Zinc in PDB 3q1d: The B-Box Domain of TRIM54

The structure of The B-Box Domain of TRIM54, PDB code: 3q1d was solved by J.R.Walker, L.Yermekbayeva, F.Mackenzie, A.Dong, J.Weigelt, C.Bountra, A.M.Edwards, C.H.Arrowsmith, S.Dhe-Paganon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.82 / 2.15
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	47.276, 47.276, 87.047, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 25.3

The binding sites of Zinc atom in the The B-Box Domain of TRIM54 (pdb code 3q1d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The B-Box Domain of TRIM54, PDB code: 3q1d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The B-Box Domain of TRIM54


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The B-Box Domain of TRIM54 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:21.7 occ:1.00 ND1 A:HIS155 2.1 25.0 1.0 SG A:CYS158 2.3 22.6 1.0 SG A:CYS138 2.3 21.7 1.0 SG A:CYS141 2.4 27.5 1.0 CE1 A:HIS155 3.1 27.0 1.0 CG A:HIS155 3.1 20.3 1.0 CB A:CYS158 3.2 22.3 1.0 CB A:CYS141 3.3 28.7 1.0 CB A:HIS155 3.4 17.7 1.0 CB A:CYS138 3.5 18.1 1.0 N A:CYS141 3.8 28.3 1.0 CA A:HIS155 3.9 17.1 1.0 NE2 A:HIS155 4.2 28.5 1.0 CA A:CYS141 4.2 29.6 1.0 CD2 A:HIS155 4.2 23.5 1.0 CB A:SER140 4.4 26.7 1.0 CA A:CYS158 4.7 24.3 1.0 C A:SER140 4.7 29.4 1.0 CA A:CYS138 4.8 18.3 1.0 O A:ALA154 4.9 20.8 1.0 C A:HIS155 4.9 16.8 1.0 O A:HIS155 4.9 17.6 1.0 N A:HIS155 4.9 17.7 1.0 CA A:SER140 5.0 28.5 1.0

Zinc binding site 2 out of 2 in the The B-Box Domain of TRIM54


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The B-Box Domain of TRIM54 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:17.5 occ:1.00 ND1 A:HIS129 2.2 19.1 1.0 SG A:CYS149 2.3 19.8 1.0 SG A:CYS146 2.3 16.8 1.0 SG A:CYS126 2.3 18.7 1.0 CE1 A:HIS129 3.1 18.1 1.0 CG A:HIS129 3.1 19.4 1.0 CB A:CYS126 3.3 18.4 1.0 CB A:CYS146 3.4 15.8 1.0 CB A:HIS129 3.5 19.8 1.0 CB A:CYS149 3.5 15.3 1.0 N A:CYS149 3.8 13.1 1.0 N A:HIS129 4.0 21.0 1.0 CA A:CYS149 4.1 14.1 1.0 O A:HOH228 4.1 28.6 1.0 NE2 A:HIS129 4.2 18.8 1.0 CD2 A:HIS129 4.3 19.2 1.0 N A:CYS146 4.3 14.5 1.0 CA A:CYS146 4.3 14.4 1.0 CA A:HIS129 4.3 21.2 1.0 OG1 A:THR145 4.6 19.5 1.0 C A:LEU148 4.7 13.1 1.0 O A:CYS146 4.7 12.5 1.0 C A:CYS146 4.7 13.4 1.0 CA A:CYS126 4.7 18.8 1.0 O A:HOH209 4.8 22.6 1.0 CB A:GLU128 4.8 22.7 1.0 CB A:LEU148 4.9 14.3 1.0 O A:HIS129 5.0 21.9 1.0

J.R.Walker, L.Yermekbayeva, F.Mackenzie, A.Dong, J.Weigelt, C.Bountra, A.M.Edwards, C.H.Arrowsmith, S.Dhe-Paganon. The B-Box Domain of TRIM54 To Be Published.