Zinc in PDB 5jw7: Crystal Structure of Sopa-TRIM56 Complex

The structure of Crystal Structure of Sopa-TRIM56 Complex, PDB code: 5jw7 was solved by S.Bhogaraju, I.Dikic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.48 / 2.85
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	71.015, 71.015, 122.944, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 27.8

The binding sites of Zinc atom in the Crystal Structure of Sopa-TRIM56 Complex (pdb code 5jw7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Sopa-TRIM56 Complex, PDB code: 5jw7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Sopa-TRIM56 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Sopa-TRIM56 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:73.0 occ:1.00 HB3 B:CYS21 2.2 96.7 1.0 SG B:CYS21 2.3 0.5 1.0 HG B:CYS24 2.4 0.1 1.0 HB2 B:CYS41 2.4 0.9 1.0 HB3 B:CYS24 2.4 74.2 1.0 SG B:CYS44 2.5 90.1 1.0 SG B:CYS41 2.5 91.7 1.0 CB B:CYS21 2.6 80.6 1.0 SG B:CYS24 2.7 95.9 1.0 HB2 B:CYS21 2.9 96.7 1.0 CB B:CYS41 2.9 0.3 1.0 CB B:CYS24 3.0 61.8 1.0 H B:CYS41 3.0 0.6 1.0 H B:CYS24 3.2 88.1 1.0 HB2 B:CYS44 3.5 0.1 1.0 HB3 B:CYS41 3.6 0.9 1.0 CB B:CYS44 3.7 0.4 1.0 HB2 B:CYS24 3.7 74.2 1.0 N B:CYS41 3.8 0.2 1.0 HB3 A:ASN340 3.8 82.3 1.0 N B:CYS24 3.9 73.4 1.0 CA B:CYS41 3.9 93.6 1.0 HB3 B:CYS44 3.9 0.1 1.0 CA B:CYS21 4.0 79.0 1.0 CA B:CYS24 4.1 67.6 1.0 HG1 A:THR338 4.1 84.7 1.0 HB B:ILE23 4.2 0.1 1.0 H B:CYS21 4.2 0.8 1.0 H B:ILE23 4.5 86.3 1.0 HB3 B:TYR40 4.5 0.9 1.0 HA B:LEU28 4.5 0.1 1.0 HD22 A:ASN340 4.5 0.1 1.0 C B:CYS21 4.5 73.8 1.0 O B:CYS21 4.5 86.4 1.0 HA B:CYS41 4.6 0.3 1.0 N B:CYS21 4.6 88.1 1.0 H B:GLU26 4.6 93.3 1.0 HA B:CYS21 4.6 94.8 1.0 H B:LEU25 4.7 93.3 1.0 CB A:ASN340 4.7 68.6 1.0 HB2 A:ASN340 4.7 82.3 1.0 HA B:CYS24 4.7 81.1 1.0 H B:CYS44 4.7 0.3 1.0 O B:GLU26 4.8 85.1 1.0 OG1 A:THR338 4.8 70.6 1.0 H B:ARG29 4.9 0.4 1.0 HA B:TYR40 4.9 0.8 1.0 C B:CYS41 4.9 98.8 1.0 C B:CYS24 4.9 82.4 1.0 C B:TYR40 5.0 85.9 1.0 CA B:CYS44 5.0 0.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Sopa-TRIM56 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Sopa-TRIM56 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:0.1 occ:1.00 ND1 B:HIS38 2.1 82.9 1.0 HE1 B:HIS38 2.3 0.0 1.0 HB3 B:CYS56 2.4 0.4 1.0 CE1 B:HIS38 2.5 90.9 1.0 HB2 B:CYS56 2.5 0.4 1.0 CB B:CYS56 2.7 0.7 1.0 SG B:CYS59 2.7 0.2 1.0 SG B:CYS36 2.7 0.4 1.0 SG B:CYS56 2.8 0.7 1.0 CG B:HIS38 3.5 88.5 1.0 HG B:CYS36 3.6 0.8 1.0 HB2 B:CYS36 3.7 0.1 1.0 H B:LEU37 3.7 0.1 1.0 H B:CYS59 3.7 0.9 1.0 NE2 B:HIS38 3.8 92.9 1.0 HB2 B:HIS38 3.8 1.0 1.0 HB2 B:GLU58 3.8 1.0 1.0 CB B:CYS36 3.9 0.6 1.0 HH B:TYR40 4.0 0.5 1.0 H B:ARG60 4.0 0.4 1.0 CA B:CYS56 4.2 97.2 1.0 HB3 B:CYS36 4.2 0.1 1.0 CB B:HIS38 4.2 90.8 1.0 CD2 B:HIS38 4.3 0.0 1.0 CB B:CYS59 4.3 0.2 1.0 N B:CYS59 4.3 0.9 1.0 HE2 B:HIS38 4.4 0.5 1.0 H B:GLU58 4.5 0.1 1.0 HA B:CYS56 4.5 0.6 1.0 N B:LEU37 4.5 1.0 1.0 OH B:TYR40 4.7 91.3 1.0 H B:CYS56 4.7 0.5 1.0 O B:ARG60 4.7 0.3 1.0 H B:HIS38 4.8 0.6 1.0 CB B:GLU58 4.8 0.1 1.0 N B:ARG60 4.8 0.5 1.0 HB3 B:CYS59 4.8 0.2 1.0 N B:HIS38 4.8 0.1 1.0 C B:CYS56 4.8 0.1 1.0 HB2 B:CYS59 4.9 0.2 1.0 CA B:CYS59 4.9 0.9 1.0 HB3 B:HIS38 4.9 1.0 1.0 N B:CYS56 5.0 97.9 1.0

E.Fiskin, S.Bhogaraju, L.Herhaus, S.Kalayil, M.Hahn, I.Dikic. Structural Basis For the Recognition and Degradation of Host Trim Proteins By Salmonella Effector Sopa. Nat Commun V. 8 14004 2017.
ISSN: ESSN 2041-1723
PubMed: 28084320
DOI: 10.1038/NCOMMS14004