Zinc in PDB 8rx0: (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub

All present enzymatic activity of (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub:
2.3.2.23; 2.3.2.24;

The structure of (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub (pdb code 8rx0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub, PDB code: 8rx0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn401 b:70.6 occ:1.00 ND1 R:HIS80 2.0 55.3 1.0 SG R:CYS45 2.2 47.5 1.0 SG R:CYS42 2.3 51.3 1.0 SG R:CYS83 2.4 53.6 1.0 HB2 R:HIS80 2.5 55.3 1.0 CG R:HIS80 2.9 55.3 1.0 H R:HIS80 2.9 55.3 1.0 CE1 R:HIS80 3.1 55.3 1.0 CB R:HIS80 3.1 55.3 1.0 HB3 R:CYS45 3.1 47.5 1.0 HB2 R:CYS83 3.2 53.6 1.0 CB R:CYS45 3.3 47.5 1.0 HE1 R:HIS80 3.3 55.3 1.0 CB R:CYS83 3.4 53.6 1.0 H R:CYS45 3.4 47.5 1.0 CB R:CYS42 3.5 51.3 1.0 HB R:ILE44 3.6 47.1 1.0 HB2 R:CYS42 3.6 51.3 1.0 N R:HIS80 3.7 55.3 1.0 HB3 R:CYS42 3.7 51.3 1.0 HB3 R:CYS83 3.8 53.6 1.0 HB3 R:HIS80 3.9 55.3 1.0 CA R:HIS80 4.0 55.3 1.0 N R:CYS45 4.0 47.5 1.0 HB2 R:CYS45 4.0 47.5 1.0 CD2 R:HIS80 4.0 55.3 1.0 NE2 R:HIS80 4.1 55.3 1.0 HA R:CYS53 4.2 64.9 1.0 CA R:CYS45 4.3 47.5 1.0 H R:CYS83 4.4 53.6 1.0 CB R:ILE44 4.5 47.1 1.0 HA R:PHE79 4.5 51.6 1.0 HB2 R:CYS53 4.6 64.9 1.0 H R:ILE44 4.6 47.1 1.0 SG R:CYS53 4.7 64.9 1.0 O R:HIS80 4.7 55.3 1.0 HG12 R:ILE44 4.7 47.1 1.0 H R:ILE54 4.7 54.5 1.0 HB2 R:ASN47 4.7 55.2 1.0 HA R:HIS80 4.7 55.3 1.0 CA R:CYS83 4.7 53.6 1.0 H R:ASN47 4.8 55.2 1.0 C R:HIS80 4.8 55.3 1.0 HB3 R:PHE79 4.8 51.6 1.0 C R:PHE79 4.8 51.6 1.0 HD2 R:HIS80 4.8 55.3 1.0 N R:CYS83 4.9 53.6 1.0 H R:ARG46 4.9 47.1 1.0 HE2 R:HIS80 4.9 55.3 1.0 CA R:CYS42 4.9 51.3 1.0 HD1 R:PHE79 4.9 51.6 1.0 HG13 R:ILE44 4.9 47.1 1.0 CB R:CYS53 5.0 64.9 1.0 CG1 R:ILE44 5.0 47.1 1.0 C R:ILE44 5.0 47.1 1.0

