Zinc in PDB 8a58: X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W

All present enzymatic activity of X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W:
2.3.2.23; 2.3.2.25; 2.3.2.27;

The structure of X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W, PDB code: 8a58 was solved by L.C.James, L.Kiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.46 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.82, 75.482, 63.835, 90, 119.31, 90
R / Rfree (%)	21.5 / 25.9

The binding sites of Zinc atom in the X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W (pdb code 8a58). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W, PDB code: 8a58:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:55.4 occ:1.00 SG C:CYS19 2.2 58.7 1.0 SG C:CYS39 2.3 56.4 1.0 SG C:CYS16 2.5 55.1 1.0 SG C:CYS36 2.5 57.4 1.0 CB C:CYS36 3.0 55.0 1.0 CB C:CYS16 3.1 42.7 1.0 CB C:CYS19 3.3 63.8 1.0 CB C:CYS39 3.5 55.4 1.0 N C:CYS19 3.6 49.5 1.0 O C:HOH208 3.8 76.8 1.0 N C:CYS36 3.9 60.5 1.0 CA C:CYS19 4.0 53.8 1.0 CA C:CYS36 4.1 56.1 1.0 CA C:CYS16 4.6 56.1 1.0 CB C:ILE18 4.6 60.5 1.0 C C:ILE18 4.7 64.5 1.0 CA C:CYS39 4.8 63.0 1.0 N C:ILE18 4.9 52.0 1.0 N C:CYS39 4.9 58.9 1.0 C C:CYS19 4.9 66.3 1.0 C C:CYS16 4.9 50.9 1.0 CA C:ILE18 5.0 49.9 1.0 O C:CYS16 5.0 53.0 1.0

Zinc binding site 2 out of 4 in the X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:49.5 occ:1.00 ND1 C:HIS33 2.0 57.4 1.0 SG C:CYS31 2.3 45.6 1.0 SG C:CYS51 2.4 45.4 1.0 SG C:CYS54 2.5 53.4 1.0 CE1 C:HIS33 3.0 45.2 1.0 CG C:HIS33 3.0 54.3 1.0 CB C:CYS51 3.2 51.1 1.0 CB C:CYS54 3.3 49.8 1.0 CB C:HIS33 3.4 40.9 1.0 CB C:CYS31 3.4 52.2 1.0 N C:CYS54 3.6 45.6 1.0 CA C:CYS54 4.0 64.5 1.0 NE2 C:HIS33 4.1 52.5 1.0 CD2 C:HIS33 4.1 53.3 1.0 CB C:VAL53 4.3 49.8 1.0 N C:HIS33 4.4 47.2 1.0 CA C:HIS33 4.5 56.1 1.0 C C:VAL53 4.5 62.7 1.0 CA C:CYS51 4.7 48.3 1.0 CA C:CYS31 4.7 54.3 1.0 C C:CYS54 4.7 64.8 1.0 N C:VAL53 4.7 47.5 1.0 CA C:VAL53 4.7 47.4 1.0 N C:ARG55 4.8 56.5 1.0 CB C:GLN56 4.8 58.6 1.0 C C:CYS31 4.9 53.3 1.0 CG1 C:VAL53 4.9 44.8 1.0 N C:GLN56 4.9 55.2 1.0 CD1 C:ILE29 5.0 55.0 1.0

Zinc binding site 3 out of 4 in the X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:64.8 occ:1.00 ND1 D:HIS33 1.9 59.4 1.0 SG D:CYS51 2.3 54.6 1.0 SG D:CYS31 2.3 110.5 1.0 SG D:CYS54 2.5 83.1 1.0 CG D:HIS33 2.8 55.0 1.0 CE1 D:HIS33 2.9 65.4 1.0 CB D:CYS54 3.1 61.0 1.0 CB D:HIS33 3.2 36.6 1.0 CB D:CYS31 3.3 82.4 1.0 CB D:CYS51 3.4 56.4 1.0 CG2 D:VAL53 3.6 83.7 1.0 N D:CYS54 3.8 73.8 1.0 CD2 D:HIS33 4.0 61.4 1.0 NE2 D:HIS33 4.0 70.1 1.0 CA D:CYS54 4.0 66.5 1.0 N D:HIS33 4.4 65.7 1.0 CA D:HIS33 4.4 61.6 1.0 CD1 D:ILE29 4.6 67.8 1.0 CA D:CYS31 4.6 58.9 1.0 CD C:ARG67 4.8 80.4 1.0 C D:CYS54 4.8 73.6 1.0 C D:VAL53 4.8 69.5 1.0 CA D:CYS51 4.8 57.7 1.0 NE C:ARG67 4.9 105.4 1.0 C D:CYS31 4.9 62.3 1.0 CB D:VAL53 4.9 73.5 1.0 N D:ARG55 4.9 67.1 1.0 N D:VAL53 5.0 63.0 1.0

Zinc binding site 4 out of 4 in the X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of TRIM21 Ring E3 Ligase in Complex with E2 Enzyme UBE2W within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:58.1 occ:1.00 SG D:CYS39 2.3 60.0 1.0 SG D:CYS19 2.4 47.8 1.0 SG D:CYS36 2.4 50.4 1.0 SG D:CYS16 2.4 48.4 1.0 CB D:CYS36 3.0 43.1 1.0 CB D:CYS19 3.2 44.0 1.0 CB D:CYS16 3.2 58.7 1.0 CB D:CYS39 3.5 52.4 1.0 N D:CYS19 3.6 49.5 1.0 CA D:CYS19 4.0 71.5 1.0 N D:CYS36 4.1 54.7 1.0 CA D:CYS36 4.2 48.4 1.0 CB D:ILE18 4.6 59.7 1.0 CA D:CYS16 4.6 51.3 1.0 C D:ILE18 4.7 70.7 1.0 CA D:CYS39 4.8 65.4 1.0 C D:CYS19 4.9 62.3 1.0 N D:CYS39 5.0 60.0 1.0 C D:CYS16 5.0 55.9 1.0

L.Kiss, T.Rhinesmith, J.Luptak, C.F.Dickson, J.Weidenhausen, S.Smyly, J.C.Yang, S.L.Maslen, I.Sinning, D.Neuhaus, D.Clift, L.C.James. Trim-Away Ubiquitinates and Degrades Lysine-Less and N-Terminally Acetylated Substrates. Nat Commun V. 14 2160 2023.
ISSN: ESSN 2041-1723
PubMed: 37061529
DOI: 10.1038/S41467-023-37504-X