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Cadmium in PDB 9ewp: Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain

Enzymatic activity of Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain

All present enzymatic activity of Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain:
2.3.2.23;

Protein crystallography data

The structure of Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain, PDB code: 9ewp was solved by A.Swarnkar, A.Stein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.24 / 1.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.139, 44.169, 97.578, 90, 90, 90
R / Rfree (%) 13.5 / 15.6

Other elements in 9ewp:

The structure of Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain (pdb code 9ewp). 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 Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain, PDB code: 9ewp:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 9ewp

Go back to Cadmium Binding Sites List in 9ewp
Cadmium binding site 1 out of 4 in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain


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 Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:14.7
occ:1.00
 OE1 A:GLU166 2.3 15.6 1.0
OE1 A:GLU163 2.3 15.9 1.0
CD A:GLU166 3.2 14.6 1.0
CD A:GLU163 3.2 15.6 1.0
OE2 A:GLU166 3.4 14.7 1.0
CD A:CD205 3.4 14.6 1.0
OE2 A:GLU163 3.7 16.4 1.0
HA A:GLU163 3.8 18.6 1.0
HB2 A:GLU163 4.1 18.6 1.0
HG12 A:VAL162 4.4 18.6 1.0
CG A:GLU163 4.4 16.1 1.0
CG A:GLU166 4.5 16.3 1.0
CB A:GLU163 4.6 15.5 1.0
O A:HOH374 4.6 19.6 0.9
CA A:GLU163 4.6 15.5 1.0
HB3 A:GLU166 4.6 19.9 1.0
HB2 A:GLU166 4.7 19.9 1.0
CB A:GLU166 4.9 16.5 1.0
HG3 A:GLU166 4.9 19.5 1.0
HG2 A:GLU163 5.0 19.3 1.0

Cadmium binding site 2 out of 4 in 9ewp

Go back to Cadmium Binding Sites List in 9ewp
Cadmium binding site 2 out of 4 in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain


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 Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:14.6
occ:0.98
 OE2 A:GLU166 2.3 14.7 1.0
OE2 A:GLU163 2.3 16.4 1.0
CD A:GLU163 3.1 15.6 1.0
CD A:GLU166 3.1 14.6 1.0
OE1 A:GLU163 3.2 15.9 1.0
CD A:CD204 3.4 14.7 1.0
OE1 A:GLU166 3.4 15.6 1.0
HZ1 A:LYS167 3.6 38.8 1.0
HZ2 A:LYS167 4.0 38.8 1.0
NZ A:LYS167 4.3 32.3 1.0
HG2 A:GLU166 4.4 19.5 1.0
CG A:GLU166 4.4 16.3 1.0
CG A:GLU163 4.6 16.1 1.0
HG3 A:GLU163 4.7 19.3 1.0
HZ3 A:LYS167 4.7 38.8 1.0
HG3 A:LYS167 4.9 33.8 1.0
HG2 A:GLU163 4.9 19.3 1.0
HG3 A:GLU166 4.9 19.5 1.0

Cadmium binding site 3 out of 4 in 9ewp

Go back to Cadmium Binding Sites List in 9ewp
Cadmium binding site 3 out of 4 in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain


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 Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:16.8
occ:0.98
 ND1 A:HIS94 2.3 16.7 1.0
OD2 A:ASP96 2.3 18.9 1.0
CL A:CL211 2.4 22.4 0.6
OD1 A:ASP96 2.4 17.8 1.0
O A:HOH362 2.4 16.8 1.0
CL A:CL210 2.5 18.8 0.9
CG A:ASP96 2.7 17.9 1.0
CE1 A:HIS94 3.2 16.0 1.0
HE1 A:HIS94 3.2 19.2 1.0
HA A:HIS94 3.3 18.1 1.0
CG A:HIS94 3.3 15.6 1.0
HB3 A:HIS94 3.4 18.5 1.0
HG1 A:THR97 3.6 21.3 1.0
CB A:HIS94 3.8 15.4 1.0
CA A:HIS94 4.0 15.0 1.0
CB A:ASP96 4.3 17.3 1.0
NE2 A:HIS94 4.3 16.9 1.0
OG1 A:THR97 4.3 17.8 1.0
O A:TYR93 4.4 15.6 1.0
O A:HOH513 4.4 33.6 0.9
H A:ASP96 4.4 19.3 1.0
CD2 A:HIS94 4.4 15.4 1.0
HG23 A:THR97 4.5 21.5 1.0
HB3 A:ASP96 4.6 20.8 1.0
H A:THR97 4.6 20.3 1.0
HB2 A:ASP96 4.6 20.8 1.0
HB2 A:HIS94 4.7 18.5 1.0
HD2 A:PRO95 4.8 19.7 1.0
C A:HIS94 4.8 14.5 1.0

Cadmium binding site 4 out of 4 in 9ewp

Go back to Cadmium Binding Sites List in 9ewp
Cadmium binding site 4 out of 4 in the Crystal Structure of Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain


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 Yeast E2 Ubiquitin-Conjugating Enzyme UBC6 Ubc Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:36.6
occ:0.24
 HD2 A:HIS130 1.5 42.3 1.0
CD2 A:HIS130 1.8 35.2 1.0
NE2 A:HIS130 2.3 37.0 1.0
CG A:HIS130 2.9 32.7 1.0
CE1 A:HIS130 3.4 37.1 1.0
HB2 A:HIS130 3.6 31.9 1.0
ND1 A:HIS130 3.7 36.5 1.0
CB A:HIS130 3.8 26.6 1.0
HA A:HIS130 3.9 25.2 1.0
HE1 A:HIS130 4.2 44.6 1.0
CA A:HIS130 4.4 21.0 1.0
HD1 A:HIS130 4.5 43.8 1.0
HB3 A:HIS130 4.6 31.9 1.0

Reference:

A.Swarnkar, F.Leidner, A.K.Rout, S.Ainatzi, C.C.Schmidt, S.Becker, H.Urlaub, C.Griesinger, H.Grubmuller, A.Stein. Determinants of Chemoselectivity in Ubiquitination By the J2 Family of Ubiquitin-Conjugating Enzymes Embo J. 2024.
ISSN: ESSN 1460-2075
DOI: 10.1038/S44318-024-00301-3
Page generated: Wed Nov 27 16:43:01 2024

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