Zinc in PDB 8v0d: UBCH5B-RING3 of MIB1 Fusion Structure

All present enzymatic activity of UBCH5B-RING3 of MIB1 Fusion Structure:
2.3.2.23; 2.3.2.24; 2.3.2.27;

The structure of UBCH5B-RING3 of MIB1 Fusion Structure, PDB code: 8v0d was solved by R.Cao, S.C.Blacklow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.16 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.985, 65.119, 135.931, 90, 93.03, 90
R / Rfree (%)	21.3 / 24.3

The binding sites of Zinc atom in the UBCH5B-RING3 of MIB1 Fusion Structure (pdb code 8v0d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the UBCH5B-RING3 of MIB1 Fusion Structure, PDB code: 8v0d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the UBCH5B-RING3 of MIB1 Fusion Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of UBCH5B-RING3 of MIB1 Fusion Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:56.0 occ:1.00 SG B:CYS963 2.3 51.5 1.0 SG B:CYS985 2.3 61.8 1.0 SG B:CYS966 2.3 67.0 1.0 SG B:CYS982 2.3 68.6 1.0 CB B:CYS963 3.0 58.9 1.0 CB B:CYS985 3.2 63.7 1.0 CB B:CYS982 3.3 62.1 1.0 CB B:CYS966 3.3 60.3 1.0 N B:CYS966 3.6 59.8 1.0 NH2 B:ARG969 3.7 70.1 1.0 N B:CYS982 3.8 58.4 1.0 CA B:CYS982 4.1 62.0 1.0 CA B:CYS966 4.1 59.8 1.0 N B:CYS985 4.2 66.2 1.0 CA B:CYS985 4.3 65.6 1.0 NE B:ARG969 4.4 67.7 1.0 CB B:VAL965 4.5 57.6 1.0 CA B:CYS963 4.5 60.7 1.0 CZ B:ARG969 4.5 71.4 1.0 C B:VAL965 4.7 59.9 1.0 C B:CYS982 4.7 63.2 1.0 O B:CYS982 4.7 63.2 1.0 N B:VAL965 4.8 56.8 1.0 CA B:VAL965 4.9 56.4 1.0 C B:CYS963 4.9 59.1 1.0 C B:THR981 5.0 59.6 1.0 CB B:THR981 5.0 62.0 1.0

Zinc binding site 2 out of 5 in the UBCH5B-RING3 of MIB1 Fusion Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of UBCH5B-RING3 of MIB1 Fusion Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1102 b:59.4 occ:1.00 ND1 B:HIS979 2.0 58.2 1.0 SG B:CYS995 2.3 65.9 1.0 SG B:CYS977 2.3 63.7 1.0 SG B:CYS992 2.3 61.3 1.0 CE1 B:HIS979 3.0 57.9 1.0 CG B:HIS979 3.1 60.1 1.0 CB B:CYS992 3.2 63.7 1.0 CB B:CYS977 3.4 65.0 1.0 CB B:CYS995 3.4 62.8 1.0 CB B:HIS979 3.5 61.2 1.0 N B:CYS995 3.8 61.2 1.0 NE2 B:HIS979 4.1 54.5 1.0 CA B:CYS995 4.2 61.6 1.0 CD2 B:HIS979 4.2 59.2 1.0 N B:HIS979 4.3 63.0 1.0 O B:CYS977 4.4 65.1 1.0 CA B:HIS979 4.5 61.3 1.0 C B:CYS977 4.5 65.3 1.0 CA B:CYS977 4.6 67.9 1.0 CA B:CYS992 4.7 63.5 1.0 CB B:ILE994 4.8 60.9 1.0 C B:CYS995 4.8 62.0 1.0 C B:ILE994 4.8 62.3 1.0 N B:ARG996 4.9 63.4 1.0

