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Cadmium in PDB 2jf5: Crystal Structure of LYS63-Linked Di-Ubiquitin

Protein crystallography data

The structure of Crystal Structure of LYS63-Linked Di-Ubiquitin, PDB code: 2jf5 was solved by D.Komander, P.Odenwaelder, D.Barford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group P 43 3 2
Cell size a, b, c (Å), α, β, γ (°) 105.021, 105.021, 105.021, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 25

Other elements in 2jf5:

The structure of Crystal Structure of LYS63-Linked Di-Ubiquitin also contains other interesting chemical elements:

Cobalt (Co) 2 atoms
Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of LYS63-Linked Di-Ubiquitin (pdb code 2jf5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of LYS63-Linked Di-Ubiquitin, PDB code: 2jf5:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 2jf5

Go back to Cadmium Binding Sites List in 2jf5
Cadmium binding site 1 out of 4 in the Crystal Structure of LYS63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of LYS63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1076

b:54.7
occ:0.50
CD A:CD1076 0.0 54.7 0.5
CD A:CD1076 1.9 37.4 0.5
OE2 A:GLU18 2.1 45.7 1.0
OD1 A:ASP21 2.2 39.8 1.0
CG A:ASP21 3.0 39.5 1.0
CD A:GLU18 3.1 42.8 1.0
OD2 A:ASP21 3.3 37.2 1.0
CG A:GLU18 3.4 41.9 1.0
O A:HOH2006 3.6 41.8 0.3
ND2 A:ASN25 4.1 36.4 1.0
OE1 A:GLU18 4.1 41.1 1.0
O A:HOH2008 4.3 35.7 1.0
CB A:ASP21 4.3 40.1 1.0
CA A:ASP21 4.6 41.0 1.0
CB A:GLU18 4.6 40.8 1.0

Cadmium binding site 2 out of 4 in 2jf5

Go back to Cadmium Binding Sites List in 2jf5
Cadmium binding site 2 out of 4 in the Crystal Structure of LYS63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of LYS63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1076

b:37.4
occ:0.50
CD A:CD1076 0.0 37.4 0.5
CD A:CD1076 1.9 54.7 0.5
OD1 A:ASP21 2.2 39.8 1.0
OD2 A:ASP21 2.6 37.2 1.0
CG A:ASP21 2.8 39.5 1.0
NZ A:LYS29 3.3 45.1 1.0
CE A:LYS29 3.5 44.1 1.0
OE2 A:GLU18 3.7 45.7 1.0
O A:HOH2006 4.0 41.8 0.3
CB A:ASP21 4.3 40.1 1.0
CD A:GLU18 4.3 42.8 1.0
CG A:GLU18 4.3 41.9 1.0
ND2 A:ASN25 4.4 36.4 1.0
N A:GLU18 4.7 40.0 1.0
CB A:ASN25 4.7 37.1 1.0
CG A:ASN25 4.9 37.8 1.0
CD A:LYS29 5.0 43.8 1.0

Cadmium binding site 3 out of 4 in 2jf5

Go back to Cadmium Binding Sites List in 2jf5
Cadmium binding site 3 out of 4 in the Crystal Structure of LYS63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of LYS63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1077

b:24.9
occ:0.50
CD B:CD1077 0.0 24.9 0.5
CD B:CD1077 1.6 26.2 0.5
OD1 B:ASP21 2.3 37.6 1.0
OD2 B:ASP21 2.6 34.9 1.0
CL B:CL1080 2.7 66.5 1.0
CG B:ASP21 2.8 37.5 1.0
NZ B:LYS29 2.9 43.2 1.0
CE B:LYS29 3.3 42.0 1.0
OE1 B:GLU18 3.7 44.2 1.0
CG B:GLU18 4.2 40.1 1.0
CB B:ASP21 4.3 35.5 1.0
ND2 B:ASN25 4.3 31.6 1.0
CD B:GLU18 4.4 43.0 1.0
N B:GLU18 4.6 36.6 1.0
CB B:ASN25 4.6 32.2 1.0
CB B:GLU18 4.8 36.3 1.0
CD B:LYS29 4.8 43.8 1.0
O B:HOH2018 4.8 25.2 1.0
CG B:ASN25 4.9 33.6 1.0
CA B:VAL17 4.9 36.7 1.0

Cadmium binding site 4 out of 4 in 2jf5

Go back to Cadmium Binding Sites List in 2jf5
Cadmium binding site 4 out of 4 in the Crystal Structure of LYS63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of LYS63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1077

b:26.2
occ:0.50
CD B:CD1077 0.0 26.2 0.5
CD B:CD1077 1.6 24.9 0.5
OE1 B:GLU18 2.3 44.2 1.0
OD1 B:ASP21 2.4 37.6 1.0
CL B:CL1080 3.2 66.5 1.0
CG B:ASP21 3.2 37.5 1.0
OD2 B:ASP21 3.3 34.9 1.0
CD B:GLU18 3.3 43.0 1.0
CG B:GLU18 3.6 40.1 1.0
CB B:GLU18 4.2 36.3 1.0
ND2 B:ASN25 4.3 31.6 1.0
NZ B:LYS29 4.4 43.2 1.0
OE2 B:GLU18 4.5 43.3 1.0
CB B:ASP21 4.6 35.5 1.0
O B:HOH2017 4.6 29.7 1.0
N B:GLU18 4.8 36.6 1.0
CA B:ASP21 4.9 35.8 1.0
CE B:LYS29 4.9 42.0 1.0

Reference:

D.Komander, F.Reyes-Turcu, J.D.F.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 Oct 28 09:59:34 2020
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