Zinc in PDB 8jav: Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)

The binding sites of Zinc atom in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) (pdb code 8jav). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer), PDB code: 8jav:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:54.2 occ:1.00 NE2 B:HIS89 2.0 29.2 1.0 NE2 A:HIS89 2.0 14.5 1.0 SG A:CYS54 2.3 13.3 1.0 SG B:CYS54 2.3 38.6 1.0 CE1 A:HIS89 2.8 14.5 1.0 CE1 B:HIS89 3.0 29.2 1.0 CD2 B:HIS89 3.0 29.2 1.0 CD2 A:HIS89 3.0 14.5 1.0 CB A:CYS54 3.5 13.3 1.0 O B:LEU53 3.5 34.0 1.0 CB B:CYS54 3.7 38.6 1.0 CA A:CYS54 3.8 13.3 1.0 ND1 A:HIS89 3.9 14.5 1.0 CG A:HIS89 4.0 14.5 1.0 CA B:CYS54 4.1 38.6 1.0 ND1 B:HIS89 4.1 29.2 1.0 CG B:HIS89 4.1 29.2 1.0 N A:CYS54 4.2 13.3 1.0 CG2 A:VAL91 4.3 20.9 1.0 C B:LEU53 4.4 34.0 1.0 N B:CYS54 4.7 38.6 1.0 C A:LEU53 4.8 13.7 1.0 O A:LEU53 4.9 13.7 1.0

Zinc binding site 2 out of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn200 b:46.3 occ:1.00 ND1 R:HIS82 2.0 34.9 1.0 SG R:CYS53 2.3 35.9 1.0 SG R:CYS68 2.3 40.3 1.0 SG R:CYS56 2.3 43.5 1.0 CE1 R:HIS82 2.7 34.9 1.0 CG R:HIS82 3.2 34.9 1.0 CB R:CYS68 3.3 40.3 1.0 CB R:CYS56 3.3 43.5 1.0 CB R:CYS53 3.3 35.9 1.0 N R:CYS53 3.7 35.9 1.0 NE2 R:HIS82 3.8 34.9 1.0 CB R:HIS82 3.8 34.9 1.0 CA R:CYS68 3.9 40.3 1.0 N R:CYS56 4.0 43.5 1.0 CA R:CYS53 4.1 35.9 1.0 CD2 R:HIS82 4.1 34.9 1.0 CA R:CYS56 4.2 43.5 1.0 C R:CYS53 4.7 35.9 1.0 O R:CYS53 4.7 35.9 1.0 N R:CYS68 4.8 40.3 1.0 C R:LEU52 4.8 35.6 1.0 C R:CYS68 5.0 40.3 1.0

Zinc binding site 3 out of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:36.2 occ:1.00 ND1 R:HIS80 2.1 28.1 1.0 SG R:CYS45 2.3 26.8 1.0 SG R:CYS83 2.3 30.5 1.0 SG R:CYS42 2.3 27.2 1.0 CG R:HIS80 2.9 28.1 1.0 CB R:CYS42 3.0 27.2 1.0 CB R:HIS80 3.0 28.1 1.0 CB R:CYS45 3.2 26.8 1.0 CE1 R:HIS80 3.2 28.1 1.0 CB R:CYS83 3.2 30.5 1.0 CB R:CYS53 3.8 35.9 1.0 N R:CYS45 4.1 26.8 1.0 CD2 R:HIS80 4.1 28.1 1.0 CA R:CYS53 4.2 35.9 1.0 NE2 R:HIS80 4.2 28.1 1.0 CA R:CYS45 4.2 26.8 1.0 N R:HIS80 4.2 28.1 1.0 CA R:HIS80 4.2 28.1 1.0 CA R:CYS42 4.5 27.2 1.0 CA R:CYS83 4.6 30.5 1.0 O R:CYS42 4.6 27.2 1.0 N R:ILE54 4.7 37.2 1.0 C R:CYS42 4.8 27.2 1.0 C R:CYS45 4.9 26.8 1.0 N R:CYS83 4.9 30.5 1.0

Zinc binding site 4 out of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn202 b:45.1 occ:1.00 SG R:CYS75 2.3 34.6 1.0 SG R:CYS94 2.3 29.3 1.0 ND1 R:HIS77 2.3 31.1 1.0 CE1 R:HIS77 3.1 31.1 1.0 CG R:HIS77 3.2 31.1 1.0 CB R:ASP97 3.3 34.5 1.0 CB R:CYS94 3.3 29.3 1.0 CB R:CYS75 3.3 34.6 1.0 N R:ASP97 3.5 34.5 1.0 CB R:HIS77 3.5 31.1 1.0 O R:ASP97 3.7 34.5 1.0 CA R:ASP97 3.8 34.5 1.0 NE2 R:HIS77 4.1 31.1 1.0 CD2 R:HIS77 4.1 31.1 1.0 C R:ASP97 4.2 34.5 1.0 CB R:LEU96 4.4 31.3 1.0 C R:LEU96 4.6 31.3 1.0 CG R:ASP97 4.6 34.5 1.0 CA R:CYS75 4.7 34.6 1.0 CA R:CYS94 4.7 29.3 1.0 O R:CYS75 4.7 34.6 1.0 N R:LEU96 4.8 31.3 1.0 CZ3 R:TRP101 4.8 30.5 1.0 C R:CYS75 4.8 34.6 1.0 CA R:LEU96 4.8 31.3 1.0 CA R:HIS77 4.9 31.1 1.0 C R:CYS94 4.9 29.3 1.0 OD2 R:ASP97 5.0 34.5 1.0