Zinc binding site 3 out of 5 in the UBCH5B-RING3 of MIB1 Fusion Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of UBCH5B-RING3 of MIB1 Fusion Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:55.4 occ:1.00 SG A:CYS982 2.3 60.8 1.0 SG A:CYS985 2.3 62.1 1.0 SG A:CYS963 2.3 58.3 1.0 SG A:CYS966 2.3 66.2 1.0 CB A:CYS985 3.2 58.5 1.0 CB A:CYS963 3.2 58.2 1.0 CB A:CYS966 3.3 62.4 1.0 CB A:CYS982 3.4 60.5 1.0 N A:CYS966 3.6 58.8 1.0 N A:CYS982 4.0 58.2 1.0 NH1 A:ARG969 4.1 75.0 1.0 CA A:CYS966 4.1 60.8 1.0 N A:CYS985 4.2 64.1 1.0 CA A:CYS982 4.2 59.6 1.0 CA A:CYS985 4.3 63.6 1.0 CB A:VAL965 4.5 57.0 1.0 CA A:CYS963 4.7 58.9 1.0 CD A:ARG969 4.7 71.1 1.0 C A:VAL965 4.7 59.1 1.0 O A:CYS982 4.8 62.6 1.0 C A:CYS982 4.8 61.9 1.0 N A:VAL965 4.9 57.0 1.0 CA A:VAL965 4.9 57.8 1.0 CZ A:ARG969 5.0 76.1 1.0

Zinc binding site 4 out of 5 in the UBCH5B-RING3 of MIB1 Fusion Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of UBCH5B-RING3 of MIB1 Fusion Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:53.2 occ:1.00 ND1 A:HIS979 2.1 55.1 1.0 SG A:CYS977 2.3 56.4 1.0 SG A:CYS992 2.3 57.4 1.0 SG A:CYS995 2.3 57.2 1.0 CE1 A:HIS979 3.1 55.2 1.0 CG A:HIS979 3.1 54.3 1.0 CB A:CYS992 3.1 57.0 1.0 CB A:CYS977 3.2 59.0 1.0 CB A:HIS979 3.4 51.4 1.0 CB A:CYS995 3.4 55.5 1.0 N A:CYS995 3.7 54.9 1.0 CA A:CYS995 4.1 56.9 1.0 NE2 A:HIS979 4.2 57.2 1.0 N A:HIS979 4.2 57.2 1.0 CD2 A:HIS979 4.2 54.8 1.0 CA A:CYS977 4.4 59.6 1.0 CA A:HIS979 4.4 55.4 1.0 C A:CYS977 4.4 60.8 1.0 O A:CYS977 4.4 60.5 1.0 CA A:CYS992 4.6 57.0 1.0 CB A:ILE994 4.6 56.3 1.0 C A:CYS995 4.7 57.5 1.0 N A:ARG996 4.7 59.0 1.0 C A:ILE994 4.8 54.7 1.0 N A:ILE994 4.9 54.6 1.0 CA A:ILE994 5.0 54.9 1.0

Zinc binding site 5 out of 5 in the UBCH5B-RING3 of MIB1 Fusion Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of UBCH5B-RING3 of MIB1 Fusion Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:76.0 occ:1.00 NE2 A:HIS32 2.3 71.9 1.0 NE2 A:HIS55 2.3 70.9 1.0 CD2 A:HIS55 2.5 70.4 1.0 CE1 A:HIS55 2.5 74.8 1.0 CG A:HIS55 2.8 65.4 1.0 ND1 A:HIS55 2.8 73.0 1.0 CE1 A:HIS32 3.1 70.6 1.0 CD2 A:HIS32 3.3 67.5 1.0 CB A:HIS55 3.8 58.5 1.0 ND1 A:HIS32 4.3 67.5 1.0 CG A:HIS32 4.4 64.7 1.0 NZ A:LYS66 4.7 70.3 1.0 CA A:HIS55 4.8 55.1 1.0 CE A:LYS66 4.8 67.2 1.0

R.Cao, S.C.Blacklow. UBCH5B-RING3 Fusion Structure To Be Published.