Zinc in PDB 8eb0: RNF216/E2-Ub/Ub Transthiolation Complex

The structure of RNF216/E2-Ub/Ub Transthiolation Complex, PDB code: 8eb0 was solved by T.R.Cotton, X.S.Wang, B.C.Lechtenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.37 / 3.03
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	152.545, 70.363, 65.152, 90, 108.7, 90
R / Rfree (%)	30.3 / 33.9

The binding sites of Zinc atom in the RNF216/E2-Ub/Ub Transthiolation Complex (pdb code 8eb0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the RNF216/E2-Ub/Ub Transthiolation Complex, PDB code: 8eb0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the RNF216/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RNF216/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:91.1 occ:1.00 SG A:CYS537 2.3 81.9 1.0 SG A:CYS518 2.3 90.9 1.0 SG A:CYS540 2.3 78.1 1.0 SG A:CYS515 2.3 89.2 1.0 CB A:CYS518 3.0 90.0 1.0 CB A:CYS540 3.0 77.0 1.0 CB A:CYS515 3.2 91.2 1.0 N A:CYS518 3.3 90.4 1.0 CB A:CYS537 3.3 83.3 1.0 CA A:CYS518 3.7 90.9 1.0 N A:CYS537 3.8 83.2 1.0 CA A:CYS537 4.1 83.0 1.0 CB A:CYS517 4.2 89.1 1.0 CA A:CYS540 4.2 75.6 1.0 N A:CYS540 4.3 76.1 1.0 C A:CYS517 4.4 91.2 1.0 CE2 A:PHE522 4.4 88.6 1.0 C A:CYS518 4.5 93.0 1.0 N A:TYR519 4.6 96.1 1.0 CA A:CYS517 4.6 90.8 1.0 N A:CYS517 4.7 92.2 1.0 CA A:CYS515 4.7 92.8 1.0 O A:CYS537 4.7 80.4 1.0 C A:CYS537 4.8 81.4 1.0 CZ A:PHE522 4.9 88.2 1.0 SG A:CYS517 5.0 87.4 1.0 C A:PHE536 5.0 86.1 1.0

Zinc binding site 2 out of 7 in the RNF216/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RNF216/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:99.4 occ:1.00 ND1 A:HIS534 2.1 98.3 1.0 SG A:CYS559 2.3 92.5 1.0 SG A:CYS564 2.3 98.6 1.0 SG A:CYS530 2.3 97.4 1.0 CB A:CYS564 2.7 99.0 1.0 CE1 A:HIS534 2.9 99.4 1.0 CB A:CYS559 3.1 91.1 1.0 CG A:HIS534 3.1 98.4 1.0 CB A:ASP532 3.5 106.8 1.0 CB A:HIS534 3.6 97.5 1.0 CB A:CYS530 3.8 95.8 1.0 NE2 A:HIS534 4.0 100.2 1.0 CD2 A:HIS534 4.2 99.6 1.0 CA A:CYS564 4.2 99.8 1.0 CG A:ASP532 4.2 107.2 1.0 OD2 A:ASP532 4.3 107.0 1.0 CA A:ASP532 4.3 107.2 1.0 N A:ASP532 4.4 105.9 1.0 N A:HIS534 4.4 99.1 1.0 CA A:CYS559 4.5 89.4 1.0 C A:ASP532 4.6 107.6 1.0 CA A:HIS534 4.6 98.6 1.0 O A:ASP532 4.9 108.5 1.0 N A:CYS564 5.0 100.3 1.0

Zinc binding site 3 out of 7 in the RNF216/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RNF216/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:87.1 occ:1.00 SG A:CYS605 2.2 87.0 1.0 SG A:CYS623 2.2 90.9 1.0 SG A:CYS628 2.3 85.0 1.0 SG A:CYS608 2.3 85.0 1.0 CB A:CYS623 2.4 90.4 1.0 CB A:CYS605 2.8 86.8 1.0 CB A:CYS628 3.3 87.3 1.0 CB A:CYS608 3.7 84.7 1.0 CA A:CYS623 3.9 91.4 1.0 N A:CYS608 3.9 82.0 1.0 CA A:CYS605 4.3 85.2 1.0 CB A:SER607 4.4 83.4 1.0 CA A:CYS608 4.4 83.0 1.0 CB A:LYS630 4.5 87.2 1.0 N A:LYS630 4.5 90.1 1.0 N A:ARG629 4.6 90.3 1.0 CA A:CYS628 4.6 89.1 1.0 C A:SER607 4.6 83.2 1.0 N A:SER607 4.7 81.2 1.0 N A:CYS623 4.7 91.1 1.0 CA A:SER607 4.8 82.3 1.0 C A:CYS623 4.8 93.7 1.0 C A:CYS605 4.9 84.2 1.0 O A:LYS630 4.9 87.0 1.0 C A:CYS628 4.9 89.7 1.0 CB A:PHE610 5.0 89.1 1.0 O A:CYS623 5.0 94.8 1.0

