Zinc in PDB 8wqg: Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)

The binding sites of Zinc atom in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) (pdb code 8wqg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1), PDB code: 8wqg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn200 b:156.9 occ:1.00 CB F:CYS53 2.1 128.5 1.0 SG F:CYS56 2.3 129.2 1.0 ND1 F:HIS82 2.3 105.3 1.0 SG F:CYS53 2.3 128.5 1.0 CB F:HIS82 2.6 105.3 1.0 CG F:HIS82 2.6 105.3 1.0 CE1 F:HIS82 3.4 105.3 1.0 CA F:CYS53 3.6 128.5 1.0 N F:HIS82 3.6 105.3 1.0 CA F:HIS82 3.6 105.3 1.0 CD2 F:HIS82 3.8 105.3 1.0 CB F:CYS56 3.9 129.2 1.0 N F:CYS56 4.1 129.2 1.0 NE2 F:HIS82 4.2 105.3 1.0 N F:CYS53 4.2 128.5 1.0 NE2 F:GLN60 4.2 143.2 1.0 N F:CYS83 4.3 89.6 1.0 C F:HIS82 4.4 105.3 1.0 CB F:CYS68 4.4 127.9 1.0 C F:CYS53 4.4 128.5 1.0 CB F:HIS80 4.5 99.7 1.0 CA F:CYS56 4.6 129.2 1.0 CA F:CYS68 4.6 127.9 1.0 NH1 F:ARG86 4.7 87.3 1.0 N F:ILE54 4.9 123.9 1.0 C F:PHE81 4.9 105.7 1.0 N F:GLU55 5.0 125.4 1.0 N F:PHE81 5.0 105.7 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:113.2 occ:1.00 ND1 F:HIS80 2.1 99.7 1.0 SG F:CYS42 2.3 88.3 1.0 SG F:CYS45 2.3 99.2 1.0 SG F:CYS83 2.3 89.6 1.0 CG F:HIS80 2.6 99.7 1.0 CB F:CYS45 2.6 99.2 1.0 CB F:HIS80 2.8 99.7 1.0 CB F:CYS42 2.8 88.3 1.0 CE1 F:HIS80 3.1 99.7 1.0 CB F:CYS83 3.1 89.6 1.0 N F:CYS45 3.6 99.2 1.0 CD2 F:HIS80 3.6 99.7 1.0 CA F:CYS45 3.7 99.2 1.0 N F:HIS80 3.8 99.7 1.0 CA F:HIS80 3.8 99.7 1.0 NE2 F:HIS80 3.9 99.7 1.0 CA F:CYS42 4.2 88.3 1.0 SG F:CYS53 4.3 128.5 1.0 O F:CYS42 4.3 88.3 1.0 CA F:CYS83 4.5 89.6 1.0 C F:CYS42 4.5 88.3 1.0 C F:CYS45 4.7 99.2 1.0 CA F:CYS53 4.7 128.5 1.0 C F:ILE44 4.7 82.3 1.0 CB F:CYS53 4.7 128.5 1.0 C F:HIS80 4.7 99.7 1.0 N F:CYS83 4.8 89.6 1.0 N F:ILE54 4.8 123.9 1.0 CB F:ILE44 4.9 82.3 1.0 C F:PHE79 4.9 82.4 1.0 O F:HIS80 4.9 99.7 1.0 N F:ARG46 4.9 100.9 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn202 b:85.8 occ:1.00 CE1 F:HIS77 2.2 74.2 1.0 SG F:CYS75 2.3 80.5 1.0 ND1 F:HIS77 2.3 74.2 1.0 SG F:CYS94 2.3 55.1 1.0 OD1 F:ASP97 2.4 64.8 1.0 CG F:ASP97 2.7 64.8 1.0 NE2 F:HIS77 2.9 74.2 1.0 N F:ASP97 2.9 64.8 1.0 CG F:HIS77 3.1 74.2 1.0 CB F:LEU96 3.1 59.8 1.0 OD2 F:ASP97 3.3 64.8 1.0 CB F:ASP97 3.3 64.8 1.0 CD2 F:HIS77 3.4 74.2 1.0 C F:LEU96 3.4 59.8 1.0 CA F:LEU96 3.5 59.8 1.0 N F:LEU96 3.6 59.8 1.0 CB F:CYS94 3.7 55.1 1.0 CA F:ASP97 3.7 64.8 1.0 CB F:CYS75 4.0 80.5 1.0 CB F:HIS77 4.1 74.2 1.0 O F:LEU96 4.3 59.8 1.0 CG F:LEU96 4.4 59.8 1.0 O F:CYS94 4.6 55.1 1.0 C