Zinc binding site 2 out of 3 in the (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn402 b:92.6 occ:1.00 HD1 R:HIS77 1.5 59.5 1.0 OD1 R:ASP97 2.0 62.5 1.0 OD2 R:ASP97 2.0 62.5 1.0 HB2 R:CYS75 2.0 64.8 1.0 ND1 R:HIS77 2.0 59.5 1.0 CG R:ASP97 2.1 62.5 1.0 SG R:CYS94 2.4 58.8 1.0 CB R:CYS75 2.4 64.8 1.0 SG R:CYS75 2.5 64.8 1.0 HB3 R:CYS75 2.6 64.8 1.0 HB2 R:HIS77 2.8 59.5 1.0 CE1 R:HIS77 2.9 59.5 1.0 CG R:HIS77 2.9 59.5 1.0 HE1 R:HIS77 3.1 59.5 1.0 CB R:HIS77 3.4 59.5 1.0 H R:ASP97 3.4 62.5 1.0 CB R:ASP97 3.5 62.5 1.0 HB2 R:CYS94 3.5 58.8 1.0 CB R:CYS94 3.5 58.8 1.0 HB3 R:ASP97 3.7 62.5 1.0 HB3 R:CYS94 3.7 58.8 1.0 H R:CYS75 3.8 64.8 1.0 H R:HIS77 3.8 59.5 1.0 NE2 R:HIS77 3.9 59.5 1.0 HB3 R:HIS77 3.9 59.5 1.0 CA R:CYS75 3.9 64.8 1.0 CD2 R:HIS77 3.9 59.5 1.0 HB2 R:ASP97 4.1 62.5 1.0 N R:ASP97 4.2 62.5 1.0 HE2 R:PHE79 4.2 51.6 1.0 HB2 R:LEU96 4.2 55.8 1.0 N R:CYS75 4.3 64.8 1.0 CA R:ASP97 4.4 62.5 1.0 HA R:CYS75 4.5 64.8 1.0 HA3 R:GLY73 4.5 63.3 1.0 N R:HIS77 4.5 59.5 1.0 CA R:HIS77 4.6 59.5 1.0 C R:CYS75 4.6 64.8 1.0 HB2 R:ARG99 4.7 64.2 1.0 HD2 R:HIS77 4.7 59.5 1.0 HE R:ARG99 4.8 64.2 1.0 O R:ASP97 4.9 62.5 1.0 H R:LEU96 4.9 55.8 1.0 C R:ASP97 4.9 62.5 1.0 CA R:CYS94 5.0 58.8 1.0 HB3 R:LEU96 5.0 55.8 1.0

Zinc binding site 3 out of 3 in the (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn403 b:113.0 occ:1.00 HB3 R:CYS53 1.6 64.9 1.0 HB2 R:HIS82 1.8 60.9 1.0 HB2 R:CYS53 2.0 64.9 1.0 CB R:CYS53 2.0 64.9 1.0 ND1 R:HIS82 2.0 60.9 1.0 SG R:CYS56 2.3 66.8 1.0 SG R:CYS68 2.4 65.2 1.0 CB R:HIS82 2.5 60.9 1.0 SG R:CYS53 2.5 64.9 1.0 CG R:HIS82 2.5 60.9 1.0 HB3 R:HIS82 2.9 60.9 1.0 CE1 R:HIS82 3.3 60.9 1.0 HB2 R:CYS56 3.4 66.8 1.0 H R:HIS82 3.5 60.9 1.0 CA R:CYS53 3.5 64.9 1.0 CB R:CYS56 3.5 66.8 1.0 H R:CYS53 3.5 64.9 1.0 H R:CYS56 3.6 66.8 1.0 HB2 R:CYS68 3.7 65.2 1.0 CB R:CYS68 3.7 65.2 1.0 HB3 R:HIS80 3.7 55.3 1.0 HE1 R:HIS82 3.7 60.9 1.0 CA R:HIS82 3.8 60.9 1.0 CD2 R:HIS82 3.8 60.9 1.0 N R:CYS53 4.0 64.9 1.0 N R:HIS82 4.0 60.9 1.0 HA R:CYS53 4.1 64.9 1.0 NE2 R:HIS82 4.1 60.9 1.0 HB3 R:CYS56 4.2 66.8 1.0 N R:CYS56 4.2 66.8 1.0 C R:CYS53 4.3 64.9 1.0 HA R:CYS68 4.4 65.2 1.0 HB2 R:GLU55 4.4 63.9 1.0 HB3 R:CYS68 4.4 65.2 1.0 HA R:HIS82 4.4 60.9 1.0 HB2 R:HIS80 4.5 55.3 1.0 C R:HIS82 4.5 60.9 1.0 CA R:CYS56 4.5 66.8 1.0 CB R:HIS80 4.5 55.3 1.0 H R:CYS83 4.5 53.6 1.0 HD2 R:HIS82 4.6 60.9 1.0 CA R:CYS68 4.6 65.2 1.0 O R:CYS53 4.7 64.9 1.0 H R:GLU55 4.7 63.9 1.0 N R:CYS83 4.8 53.6 1.0 HA R:CYS56 4.8 66.8 1.0 HE2 R:HIS82 5.0 60.9 1.0

C.Crowe, M.A.Nakasone. (NEDD8)-CRL2VHL-MZ1-BRD4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub To Be Published.