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Zinc in PDB 2w9n: Crystal Structure of Linear Di-Ubiquitin

Protein crystallography data

The structure of Crystal Structure of Linear Di-Ubiquitin, PDB code: 2w9n was solved by D.Komander, F.Reyes-Turcu, K.D.Wilkinson, D.Barford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.25
Space group P 43 3 2
Cell size a, b, c (Å), α, β, γ (°) 105.572, 105.572, 105.572, 90.00, 90.00, 90.00
R / Rfree (%) 25.9 / 27.6

Other elements in 2w9n:

The structure of Crystal Structure of Linear Di-Ubiquitin also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Linear Di-Ubiquitin (pdb code 2w9n). 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 Linear Di-Ubiquitin, PDB code: 2w9n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2w9n

Go back to Zinc Binding Sites List in 2w9n
Zinc binding site 1 out of 4 in the Crystal Structure of Linear Di-Ubiquitin


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 Linear Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1150

b:52.7
occ:1.00
OE2 A:GLU18 2.2 23.2 1.0
OE1 A:GLU18 2.6 30.1 1.0
CD A:GLU18 2.7 29.2 1.0
O A:HOH2003 3.0 57.3 0.3
O A:HOH2002 3.2 64.9 0.3
CG A:GLU18 4.2 29.5 1.0

Zinc binding site 2 out of 4 in 2w9n

Go back to Zinc Binding Sites List in 2w9n
Zinc binding site 2 out of 4 in the Crystal Structure of Linear Di-Ubiquitin


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 Linear Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1151

b:44.6
occ:1.00
O A:HOH2026 1.8 20.7 1.0
OD1 A:ASP97 2.0 33.6 1.0
OD2 A:ASP97 2.6 35.4 1.0
CG A:ASP97 2.7 36.0 1.0
NZ A:LYS105 2.9 45.0 1.0
O A:HOH2025 3.0 57.6 1.0
CE A:LYS105 3.9 42.7 1.0
OD1 A:ASN101 4.1 33.3 1.0
CB A:ASP97 4.1 37.1 1.0
OE1 A:GLU94 4.5 34.1 1.0
CG A:GLU94 4.6 37.8 1.0
CB A:ASN101 4.7 34.8 1.0
CG A:ASN101 4.7 32.9 1.0
N A:GLU94 4.8 37.9 1.0
CA A:ASP97 4.9 37.6 1.0
CB A:GLU94 4.9 37.3 1.0

Zinc binding site 3 out of 4 in 2w9n

Go back to Zinc Binding Sites List in 2w9n
Zinc binding site 3 out of 4 in the Crystal Structure of Linear Di-Ubiquitin


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 Linear Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1152

b:69.5
occ:1.00
OE1 A:GLU140 2.1 47.1 1.0
OE2 A:GLU140 2.3 46.0 1.0
CD A:GLU140 2.6 45.4 1.0
O A:HOH2023 3.3 44.3 1.0
CG A:GLU140 4.1 43.9 1.0
CE A:LYS139 4.4 56.2 1.0
CB A:GLU140 4.7 43.2 1.0
NZ A:LYS139 4.8 58.4 1.0

Zinc binding site 4 out of 4 in 2w9n

Go back to Zinc Binding Sites List in 2w9n
Zinc binding site 4 out of 4 in the Crystal Structure of Linear Di-Ubiquitin


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 Linear Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1153

b:0.7
occ:1.00
OD2 A:ASP128 2.0 53.8 1.0
CG A:ASP128 2.9 51.6 1.0
OD1 A:ASP128 3.2 55.1 1.0
NZ A:LYS103 3.4 50.1 1.0
OD1 A:ASP115 3.9 56.5 1.0
CD A:LYS103 4.0 41.1 1.0
CB A:ASP128 4.2 49.8 1.0
CE A:LYS103 4.3 45.1 1.0
O A:PRO114 4.5 48.0 1.0
C A:PRO114 4.9 47.5 1.0

Reference:

D.Komander, F.Reyes-Turcu, J.D.Licchesi, P.Odenwaelder, K.D.Wilkinson, D.Barford. Molecular Discrimination of Structurally Equivalent Lys 63-Linked and Linear Polyubiquitin Chains. Embo Rep. V. 10 466 2009.
ISSN: ISSN 1469-221X
PubMed: 19373254
DOI: 10.1038/EMBOR.2009.55
Page generated: Wed Dec 16 03:57:06 2020

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