Zinc binding site 4 out of 7 in the RNF216/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RNF216/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:81.0 occ:1.00 NE2 A:HIS643 2.1 79.9 1.0 SG A:CYS633 2.3 82.9 1.0 SG A:CYS636 2.3 79.3 1.0 SG A:CYS648 2.3 75.7 1.0 CD2 A:HIS643 2.6 80.6 1.0 CE1 A:HIS643 3.0 80.5 1.0 CB A:CYS633 3.1 83.7 1.0 CG A:HIS643 3.6 81.7 1.0 CB A:CYS648 3.8 74.8 1.0 ND1 A:HIS643 3.8 81.6 1.0 CB A:CYS636 3.8 78.4 1.0 NZ A:LYS635 4.0 85.4 1.0 N A:CYS636 4.1 79.0 1.0 CA A:CYS648 4.1 75.0 1.0 N A:CYS648 4.4 75.4 1.0 CA A:CYS633 4.5 84.5 1.0 CA A:CYS636 4.5 78.5 1.0 CE A:LYS635 4.6 84.4 1.0 CB A:LYS635 4.6 83.7 1.0 C A:CYS633 4.9 83.6 1.0 O A:CYS633 4.9 82.8 1.0 CB A:HIS643 4.9 83.0 1.0 C A:LYS635 4.9 83.1 1.0 N A:LYS635 5.0 84.8 1.0

Zinc binding site 5 out of 7 in the RNF216/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of RNF216/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:69.5 occ:1.00 SG A:CYS695 2.2 68.5 1.0 SG A:CYS678 2.3 65.2 1.0 SG A:CYS693 2.3 65.6 1.0 SG A:CYS675 2.3 64.4 1.0 CB A:CYS693 3.1 66.3 1.0 CB A:CYS675 3.2 63.2 1.0 CB A:CYS695 3.5 69.2 1.0 CB A:CYS678 3.5 65.7 1.0 N A:CYS678 3.5 65.7 1.0 CA A:CYS678 4.1 65.5 1.0 N A:CYS695 4.2 69.3 1.0 CB A:LYS677 4.2 68.4 1.0 CA A:CYS695 4.4 69.9 1.0 CA A:CYS693 4.5 67.1 1.0 C A:LYS677 4.6 67.2 1.0 CA A:CYS675 4.6 62.6 1.0 C A:CYS678 4.7 64.4 1.0 N A:GLY679 4.7 63.1 1.0 CB A:ALA697 4.7 66.9 1.0 CA A:LYS677 4.7 67.6 1.0 N A:LYS677 4.8 66.6 1.0 OG1 A:THR680 4.8 61.8 1.0 N A:ARG694 4.8 69.9 1.0 C A:CYS693 4.9 67.8 1.0 CB A:THR680 4.9 61.2 1.0 N A:THR680 4.9 60.7 1.0

Zinc binding site 6 out of 7 in the RNF216/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of RNF216/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:71.5 occ:1.00 NE2 A:HIS712 2.1 78.8 1.0 SG A:CYS730 2.3 77.9 1.0 SG A:CYS700 2.3 71.4 1.0 SG A:CYS703 2.3 68.9 1.0 CB A:CYS730 2.9 79.5 1.0 CD2 A:HIS712 3.0 80.1 1.0 CB A:CYS700 3.1 70.6 1.0 CE1 A:HIS712 3.2 78.9 1.0 CB A:CYS703 3.4 67.8 1.0 N A:CYS703 3.8 67.4 1.0 CG A:HIS712 4.2 80.9 1.0 CA A:CYS703 4.2 66.8 1.0 ND1 A:HIS712 4.3 80.2 1.0 CA A:CYS730 4.3 81.1 1.0 CB A:LEU702 4.4 70.1 1.0 CA A:CYS700 4.6 70.2 1.0 CE1 A:PHE713 4.6 82.5 1.0 N A:CYS730 4.6 81.8 1.0 C A:LEU702 4.7 67.7 1.0 N A:LEU702 4.9 68.8 1.0 CA A:LEU702 4.9 68.6 1.0

Zinc binding site 7 out of 7 in the RNF216/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of RNF216/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:89.8 occ:1.00 ND1 A:HIS716 2.1 103.7 1.0 SG A:CYS724 2.3 88.6 1.0 SG A:CYS727 2.3 87.4 1.0 SG A:CYS714 2.3 97.3 1.0 CE1 A:HIS716 2.9 103.9 1.0 CG A:HIS716 2.9 106.1 1.0 CB A:HIS716 3.4 106.7 1.0 CB A:CYS727 3.6 87.5 1.0 N A:CYS727 3.6 89.2 1.0 NE2 A:HIS716 3.7 106.3 1.0 CB A:CYS714 3.7 94.7 1.0 CD2 A:HIS716 3.8 107.7 1.0 CB A:CYS724 4.0 87.8 1.0 CA A:CYS727 4.1 87.3 1.0 O A:CYS727 4.2 85.1 1.0 C A:GLU726 4.2 87.0 1.0 CB A:GLU726 4.3 91.1 1.0 N A:HIS716 4.3 105.1 1.0 CA A:CYS714 4.5 94.9 1.0 CA A:HIS716 4.5 107.2 1.0 N A:GLU726 4.6 88.2 1.0 NH2 A:ARG729 4.6 95.0 1.0 CA A:GLU726 4.6 89.0 1.0 C A:CYS727 4.6 85.1 1.0 N A:GLN715 4.6 104.5 1.0 C A:CYS714 4.9 96.7 1.0

X.S.Wang, T.R.Cotton, S.J.Trevelyan, L.W.Richardson, W.T.Lee, J.Silke, B.C.Lechtenberg. The Unifying Catalytic Mechanism of the Ring-Between-Ring E3 Ubiquitin Ligase Family. Nat Commun V. 14 168 2023.
ISSN: ESSN 2041-1723
PubMed: 36631489
DOI: 10.1038/S41467-023-35871-Z