Zinc in PDB 5khy: Crystal Structure of Oxime-Linked K6 Diubiquitin

The structure of Crystal Structure of Oxime-Linked K6 Diubiquitin, PDB code: 5khy was solved by M.Stanley, S.Virdee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.79 / 3.50
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	103.975, 103.975, 103.975, 90.00, 90.00, 90.00
R / Rfree (%)	28.2 / 33.1

The binding sites of Zinc atom in the Crystal Structure of Oxime-Linked K6 Diubiquitin (pdb code 5khy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Oxime-Linked K6 Diubiquitin, PDB code: 5khy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of Oxime-Linked K6 Diubiquitin


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 Oxime-Linked K6 Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:0.5 occ:1.00 NE2 A:HIS68 1.8 0.2 1.0 CE1 A:HIS68 2.6 0.9 1.0 CD2 A:HIS68 2.9 0.0 1.0 ND1 A:HIS68 3.8 0.3 1.0 CG A:HIS68 3.9 0.4 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Oxime-Linked K6 Diubiquitin


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 Oxime-Linked K6 Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:0.7 occ:1.00 OE1 A:GLU18 0.9 0.9 1.0 CD A:GLU18 1.7 0.3 1.0 OE2 A:GLU18 2.3 0.2 1.0 CG A:GLU18 2.9 0.8 1.0 ND2 A:ASN25 3.9 0.0 1.0 CE A:LYS29 3.9 0.5 1.0 CG A:ASN25 4.0 0.7 1.0 CB A:GLU18 4.1 0.2 1.0 NZ A:LYS29 4.2 0.3 1.0 OD1 A:ASN25 4.3 0.1 1.0 CB A:ASN25 4.6 0.6 1.0 CB A:ASP21 4.8 0.6 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Oxime-Linked K6 Diubiquitin


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 Oxime-Linked K6 Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:0.6 occ:1.00 N A:MET1 1.5 0.7 1.0 CA A:MET1 2.9 98.3 1.0 CB A:MET1 3.3 93.1 1.0 O A:MET1 3.4 0.7 1.0 C A:MET1 3.6 0.8 1.0 O A:GLU16 3.7 0.2 1.0 O A:VAL17 4.5 0.3 1.0 C A:GLU16 4.7 0.5 1.0 CG A:MET1 4.8 90.5 1.0 N A:GLN2 4.9 0.0 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Oxime-Linked K6 Diubiquitin


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 Oxime-Linked K6 Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:1.0 occ:1.00 OD2 A:ASP58 2.5 0.9 1.0 OD1 A:ASP58 3.1 0.8 1.0 CG A:ASP58 3.1 0.1 1.0 CB A:ASP58 4.6 0.0 1.0 OG1 A:THR55 4.8 0.9 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Oxime-Linked K6 Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Oxime-Linked K6 Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:0.5 occ:1.00 OD2 A:ASP52 2.2 0.1 1.0 CG A:ASP52 3.3 0.7 1.0 OD1 A:ASP52 3.6 0.9 1.0 CB A:ASP52 4.6 0.6 1.0 O A:PRO38 4.6 0.5 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Oxime-Linked K6 Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Oxime-Linked K6 Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:0.2 occ:1.00 OD2 A:ASP39 2.1 0.0 1.0 CG A:ASP39 3.2 0.4 1.0 OD1 A:ASP39 3.6 0.2 1.0 CB A:ASP39 4.4 0.0 1.0 CB A:PRO37 4.4 0.8 1.0 CG A:PRO37 4.9 0.1 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Oxime-Linked K6 Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Oxime-Linked K6 Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:0.2 occ:1.00 OD2 B:ASP32 2.5 0.5 1.0 CG B:ASP32 2.9 0.8 1.0 OD1 B:ASP32 3.0 0.4 1.0 CB B:ASP32 4.1 0.5 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Oxime-Linked K6 Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Oxime-Linked K6 Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:0.5 occ:1.00 OE2 B:GLU18 2.3 0.5 1.0 CD B:GLU18 3.0 0.5 1.0 OE1 B:GLU18 3.2 0.8 1.0 CG B:GLU18 4.3 0.3 1.0 CB B:GLU18 4.8 0.7 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Oxime-Linked K6 Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Oxime-Linked K6 Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:1.0 occ:1.00 OD2 B:ASP58 3.1 0.7 1.0 O B:GLY53 3.8 0.5 1.0 CG B:ASP58 4.2 0.6 1.0 OG1 B:THR55 4.5 0.2 1.0 CA B:ARG54 4.5 0.2 1.0 N B:THR55 4.8 0.8 1.0 OD1 B:ASP58 4.8 0.5 1.0 C B:GLY53 4.9 0.1 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Oxime-Linked K6 Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Oxime-Linked K6 Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:0.3 occ:1.00 OE1 B:GLU24 2.2 0.9 1.0 NZ B:LYS27 2.8 0.7 1.0 CD B:GLU24 3.1 0.7 1.0 OE2 B:GLU24 3.3 0.1 1.0 OD1 B:ASP39 4.1 0.0 1.0 CE B:LYS27 4.2 0.3 1.0 CG B:GLU24 4.5 0.5 1.0 CG B:ASP39 4.5 0.6 1.0 CA B:ASP39 4.6 0.6 1.0 CD B:LYS27 4.7 0.4 1.0 N B:ASP39 4.8 0.6 1.0 OD2 B:ASP39 4.8 0.4 1.0 CB B:ASP52 4.9 0.9 1.0

M.Stanley, S.Virdee. Genetically Directed Production of Recombinant, Isosteric and Nonhydrolysable Ubiquitin Conjugates. Chembiochem V. 17 1472 2016.
ISSN: ESSN 1439-7633
PubMed: 27197715
DOI: 10.1002/CBIC.201600138