Zinc in PDB 5olm: TRIM21

All present enzymatic activity of TRIM21:
2.3.2.27;

The structure of TRIM21, PDB code: 5olm was solved by L.C.James, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.95 / 1.95
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.400, 83.260, 117.588, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 26.2

The binding sites of Zinc atom in the TRIM21 (pdb code 5olm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the TRIM21, PDB code: 5olm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the TRIM21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of TRIM21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:35.5 occ:1.00 SG A:CYS36 2.3 34.5 1.0 SG A:CYS19 2.3 38.1 1.0 SG A:CYS39 2.4 34.7 1.0 SG A:CYS16 2.4 33.8 1.0 CB A:CYS16 3.0 34.1 1.0 CB A:CYS19 3.3 36.0 1.0 CB A:CYS36 3.3 39.4 1.0 CB A:CYS39 3.4 34.1 1.0 N A:CYS19 3.6 43.9 1.0 N A:CYS36 4.0 35.6 1.0 CA A:CYS19 4.0 39.0 1.0 CA A:CYS36 4.2 36.1 1.0 CA A:CYS16 4.4 28.8 1.0 CB A:ILE18 4.6 34.9 1.0 C A:ILE18 4.7 35.1 1.0 CA A:CYS39 4.8 32.7 1.0 C A:CYS19 4.9 41.1 1.0 C A:CYS16 5.0 32.8 1.0

Zinc binding site 2 out of 8 in the TRIM21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of TRIM21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:44.4 occ:1.00 ND1 A:HIS33 2.0 45.0 1.0 SG A:CYS31 2.2 32.9 1.0 SG A:CYS54 2.3 45.3 1.0 SG A:CYS51 2.4 45.8 1.0 CE1 A:HIS33 3.0 44.8 1.0 CG A:HIS33 3.0 37.6 1.0 CB A:CYS31 3.2 42.6 1.0 CB A:CYS51 3.3 49.5 1.0 CB A:HIS33 3.4 35.8 1.0 CB A:CYS54 3.5 49.9 1.0 N A:CYS54 3.9 39.4 1.0 NE2 A:HIS33 4.1 42.7 1.0 CD2 A:HIS33 4.1 44.5 1.0 CA A:CYS54 4.3 52.5 1.0 CB A:VAL53 4.3 47.8 1.0 N A:HIS33 4.6 36.4 1.0 CA A:HIS33 4.6 34.2 1.0 CA A:CYS31 4.6 37.6 1.0 CA A:CYS51 4.7 45.7 1.0 N A:ARG55 4.8 52.1 1.0 C A:VAL53 4.9 48.8 1.0 CD1 A:ILE29 4.9 42.7 1.0 C A:CYS54 4.9 56.0 1.0 C A:CYS31 4.9 37.2 1.0 N A:VAL53 5.0 41.0 1.0 O A:CYS31 5.0 44.7 1.0 CG1 A:VAL53 5.0 45.2 1.0 CA A:VAL53 5.0 44.2 1.0

Zinc binding site 3 out of 8 in the TRIM21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of TRIM21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:31.2 occ:1.00 ND1 A:HIS95 2.2 29.4 1.0 SG A:CYS111 2.3 30.7 1.0 SG A:CYS114 2.3 34.8 1.0 SG A:CYS92 2.3 36.0 1.0 CE1 A:HIS95 3.1 31.2 1.0 CG A:HIS95 3.1 28.5 1.0 CB A:CYS92 3.2 33.1 1.0 CB A:HIS95 3.4 30.3 1.0 CB A:CYS111 3.4 33.1 1.0 CB A:CYS114 3.5 31.0 1.0 N A:CYS114 3.7 32.9 1.0 N A:CYS111 3.9 29.5 1.0 CG2 A:VAL94 4.1 37.4 1.0 CA A:CYS114 4.1 31.3 1.0 CA A:CYS111 4.1 30.1 1.0 N A:HIS95 4.2 34.5 1.0 NE2 A:HIS95 4.3 30.9 1.0 CD2 A:HIS95 4.3 30.2 1.0 CA A:HIS95 4.4 32.3 1.0 O A:HOH607 4.5 39.5 1.0 C A:CYS111 4.6 26.4 1.0 CA A:CYS92 4.6 34.4 1.0 C A:VAL113 4.7 32.3 1.0 O A:CYS111 4.7 28.1 1.0 CB A:VAL113 4.8 28.8 1.0

