Zinc in PDB 2xk5: Crystal Structure of K6-Linked Diubiquitin

The structure of Crystal Structure of K6-Linked Diubiquitin, PDB code: 2xk5 was solved by S.Virdee, J.W.Chin, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.947 / 3.00
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	104.840, 104.840, 104.840, 90.00, 90.00, 90.00
R / Rfree (%)	21.34 / 24.85

The binding sites of Zinc atom in the Crystal Structure of K6-Linked Diubiquitin (pdb code 2xk5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of K6-Linked Diubiquitin, PDB code: 2xk5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of K6-Linked 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 K6-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1074 b:77.1 occ:1.00 N A:MET1 2.3 73.0 1.0 OE2 A:GLU16 2.7 78.1 1.0 OE1 A:GLU16 2.7 75.4 1.0 CA A:MET1 2.8 71.9 1.0 CD A:GLU16 3.1 75.0 1.0 C A:MET1 3.2 74.2 1.0 O A:MET1 3.6 72.3 1.0 N A:GLN2 4.0 78.5 1.0 CB A:MET1 4.2 68.0 1.0 CG A:GLU16 4.6 69.9 1.0 O A:VAL17 4.8 68.1 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of K6-Linked 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 K6-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1075 b:77.0 occ:1.00 OE1 A:GLU18 2.5 88.2 1.0 OE2 A:GLU18 2.5 88.9 1.0 CD A:GLU18 2.9 85.2 1.0 CG A:GLU18 4.4 75.7 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of K6-Linked 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 K6-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1076 b:0.4 occ:1.00 NE2 A:HIS68 2.5 89.1 1.0 CD2 A:HIS68 2.8 85.3 1.0 CE1 A:HIS68 3.8 92.2 1.0 CG A:HIS68 4.2 86.0 1.0 O A:THR66 4.4 80.3 1.0 ND1 A:HIS68 4.6 91.4 1.0 CB A:THR66 4.7 81.6 1.0 CG2 A:THR66 4.7 82.3 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of K6-Linked 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 K6-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1077 b:0.3 occ:1.00 OD2 A:ASP52 2.4 94.9 1.0 CG A:ASP52 3.1 91.4 1.0 NZ A:LYS27 3.4 80.9 1.0 OD1 A:ASP52 3.6 89.7 1.0 CB A:ASP52 4.0 88.5 1.0 CD A:LYS27 4.1 74.6 1.0 CE A:LYS27 4.2 77.1 1.0 CB A:GLU24 4.8 68.3 1.0 O A:PRO38 4.9 74.5 1.0 CB A:PRO38 4.9 72.7 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of K6-Linked 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 K6-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1076 b:94.4 occ:1.00 OD1 B:ASP21 2.5 84.4 1.0 OE2 B:GLU18 2.6 1.0 1.0 OD2 B:ASP21 2.9 78.0 1.0 OE1 B:GLU18 2.9 1.0 1.0 CD B:GLU18 2.9 0.8 1.0 CG B:ASP21 3.0 80.2 1.0 CE B:LYS29 3.5 91.5 1.0 NZ B:LYS29 3.8 94.7 1.0 CG B:GLU18 4.3 0.8 1.0 ND2 B:ASN25 4.4 82.2 1.0 CB B:ASP21 4.5 76.7 1.0 N B:GLU18 4.7 88.6 1.0 CB B:GLU18 4.8 98.1 1.0 CD B:LYS29 4.9 87.7 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of K6-Linked 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 K6-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1077 b:0.4 occ:1.00 OD2 B:ASP32 2.8 0.1 1.0 CG B:ASP32 3.3 99.8 1.0 OD1 B:ASP32 3.4 0.8 1.0 CB B:ASP32 4.4 98.9 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of K6-Linked 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 K6-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1078 b:0.4 occ:1.00 OD1 B:ASP58 2.9 0.7 1.0 OD2 B:ASP58 3.0 1.0 1.0 CG B:ASP58 3.3 0.7 1.0 OG1 B:THR55 3.9 78.4 1.0 CG2 B:THR55 4.1 80.0 1.0 CB B:THR55 4.6 78.8 1.0 CB B:ASP58 4.7 0.6 1.0 N B:THR55 4.8 84.1 1.0

S.Virdee, Y.Ye, D.P.Nguyen, D.Komander, J.W.Chin. Engineered Diubiquitin Synthesis Reveals K29-Isopeptide Specificity of An Otu Deubiquitinase Nat.Chem.Biol. V. 6 750 2010.
ISSN: ISSN 1552-4450
PubMed: 20802491
DOI: 10.1038/NCHEMBIO.426