F:ASP97 4.6 64.8 1.0 C F:CYS94 4.6 55.1 1.0 CD1 F:LEU96 4.7 59.8 1.0 CA F:CYS94 4.8 55.1 1.0 O F:CYS75 4.8 80.5 1.0 N F:ASN98 4.8 65.9 1.0 C F:PRO95 4.9 53.5 1.0 CZ F:PHE79 4.9 82.4 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn200 b:167.6 occ:1.00 CD2 J:HIS82 2.0 128.2 1.0 NE2 J:HIS82 2.1 128.2 1.0 SG J:CYS53 2.3 136.8 1.0 SG J:CYS56 2.3 136.6 1.0 SG J:CYS68 2.3 146.4 1.0 CG J:HIS82 2.6 128.2 1.0 CE1 J:HIS82 2.7 128.2 1.0 ND1 J:HIS82 3.0 128.2 1.0 OE2 J:GLU55 3.1 142.6 1.0 CB J:CYS56 3.1 136.6 1.0 CB J:HIS82 3.7 128.2 1.0 CB J:CYS68 3.9 146.4 1.0 CB J:CYS53 4.0 136.8 1.0 CD J:GLU55 4.1 142.6 1.0 N J:CYS56 4.3 136.6 1.0 CA J:CYS56 4.3 136.6 1.0 CG J:GLU55 4.7 142.6 1.0 CA J:CYS68 4.7 146.4 1.0 N J:CYS53 4.8 136.8 1.0 CD1 J:LEU52 4.9 137.4 1.0 CG J:LEU52 4.9 137.4 1.0 CA J:CYS53 4.9 136.8 1.0 CA J:HIS82 5.0 128.2 1.0 OE1 J:GLU55 5.0 142.6 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn201 b:114.5 occ:1.00 ND1 J:HIS80 2.1 122.4 1.0 SG J:CYS42 2.3 119.5 1.0 SG J:CYS45 2.3 114.3 1.0 SG J:CYS83 2.3 102.9 1.0 CG J:HIS80 2.8 122.4 1.0 CB J:CYS45 2.9 114.3 1.0 CB J:HIS80 2.9 122.4 1.0 CB J:CYS42 3.2 119.5 1.0 CE1 J:HIS80 3.2 122.4 1.0 CB J:CYS83 3.2 102.9 1.0 CB J:CYS53 3.5 136.8 1.0 N J:CYS45 3.7 114.3 1.0 N J:HIS80 3.9 122.4 1.0 CA J:CYS45 3.9 114.3 1.0 CA J:HIS80 4.0 122.4 1.0 CA J:CYS53 4.0 136.8 1.0 O J:CYS42 4.0 119.5 1.0 CD2 J:HIS80 4.0 122.4 1.0 NE2 J:HIS80 4.2 122.4 1.0 CA J:CYS42 4.4 119.5 1.0 C J:CYS42 4.5 119.5 1.0 CA J:CYS83 4.6 102.9 1.0 O J:HIS80 4.6 122.4 1.0 N J:CYS83 4.7 102.9 1.0 C J:HIS80 4.7 122.4 1.0 C J:ILE44 4.8 106.8 1.0 C J:CYS45 4.8 114.3 1.0 N J:CYS53 4.9 136.8 1.0 CB J:ILE44 4.9 106.8 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn202 b:130.2 occ:1.00 CB J:CYS75 1.8 106.7 1.0 OD1 J:ASP97 2.1 90.0 1.0 SG J:CYS94 2.3 84.0 1.0 SG J:CYS75 2.3 106.7 1.0 ND1 J:HIS77 2.3 88.7 1.0 CE1 J:HIS77 2.8 88.7 1.0 CA J:CYS75 3.0 106.7 1.0 CB J:CYS94 3.0 84.0 1.0 CG J:ASP97 3.1 90.0 1.0 O J:CYS75 3.4 106.7 1.0 OD2 J:ASP97 3.5 90.0 1.0 C J:CYS75 3.5 106.7 1.0 CG J:HIS77 3.6 88.7 1.0 NE2 J:HIS77 4.0 88.7 1.0 N J:CYS75 4.2 106.7 1.0 CB J:HIS77 4.3 88.7 1.0 N J:ASP97 4.3 90.0 1.0 CZ3 J:TRP101 4.3 84.3 1.0 CD2 J:HIS77 4.4 88.7 1.0 O J:ASP97 4.4 90.0 1.0 CB J:ASP97 4.4 90.0 1.0 CE3 J:TRP101 4.5 84.3 1.0 CA J:CYS94 4.5 84.0 1.0 N J:ASN76 4.6 100.0 1.0 CB J:LEU96 4.7 84.2 1.0 N J:HIS77 4.8 88.7 1.0 CA J:ASP97 4.8 90.0 1.0

X.Chen, K.Zhang, C.Xu. Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) To Be Published.