Zinc binding site 4 out of 8 in the TRIM21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of TRIM21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:39.2 occ:1.00 OD2 A:ASP106 1.9 47.1 1.0 ND1 A:HIS123 2.0 39.2 1.0 ND1 A:HIS120 2.0 33.0 1.0 SG A:CYS103 2.3 37.0 1.0 CG A:ASP106 2.7 60.9 1.0 CE1 A:HIS123 2.8 41.0 1.0 CE1 A:HIS120 3.0 32.9 1.0 CG A:HIS120 3.0 28.5 1.0 CG A:HIS123 3.1 40.9 1.0 OD1 A:ASP106 3.2 63.7 1.0 CB A:HIS120 3.4 30.9 1.0 CB A:CYS103 3.4 36.8 1.0 CB A:HIS123 3.6 42.1 1.0 CB A:ASP106 3.7 50.8 1.0 CA A:HIS120 3.9 31.0 1.0 NE2 A:HIS123 4.0 40.3 1.0 NE2 A:HIS120 4.1 30.6 1.0 CD2 A:HIS123 4.1 34.6 1.0 CD2 A:HIS120 4.1 28.8 1.0 N A:ASP106 4.2 46.9 1.0 O A:LYS119 4.5 36.2 1.0 CA A:ASP106 4.6 45.0 1.0 O A:HIS120 4.7 34.6 1.0 CA A:CYS103 4.8 38.1 1.0 CB A:LYS105 4.8 52.9 1.0 CD1 A:LEU110 4.8 34.9 1.0 C A:HIS120 4.9 30.2 1.0 N A:HIS120 4.9 30.0 1.0

Zinc binding site 5 out of 8 in the TRIM21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of TRIM21 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:32.5 occ:1.00 SG B:CYS36 2.3 29.2 1.0 SG B:CYS19 2.3 35.3 1.0 SG B:CYS16 2.4 34.3 1.0 SG B:CYS39 2.4 31.1 1.0 CB B:CYS16 2.9 31.9 1.0 CB B:CYS36 3.1 32.8 1.0 CB B:CYS19 3.3 36.8 1.0 CB B:CYS39 3.4 29.4 1.0 N B:CYS19 3.7 36.4 1.0 N B:CYS36 3.9 25.6 1.0 CA B:CYS36 4.1 28.0 1.0 CA B:CYS19 4.1 32.8 1.0 CA B:CYS16 4.4 30.9 1.0 CB B:ILE18 4.7 32.0 1.0 CA B:CYS39 4.8 29.9 1.0 C B:ILE18 4.8 36.2 1.0 C B:CYS19 4.9 35.4 1.0 N B:LEU20 5.0 34.1 1.0 C B:CYS16 5.0 31.5 1.0

Zinc binding site 6 out of 8 in the TRIM21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of TRIM21 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:38.9 occ:1.00 ND1 B:HIS33 2.1 40.5 1.0 SG B:CYS31 2.2 37.2 1.0 SG B:CYS54 2.4 43.0 1.0 SG B:CYS51 2.4 36.6 1.0 CE1 B:HIS33 3.1 45.9 1.0 CB B:CYS51 3.1 37.9 1.0 CG B:HIS33 3.2 41.3 1.0 CB B:CYS31 3.3 37.8 1.0 CB B:CYS54 3.4 41.8 1.0 CB B:HIS33 3.5 34.8 1.0 N B:CYS54 3.8 40.2 1.0 CA B:CYS54 4.2 44.8 1.0 NE2 B:HIS33 4.2 47.0 1.0 CD2 B:HIS33 4.3 43.1 1.0 CD1 B:ILE29 4.5 34.0 1.0 N B:HIS33 4.5 35.6 1.0 CA B:CYS51 4.6 35.6 1.0 CA B:HIS33 4.6 37.3 1.0 CB B:VAL53 4.6 47.2 1.0 CA B:CYS31 4.7 38.8 1.0 C B:CYS54 4.8 50.3 1.0 C B:CYS31 4.9 45.7 1.0 C B:VAL53 4.9 43.8 1.0 O B:CYS31 4.9 42.8 1.0 CB B:GLN56 5.0 49.7 1.0

