Zinc in PDB 7cap: Cyclic LYS48-Linked Triubiquitin

The structure of Cyclic LYS48-Linked Triubiquitin, PDB code: 7cap was solved by M.Hiranyakorn, S.Yanaka, T.Satoh, T.Wilasri, B.Jityuti, T.Yagi-Utsumi, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.33
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.429, 54.820, 60.954, 90.00, 121.99, 90.00
R / Rfree (%)	13.5 / 17.4

The binding sites of Zinc atom in the Cyclic LYS48-Linked Triubiquitin (pdb code 7cap). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cyclic LYS48-Linked Triubiquitin, PDB code: 7cap:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cyclic LYS48-Linked Triubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cyclic LYS48-Linked Triubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:23.0 occ:1.00 O A:HOH290 1.9 33.6 1.0 OE1 A:GLU18 2.1 28.2 1.0 O A:HOH267 2.2 23.1 1.0 CD A:GLU18 3.0 25.5 1.0 OE2 A:GLU18 3.4 32.9 1.0 O A:HOH237 3.9 24.9 1.0 O A:HOH292 4.1 41.6 1.0 O A:HOH284 4.2 31.1 1.0 CG A:GLU18 4.3 24.8 1.0 O A:HOH238 4.9 27.8 1.0

Zinc binding site 2 out of 6 in the Cyclic LYS48-Linked Triubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cyclic LYS48-Linked Triubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:25.8 occ:1.00 NE2 A:HIS68 2.0 21.1 1.0 O A:HOH287 2.1 23.4 1.0 O A:HOH288 2.3 20.4 1.0 O B:HOH280 2.7 44.8 1.0 CE1 A:HIS68 3.1 21.4 1.0 CD2 A:HIS68 3.1 19.5 1.0 ND1 A:HIS68 4.2 22.0 1.0 CG A:HIS68 4.2 19.9 1.0 O B:HOH298 4.3 39.6 1.0 CG A:LYS6 4.3 23.7 1.0 O A:HOH235 4.6 37.3 1.0 CE A:LYS6 4.7 30.9 1.0 CB A:LYS6 4.8 19.8 1.0 CD A:LYS6 4.8 27.3 1.0 OE1 B:GLN40 4.9 29.9 1.0

Zinc binding site 3 out of 6 in the Cyclic LYS48-Linked Triubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cyclic LYS48-Linked Triubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:19.4 occ:1.00 OE1 B:GLU18 1.9 18.5 1.0 O B:HOH279 2.0 19.7 1.0 CD B:GLU18 2.6 15.8 1.0 OE2 B:GLU18 2.7 19.1 1.0 O B:HOH284 3.9 32.4 1.0 CG B:GLU18 4.1 17.3 1.0 O B:HOH230 4.2 22.6 1.0 O B:HOH287 4.8 31.7 1.0 CB B:GLU18 4.9 15.6 1.0

Zinc binding site 4 out of 6 in the Cyclic LYS48-Linked Triubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cyclic LYS48-Linked Triubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:26.5 occ:1.00 O B:HOH283 2.0 31.3 1.0 NE2 B:HIS68 2.1 19.8 1.0 O B:HOH281 2.2 34.6 1.0 O B:HOH282 2.2 26.7 1.0 CD2 B:HIS68 3.1 21.1 1.0 CE1 B:HIS68 3.1 20.5 1.0 O B:HOH270 4.2 35.5 1.0 ND1 B:HIS68 4.2 23.2 1.0 CG B:HIS68 4.2 18.6 1.0 O C:HOH244 4.3 25.7 1.0 CD1 C:LEU8 4.3 28.1 1.0 CD B:LYS6 4.3 24.8 1.0 O C:HOH232 4.6 48.0 1.0 CD2 C:LEU71 4.6 21.2 1.0 O B:HOH297 4.8 44.8 1.0

Zinc binding site 5 out of 6 in the Cyclic LYS48-Linked Triubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cyclic LYS48-Linked Triubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:28.6 occ:1.00 NE2 C:HIS68 1.9 21.2 1.0 O C:HOH259 2.2 74.2 1.0 O C:HOH263 2.2 25.6 1.0 O C:HOH262 2.7 37.0 1.0 CE1 C:HIS68 2.9 26.6 1.0 CD2 C:HIS68 3.0 23.2 1.0 ND1 C:HIS68 4.0 23.5 1.0 O A:HOH295 4.0 28.9 1.0 O A:HOH209 4.1 32.9 1.0 CG C:HIS68 4.1 19.2 1.0 CD C:LYS6 4.4 44.8 1.0 CD1 A:LEU71 4.5 23.5 1.0 CD2 A:LEU8 5.0 36.7 1.0

Zinc binding site 6 out of 6 in the Cyclic LYS48-Linked Triubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cyclic LYS48-Linked Triubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:18.3 occ:1.00 OE2 C:GLU18 2.0 17.7 1.0 CD C:GLU18 2.7 18.3 1.0 OE1 C:GLU18 2.7 19.4 1.0 CG C:GLU18 4.2 17.6 1.0 O C:HOH269 4.5 40.0 1.0

M.Hiranyakorn, S.Yanaka, T.Satoh, T.Wilasri, B.Jityuti, M.Yagi-Utsumi, K.Kato. uc(Nmr) Characterization of Conformational Interconversions of LYS48-Linked Ubiquitin Chains. Int J Mol Sci V. 21 2020.
ISSN: ESSN 1422-0067
PubMed: 32731397
DOI: 10.3390/IJMS21155351