Zinc in PDB 2zcc: Ubiquitin Crystallized Under High Pressure

The structure of Ubiquitin Crystallized Under High Pressure, PDB code: 2zcc was solved by R.Kitahara, T.Tanaka, M.Yamashita, K.Araya, S.Yokoyama, K.Akasaka, Y.Taniguchi, M.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.031, 50.544, 93.863, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 23.7

The binding sites of Zinc atom in the Ubiquitin Crystallized Under High Pressure (pdb code 2zcc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Ubiquitin Crystallized Under High Pressure, PDB code: 2zcc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Ubiquitin Crystallized Under High Pressure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ubiquitin Crystallized Under High Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn77 b:12.2 occ:1.00 OD1 A:ASP21 2.0 11.8 1.0 O A:HOH80 2.1 12.9 1.0 O A:HOH106 2.2 20.9 1.0 CG A:ASP21 2.8 11.8 1.0 OD2 A:ASP21 2.8 12.9 1.0 O A:HOH167 3.1 29.4 1.0 O A:HOH139 3.8 27.6 1.0 ND2 A:ASN25 4.0 12.5 1.0 O A:HOH145 4.1 29.3 1.0 NZ A:LYS29 4.2 14.6 1.0 CB A:ASP21 4.2 10.9 1.0 CE A:LYS29 4.3 12.5 1.0 OE2 A:GLU18 4.4 17.1 1.0 O A:HOH189 4.6 37.6 1.0 CA A:ASP21 4.7 10.3 1.0 CG A:ASN25 4.8 12.2 1.0 CB A:ASN25 4.9 10.1 1.0 O A:HOH190 4.9 30.4 1.0

Zinc binding site 2 out of 6 in the Ubiquitin Crystallized Under High Pressure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ubiquitin Crystallized Under High Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn78 b:14.4 occ:1.00 OE2 A:GLU18 2.0 17.1 1.0 O A:HOH138 2.3 32.5 1.0 CD A:GLU18 2.7 14.3 1.0 OE1 A:GLU18 2.8 16.4 1.0 O A:HOH106 3.9 20.9 1.0 O A:HOH139 3.9 27.6 1.0 O A:HOH176 4.2 27.1 1.0 CG A:GLU18 4.2 14.8 1.0 O A:HOH167 4.6 29.4 1.0 CB A:GLU18 4.9 11.9 1.0

Zinc binding site 3 out of 6 in the Ubiquitin Crystallized Under High Pressure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ubiquitin Crystallized Under High Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn79 b:18.3 occ:1.00 NE2 C:HIS68 2.1 14.6 1.0 NE2 A:HIS68 2.1 16.7 1.0 O C:HOH150 2.2 23.0 1.0 O A:HOH161 2.5 33.8 1.0 O C:HOH117 3.0 22.6 1.0 CD2 C:HIS68 3.0 15.5 1.0 CE1 C:HIS68 3.1 14.5 1.0 CD2 A:HIS68 3.1 16.6 1.0 CE1 A:HIS68 3.1 17.9 1.0 ND1 C:HIS68 4.2 15.0 1.0 CG C:HIS68 4.2 14.1 1.0 ND1 A:HIS68 4.2 17.8 1.0 CG A:HIS68 4.2 15.8 1.0 O C:HOH180 4.3 33.5 1.0 O A:HOH131 4.7 45.7 1.0 O C:HOH100 4.8 19.6 1.0 CD A:LYS6 4.8 26.0 1.0 CG2 C:THR66 4.9 15.2 1.0

Zinc binding site 4 out of 6 in the Ubiquitin Crystallized Under High Pressure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ubiquitin Crystallized Under High Pressure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn77 b:23.4 occ:1.00 OD2 C:ASP39 2.1 23.2 1.0 O B:HOH107 2.2 30.3 1.0 CE1 B:HIS68 2.3 16.2 1.0 O B:HOH145 2.3 29.2 1.0 NE2 B:HIS68 2.9 19.0 1.0 O B:HOH143 2.9 27.3 1.0 CG C:ASP39 3.0 20.5 1.0 OD1 C:ASP39 3.1 23.9 1.0 O B:HOH165 3.3 35.1 1.0 ND1 B:HIS68 3.4 17.8 1.0 CD2 B:HIS68 4.1 15.2 1.0 O B:HOH115 4.2 25.2 1.0 O C:HOH104 4.3 22.5 1.0 CG B:HIS68 4.3 16.6 1.0 O B:HOH159 4.3 33.2 1.0 CB C:ASP39 4.3 19.8 1.0 O B:HOH144 4.5 40.7 1.0 NE2 C:GLN40 4.8 29.0 1.0 CB C:PRO37 4.8 16.9 1.0

Zinc binding site 5 out of 6 in the Ubiquitin Crystallized Under High Pressure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ubiquitin Crystallized Under High Pressure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn78 b:23.9 occ:1.00 OD1 B:ASP21 2.1 18.7 1.0 CG B:ASP21 2.8 16.6 1.0 OD2 B:ASP21 2.8 17.7 1.0 ND2 B:ASN25 3.8 11.5 1.0 O B:HOH99 4.0 35.3 1.0 CB B:ASP21 4.2 15.8 1.0 OE1 B:GLU18 4.3 14.1 1.0 CE B:LYS29 4.5 20.5 1.0 CG B:ASN25 4.5 10.9 1.0 NZ B:LYS29 4.6 22.6 1.0 CB B:ASN25 4.6 11.1 1.0 CA B:ASP21 4.8 14.6 1.0 CG B:GLU18 5.0 11.7 1.0

Zinc binding site 6 out of 6 in the Ubiquitin Crystallized Under High Pressure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ubiquitin Crystallized Under High Pressure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn79 b:23.8 occ:1.00 N B:MET1 2.0 18.1 1.0 OE2 B:GLU16 2.1 22.2 1.0 O B:HOH138 2.2 23.1 1.0 CA B:MET1 3.0 21.0 1.0 CD B:GLU16 3.1 20.7 1.0 OE1 B:GLU16 3.3 21.9 1.0 C B:MET1 3.4 19.1 1.0 O B:HOH109 3.6 25.7 1.0 O B:MET1 3.9 20.2 1.0 O B:VAL17 4.0 17.0 1.0 N B:GLN2 4.0 17.8 1.0 CB B:MET1 4.3 22.6 1.0 CG B:GLU16 4.4 19.2 1.0

R.Kitahara, T.Tanaka, M.Yamashita, K.Araya, S.Yokoyama, K.Akasaka, Y.Taniguchi, M.Kato. Structure of Ubiquitin Crystallized Under High Pressure To Be Published.