Zinc binding site 7 out of 8 in the TRIM21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of TRIM21 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:28.7 occ:1.00 ND1 B:HIS95 2.1 25.5 1.0 SG B:CYS111 2.3 27.0 1.0 SG B:CYS92 2.3 28.1 1.0 SG B:CYS114 2.3 29.7 1.0 CE1 B:HIS95 3.1 26.6 1.0 CG B:HIS95 3.1 25.8 1.0 CB B:CYS92 3.2 28.6 1.0 CB B:CYS111 3.4 31.9 1.0 CB B:CYS114 3.4 31.0 1.0 CB B:HIS95 3.4 30.0 1.0 N B:CYS114 3.7 28.8 1.0 N B:CYS111 3.8 29.5 1.0 CA B:CYS114 4.0 31.4 1.0 CA B:CYS111 4.1 28.4 1.0 N B:HIS95 4.1 26.9 1.0 NE2 B:HIS95 4.2 24.5 1.0 CD2 B:HIS95 4.2 27.0 1.0 CA B:HIS95 4.4 28.2 1.0 CG1 B:VAL94 4.5 33.8 1.0 C B:CYS111 4.6 30.8 1.0 CB B:VAL113 4.7 29.8 1.0 CA B:CYS92 4.7 32.3 1.0 O B:CYS111 4.7 28.7 1.0 C B:VAL113 4.7 32.5 1.0 C B:LEU110 5.0 31.9 1.0

Zinc binding site 8 out of 8 in the TRIM21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of TRIM21 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:39.6 occ:1.00 ND1 B:HIS120 2.0 38.4 1.0 ND1 B:HIS123 2.0 44.7 1.0 OD2 B:ASP106 2.0 38.0 1.0 SG B:CYS103 2.3 38.3 1.0 CE1 B:HIS123 2.9 50.0 1.0 CE1 B:HIS120 2.9 34.4 1.0 CG B:ASP106 3.1 38.8 1.0 CG B:HIS120 3.1 35.9 1.0 CG B:HIS123 3.1 51.5 1.0 CB B:CYS103 3.4 36.8 1.0 CB B:HIS120 3.5 38.9 1.0 CB B:HIS123 3.6 52.5 1.0 CB B:ASP106 3.7 36.4 1.0 CA B:HIS120 3.9 37.4 1.0 NE2 B:HIS123 4.0 49.9 1.0 NE2 B:HIS120 4.0 35.5 1.0 OD1 B:ASP106 4.0 42.0 1.0 CD2 B:HIS120 4.1 34.9 1.0 CD2 B:HIS123 4.2 51.2 1.0 O B:LYS119 4.3 43.6 1.0 N B:ASP106 4.3 41.2 1.0 CB B:LYS105 4.6 49.2 1.0 O B:HIS120 4.6 45.7 1.0 CA B:ASP106 4.7 39.7 1.0 CD1 B:LEU110 4.7 35.5 1.0 CA B:CYS103 4.8 33.6 1.0 C B:HIS120 4.8 42.9 1.0 N B:HIS120 4.9 38.3 1.0 C B:LYS119 5.0 37.9 1.0

C.Dickson, A.Fletcher, M.Vaysburd, J.C.Yang, D.L.Mallery, J.Zeng, C.M.Johnson, S.H.Mclaughlin, M.Skehel, S.Maslen, J.Cruickshank, N.Huguenin-Dezot, J.W.Chin, D.Neuhaus, L.C.James. Intracellular Antibody Signalling Is Regulated By Phosphorylation of the Fc Receptor TRIM21. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29667579
DOI: 10.7554/ELIFE.32660