Zinc in PDB 5zbu: Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub

All present enzymatic activity of Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub:
2.3.2.23; 2.3.2.24; 2.3.2.27;

The structure of Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub, PDB code: 5zbu was solved by A.B.Datta, S.Sarkar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.26 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.559, 105.740, 60.790, 90.00, 115.49, 90.00
R / Rfree (%)	21.4 / 26.2

The binding sites of Zinc atom in the Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub (pdb code 5zbu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub, PDB code: 5zbu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:74.0 occ:1.00 ND1 A:HIS263 2.1 0.5 1.0 SG A:CYS243 2.3 76.0 1.0 SG A:CYS240 2.3 90.3 1.0 SG A:CYS266 2.4 74.8 1.0 CB A:CYS240 2.9 94.5 1.0 CG A:HIS263 3.0 76.8 1.0 CE1 A:HIS263 3.1 83.4 1.0 CB A:HIS263 3.3 65.5 1.0 CB A:CYS266 3.3 74.6 1.0 CB A:CYS243 3.5 71.2 1.0 N A:HIS263 4.0 64.5 1.0 N A:CYS243 4.0 95.0 1.0 NE2 A:HIS263 4.2 85.2 1.0 CD2 A:HIS263 4.2 83.6 1.0 CA A:HIS263 4.3 71.3 1.0 CA A:CYS243 4.4 77.7 1.0 CA A:CYS240 4.4 0.0 1.0 CA A:CYS266 4.8 65.0 1.0 C A:CYS240 4.8 97.8 1.0 CE1 A:TYR247 4.9 79.4 1.0 CB A:ILE242 4.9 65.8 1.0 O A:CYS240 4.9 98.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:70.2 occ:1.00 ND1 A:HIS260 2.1 97.9 1.0 SG A:CYS258 2.2 67.4 1.0 SG A:CYS281 2.3 68.9 1.0 SG A:CYS278 2.3 84.4 1.0 CG A:HIS260 3.1 92.0 1.0 CE1 A:HIS260 3.1 0.2 1.0 CB A:CYS278 3.1 79.4 1.0 CB A:HIS260 3.4 91.3 1.0 CB A:CYS258 3.4 59.5 1.0 CB A:CYS281 3.6 65.0 1.0 N A:CYS281 3.8 55.9 1.0 NE2 A:HIS260 4.2 95.2 1.0 CD2 A:HIS260 4.2 94.5 1.0 CA A:CYS281 4.2 57.3 1.0 N A:HIS260 4.5 97.6 1.0 CA A:HIS260 4.5 84.8 1.0 CA A:CYS278 4.6 87.5 1.0 CB A:VAL280 4.6 63.8 1.0 CA A:CYS258 4.7 70.6 1.0 C A:CYS258 4.8 75.2 1.0 O A:CYS258 4.8 82.1 1.0 C A:VAL280 4.9 73.5 1.0 N A:VAL280 4.9 77.7 1.0 C A:CYS281 4.9 57.4 1.0 CD1 A:LEU256 4.9 51.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:71.7 occ:1.00 ND1 D:HIS263 2.2 83.3 1.0 SG D:CYS243 2.3 94.7 1.0 SG D:CYS240 2.4 59.2 1.0 SG D:CYS266 2.4 79.8 1.0 CB D:CYS240 2.9 72.6 1.0 CB D:CYS243 3.0 72.2 1.0 CG D:HIS263 3.1 80.8 1.0 CE1 D:HIS263 3.2 71.0 1.0 CB D:HIS263 3.3 71.9 1.0 CB D:CYS266 3.6 70.8 1.0 N D:CYS243 3.9 66.8 1.0 CA D:CYS243 4.0 71.1 1.0 CD2 D:HIS263 4.2 88.4 1.0 NE2 D:HIS263 4.2 77.2 1.0 CA D:CYS240 4.4 59.2 1.0 N D:HIS263 4.5 73.2 1.0 CE D:LYS265 4.5 86.0 1.0 CA D:HIS263 4.5 66.8 1.0 C D:CYS243 4.8 81.7 1.0 O D:CYS240 4.9 60.8 1.0 C D:CYS240 5.0 66.6 1.0 CA D:CYS266 5.0 55.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1002 b:88.0 occ:1.00 ND1 D:HIS260 2.0 0.4 1.0 SG D:CYS258 2.2 76.9 1.0 SG D:CYS281 2.3 70.3 1.0 SG D:CYS278 2.3 70.2 1.0 CE1 D:HIS260 2.9 0.4 1.0 CG D:HIS260 2.9 91.2 1.0 CB D:CYS278 3.0 71.1 1.0 CB D:HIS260 3.3 89.0 1.0 CB D:CYS258 3.4 90.2 1.0 CB D:CYS281 3.6 85.3 1.0 NE2 D:HIS260 4.0 0.9 1.0 CD2 D:HIS260 4.0 98.5 1.0 N D:CYS281 4.1 68.4 1.0 CA D:CYS278 4.4 81.5 1.0 CD2 D:LEU256 4.4 92.8 1.0 CA D:CYS281 4.5 70.1 1.0 N D:HIS260 4.5 79.5 1.0 CA D:HIS260 4.5 73.9 1.0 CA D:CYS258 4.6 95.6 1.0 OH D:TYR262 4.7 66.5 1.0 C D:CYS258 4.8 0.0 1.0 CB D:GLN283 4.8 0.4 1.0 O D:CYS258 4.8 0.3 1.0 CB D:VAL280 5.0 65.5 1.0

S.Sarkar, A.B.Datta. Crystal Structure of Pa-Tm-Ring E3 Ligase RNF13 Ring Domain in Complex with E2~Ub To Be Published.