1 1.0 CA D:ASP111 4.6 37.6 1.0 CA D:CYS108 4.7 28.3 1.0 HG22 D:THR130 4.7 47.3 1.0 HE2 D:HIS125 4.7 43.3 1.0 H D:GLU110 4.8 37.0 1.0 CB D:GLU110 4.8 36.6 1.0 HA D:CYS108 4.8 34.0 1.0 HE2 D:HIS128 4.8 42.3 1.0 N D:HIS125 4.9 40.5 1.0 C D:HIS125 4.9 33.0 1.0 HB3 D:GLU110 4.9 43.9 1.0 O D:HIS125 4.9 33.8 1.0

Zinc binding site 4 out of 4 in the Mini TRIM5 B-Box 2 Dimer C2 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mini TRIM5 B-Box 2 Dimer C2 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn702 b:38.0 occ:1.00 ND1 D:HIS100 2.0 37.3 1.0 SG D:CYS119 2.3 44.9 1.0 SG D:CYS116 2.3 38.1 1.0 SG D:CYS97 2.3 40.7 1.0 H D:CYS119 2.9 37.6 1.0 CE1 D:HIS100 2.9 45.2 1.0 HB2 D:HIS100 3.0 48.9 1.0 HE1 D:HIS100 3.0 54.3 1.0 HB2 D:CYS97 3.1 46.4 1.0 CG D:HIS100 3.1 39.5 1.0 CB D:CYS97 3.2 38.6 1.0 HB3 D:CYS97 3.3 46.4 1.0 H D:CYS116 3.3 42.8 1.0 HB3 D:CYS116 3.4 39.5 1.0 N D:CYS119 3.5 31.4 1.0 CB D:CYS116 3.5 32.9 1.0 CB D:CYS119 3.5 40.9 1.0 CB D:HIS100 3.5 40.8 1.0 HB2 D:CYS119 3.7 49.0 1.0 H D:HIS100 3.9 54.1 1.0 HB2 D:LEU118 3.9 39.1 1.0 CA D:CYS119 3.9 31.6 1.0 N D:CYS116 4.0 35.7 1.0 HA D:CYS119 4.1 37.9 1.0 HB3 D:ARG99 4.1 77.4 1.0 NE2 D:HIS100 4.1 40.9 1.0 CD2 D:HIS100 4.2 40.0 1.0 HB3 D:HIS100 4.2 48.9 1.0 CA D:CYS116 4.3 29.6 1.0 HB2 D:CYS116 4.3 39.5 1.0 N D:HIS100 4.3 45.1 1.0 HB3 D:CYS119 4.3 49.0 1.0 C D:LEU118 4.5 34.3 1.0 H D:ARG99 4.5 58.6 1.0 H D:LEU118 4.6 41.3 1.0 CA D:HIS100 4.6 44.8 1.0 O D:CYS116 4.6 34.0 1.0 C D:CYS116 4.6 32.9 1.0 CA D:CYS97 4.7 47.6 1.0 HB D:ILE115 4.7 51.8 1.0 HB2 D:GLU102 4.7 47.0 1.0 CB D:LEU118 4.7 32.6 1.0 HE2 D:HIS100 4.8 49.1 1.0 HA D:CYS97 4.9 57.1 1.0 HD3 D:ARG99 4.9 91.7 1.0 H D:GLU102 4.9 54.0 1.0 HG2 D:ARG99 4.9 0.5 1.0 HB3 D:LEU118 4.9 39.1 1.0 CA D:LEU118 4.9 31.4 1.0 CB D:ARG99 4.9 64.5 1.0 N D:LEU118 5.0 34.4 1.0

J.M.Wagner, M.D.Roganowicz, K.Skorupka, S.L.Alam, D.E.Christensen, G.L.Doss, Y.Wan, G.A.Frank, B.K.Ganser-Pornillos, W.I.Sundquist, O.Pornillos. Mechanism of B-Box 2 Domain-Mediated Higher-Order Assembly of the Retroviral Restriction Factor TRIM5 Alpha. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27253059
DOI: 10.7554/ELIFE.16309