Zinc binding site 5 out of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn601 b:48.2 occ:1.00 NE2 K:HIS89 2.0 25.6 1.0 NE2 J:HIS89 2.0 18.7 1.0 SG J:CYS54 2.3 9.9 1.0 SG K:CYS54 2.3 27.9 1.0 CE1 K:HIS89 2.6 25.6 1.0 CE1 J:HIS89 2.8 18.7 1.0 CD2 J:HIS89 3.1 18.7 1.0 CD2 K:HIS89 3.3 25.6 1.0 CB K:CYS54 3.6 27.9 1.0 CB J:CYS54 3.6 9.9 1.0 ND1 K:HIS89 3.8 25.6 1.0 CA J:CYS54 3.8 9.9 1.0 CA K:CYS54 3.8 27.9 1.0 ND1 J:HIS89 3.9 18.7 1.0 CG J:HIS89 4.1 18.7 1.0 CG K:HIS89 4.2 25.6 1.0 N J:CYS54 4.3 9.9 1.0 N K:CYS54 4.3 27.9 1.0 C J:LEU53 4.9 15.4 1.0 C K:LEU53 5.0 25.6 1.0

Zinc binding site 6 out of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range: probe atom residue distance (Å) B Occ V:Zn200 b:79.5 occ:1.00 ND1 V:HIS82 2.1 70.7 1.0 SG V:CYS53 2.3 72.2 1.0 SG V:CYS68 2.3 75.9 1.0 SG V:CYS56 2.3 78.9 1.0 CG V:HIS82 2.8 70.7 1.0 CB V:HIS82 2.8 70.7 1.0 CB V:CYS56 3.1 78.9 1.0 CB V:CYS53 3.2 72.2 1.0 CE1 V:HIS82 3.2 70.7 1.0 CB V:CYS68 3.3 75.9 1.0 N V:CYS56 3.9 78.9 1.0 N V:CYS53 3.9 72.2 1.0 CD2 V:HIS82 4.0 70.7 1.0 CA V:CYS56 4.0 78.9 1.0 CA V:CYS53 4.1 72.2 1.0 CA V:CYS68 4.2 75.9 1.0 NE2 V:HIS82 4.2 70.7 1.0 CA V:HIS82 4.2 70.7 1.0 N V:HIS82 4.6 70.7 1.0 C V:CYS53 4.7 72.2 1.0 O V:CYS53 4.8 72.2 1.0 C V:GLU55 4.9 74.9 1.0 C V:HIS82 4.9 70.7 1.0

Zinc binding site 7 out of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range: probe atom residue distance (Å) B Occ V:Zn201 b:67.2 occ:1.00 ND1 V:HIS80 2.1 62.4 1.0 SG V:CYS45 2.3 55.6 1.0 SG V:CYS83 2.3 64.5 1.0 SG V:CYS42 2.3 57.3 1.0 CG V:HIS80 2.9 62.4 1.0 CB V:CYS45 3.1 55.6 1.0 CB V:HIS80 3.1 62.4 1.0 CE1 V:HIS80 3.2 62.4 1.0 CB V:CYS42 3.2 57.3 1.0 CB V:CYS83 3.3 64.5 1.0 CB V:CYS53 4.0 72.2 1.0 N V:CYS45 4.0 55.6 1.0 CD2 V:HIS80 4.1 62.4 1.0 N V:HIS80 4.1 62.4 1.0 CA V:CYS45 4.1 55.6 1.0 NE2 V:HIS80 4.2 62.4 1.0 CA V:HIS80 4.2 62.4 1.0 CA V:CYS53 4.3 72.2 1.0 CA V:CYS42 4.6 57.3 1.0 O V:CYS42 4.6 57.3 1.0 CA V:CYS83 4.7 64.5 1.0 C V:CYS42 4.8 57.3 1.0 C V:CYS45 4.9 55.6 1.0 N V:ILE54 4.9 71.9 1.0

Zinc binding site 8 out of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range: probe atom residue distance (Å) B Occ V:Zn202 b:79.2 occ:1.00 OD1 V:ASP97 2.1 71.2 1.0 SG V:CYS75 2.3 74.3 1.0 SG V:CYS94 2.3 63.8 1.0 ND1 V:HIS77 2.3 69.6 1.0 CG V:HIS77 2.9 69.6 1.0 CB V:HIS77 2.9 69.6 1.0 CG V:ASP97 3.0 71.2 1.0 CB V:CYS75 3.2 74.3 1.0 OD2 V:ASP97 3.3 71.2 1.0 CE1 V:HIS77 3.4 69.6 1.0 CB V:CYS94 3.4 63.8 1.0 CD2 V:HIS77 4.1 69.6 1.0 N V:ASP97 4.1 71.2 1.0 CA V:HIS77 4.2 69.6 1.0 NE2 V:HIS77 4.3 69.6 1.0 O V:CYS75 4.3 74.3 1.0 N V:HIS77 4.4 69.6 1.0 CB V:LEU96 4.4 66.0 1.0 CB V:ASP97 4.4 71.2 1.0 O V:ASP97 4.4 71.2 1.0 CA V:CYS75 4.4 74.3 1.0 C V:CYS75 4.5 74.3 1.0 CA V:ASP97 4.8 71.2 1.0 CA V:CYS94 4.8 63.8 1.0 O V:HIS77 4.9 69.6 1.0 CZ3 V:TRP101 5.0 65.5 1.0 CZ V:PHE79 5.0 59.5 1.0 N V:LEU96 5.0 66.0 1.0

S.Zhao, K.Zhang, C.Xu. Molecular Basis For CRL2APPBP2-Mediated C-Degron Recognition To Be Published.