Zinc in PDB 5zc4: Crystal Structure of RNF13 Ring Domain

All present enzymatic activity of Crystal Structure of RNF13 Ring Domain:
2.3.2.27;

The structure of Crystal Structure of RNF13 Ring Domain, PDB code: 5zc4 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)	22.62 / 1.91
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	90.338, 90.338, 45.445, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 18.6

The binding sites of Zinc atom in the Crystal Structure of RNF13 Ring Domain (pdb code 5zc4). 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 RNF13 Ring Domain, PDB code: 5zc4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of RNF13 Ring Domain


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 RNF13 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:46.9 occ:1.00 ND1 A:HIS263 2.1 51.8 1.0 SG A:CYS243 2.3 47.0 1.0 SG A:CYS240 2.3 41.7 1.0 SG A:CYS266 2.4 45.9 1.0 CB A:CYS240 3.0 39.2 1.0 CE1 A:HIS263 3.0 52.4 1.0 CG A:HIS263 3.1 53.9 1.0 CB A:CYS266 3.2 43.9 1.0 CB A:CYS243 3.3 46.2 1.0 CB A:HIS263 3.5 53.2 1.0 N A:CYS243 3.7 39.0 1.0 CA A:CYS243 4.1 41.4 1.0 NE2 A:HIS263 4.1 54.3 1.0 N A:HIS263 4.1 48.5 1.0 CD2 A:HIS263 4.2 54.4 1.0 CA A:HIS263 4.4 48.3 1.0 CA A:CYS240 4.4 39.4 1.0 CE A:LYS265 4.6 60.2 0.5 CA A:CYS266 4.6 51.1 1.0 C A:CYS240 4.9 41.0 1.0 O A:CYS240 4.9 38.5 1.0 C A:ILE242 4.9 44.0 1.0 N A:CYS266 4.9 49.1 1.0 C A:CYS243 4.9 40.1 1.0 CB A:ILE242 4.9 35.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of RNF13 Ring Domain


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 RNF13 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:41.0 occ:1.00 ND1 A:HIS260 2.1 41.4 1.0 SG A:CYS278 2.2 38.7 1.0 SG A:CYS281 2.3 45.3 1.0 SG A:CYS258 2.4 43.1 1.0 CB A:CYS278 3.0 38.6 1.0 CG A:HIS260 3.1 40.1 1.0 CE1 A:HIS260 3.1 41.2 1.0 CB A:CYS258 3.2 42.1 1.0 CB A:HIS260 3.4 39.7 1.0 CB A:CYS281 3.5 45.0 1.0 N A:CYS281 3.8 38.3 1.0 CA A:CYS281 4.2 39.5 1.0 NE2 A:HIS260 4.2 41.9 1.0 CD2 A:HIS260 4.2 40.5 1.0 CA A:CYS278 4.5 37.9 1.0 N A:HIS260 4.5 39.4 1.0 O A:HOH1135 4.5 48.8 1.0 CA A:CYS258 4.5 49.3 1.0 CB A:VAL280 4.5 33.3 1.0 CA A:HIS260 4.6 38.1 1.0 C A:CYS258 4.7 50.6 1.0 O A:CYS258 4.8 48.6 1.0 C A:VAL280 4.8 38.2 1.0 N A:VAL280 4.9 33.9 1.0 C A:CYS281 4.9 42.2 1.0 C A:CYS278 5.0 40.0 1.0 CA A:VAL280 5.0 33.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of RNF13 Ring Domain


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 RNF13 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:41.4 occ:1.00 ND1 D:HIS263 2.1 47.0 1.0 SG D:CYS266 2.3 39.1 1.0 SG D:CYS243 2.3 40.1 1.0 SG D:CYS240 2.3 41.5 1.0 CB D:CYS240 2.9 41.5 1.0 CE1 D:HIS263 3.0 49.6 1.0 CG D:HIS263 3.1 45.9 1.0 CB D:CYS266 3.3 37.5 1.0 CB D:CYS243 3.3 36.5 1.0 CB D:HIS263 3.5 43.0 1.0 N D:CYS243 3.8 35.6 1.0 CA D:CYS243 4.1 33.0 1.0 NE2 D:HIS263 4.2 48.5 1.0 N D:HIS263 4.2 41.2 1.0 O A:HOH1143 4.2 47.5 1.0 CD2 D:HIS263 4.3 50.6 1.0 CA D:CYS240 4.4 47.2 1.0 CA D:HIS263 4.5 41.3 1.0 O D:CYS240 4.7 42.5 1.0 CA D:CYS266 4.7 38.0 1.0 CB D:ILE242 4.8 34.2 1.0 C D:CYS240 4.8 47.4 1.0 C D:ILE242 4.9 38.9 1.0 C D:CYS243 5.0 34.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of RNF13 Ring Domain


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 RNF13 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1002 b:61.7 occ:1.00 ND1 D:HIS260 2.1 62.5 1.0 SG D:CYS281 2.2 67.2 1.0 SG D:CYS278 2.3 53.9 1.0 SG D:CYS258 2.4 60.9 1.0 CB D:CYS278 3.0 52.4 1.0 CE1 D:HIS260 3.1 64.8 1.0 CG D:HIS260 3.1 58.8 1.0 CB D:CYS258 3.2 71.3 1.0 CB D:HIS260 3.4 55.0 1.0 CB D:CYS281 3.4 67.5 1.0 N D:CYS281 3.9 59.6 1.0 NE2 D:HIS260 4.2 65.1 1.0 CA D:CYS281 4.2 63.6 1.0 CD2 D:HIS260 4.2 58.7 1.0 CA D:CYS278 4.5 49.8 1.0 CA D:CYS258 4.5 75.8 1.0 N D:HIS260 4.6 63.0 1.0 CA D:HIS260 4.6 57.7 1.0 O D:HOH1120 4.7 57.2 1.0 C D:CYS281 4.8 64.2 1.0 OH D:TYR262 4.8 47.8 1.0 C D:CYS258 4.8 78.0 1.0 CB D:GLN283 4.8 74.7 1.0 O D:CYS258 4.9 82.6 1.0 N D:GLN283 4.9 69.5 1.0 C D:VAL280 4.9 56.8 1.0 N D:LYS282 5.0 61.9 1.0

S.Sarkar, A.B.Datta. Crystal Structure of RNF13 Ring Domain To Be Published.