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Zinc in PDB 5ojj: Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T

Enzymatic activity of Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T

All present enzymatic activity of Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T:
2.3.2.23;

Protein crystallography data

The structure of Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T, PDB code: 5ojj was solved by F.E.Morreale, A.Testa, V.K.Chaugule, A.Bortoluzzi, A.Ciulli, H.Walden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.75 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.020, 96.383, 89.996, 90.00, 93.28, 90.00
R / Rfree (%) 17.8 / 19.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T (pdb code 5ojj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T, PDB code: 5ojj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ojj

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Zinc binding site 1 out of 8 in the Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T


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 the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:21.6
occ:1.00
 O A:ACT201 2.0 25.1 1.0
NZ A:LYS91 2.2 26.8 1.0
ND1 C:HIS150 2.2 25.4 1.0
SG A:CYS86 2.3 20.5 1.0
C A:ACT201 2.9 26.4 1.0
OXT A:ACT201 3.0 28.6 1.0
CE1 C:HIS150 3.0 27.1 1.0
CE A:LYS91 3.1 27.4 1.0
CB A:CYS86 3.2 19.5 1.0
CG C:HIS150 3.4 25.1 1.0
CA A:CYS86 3.7 19.4 1.0
O C:LYS149 3.9 24.9 1.0
CB C:HIS150 3.9 24.7 1.0
CA C:HIS150 3.9 27.4 1.0
O A:HOH334 3.9 27.4 1.0
NE2 C:HIS150 4.2 27.1 1.0
CG C:LYS149 4.2 32.2 1.0
CH3 A:ACT201 4.3 26.0 1.0
C C:LYS149 4.3 28.6 1.0
CD2 C:HIS150 4.4 25.5 1.0
N C:HIS150 4.4 27.7 1.0
CD A:LYS91 4.5 26.8 1.0
C A:CYS86 4.6 20.2 1.0
CD2 A:LEU124 4.7 22.3 1.0
N A:CYS86 4.8 18.9 1.0
O A:HOH389 4.8 26.6 1.0
N A:LEU87 4.9 19.6 1.0
CD C:LYS149 5.0 34.8 1.0

Zinc binding site 2 out of 8 in 5ojj

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Zinc binding site 2 out of 8 in the Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T


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 the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:25.6
occ:1.00
 OD2 C:ASP127 2.0 24.8 1.0
OD2 B:ASP127 2.1 23.4 1.0
NE2 E:HIS12 2.1 22.4 1.0
OD2 A:ASP127 2.1 23.1 1.0
CG C:ASP127 2.8 27.8 1.0
CG A:ASP127 2.9 25.8 1.0
OD1 A:ASP127 3.0 26.0 1.0
OD1 C:ASP127 3.0 26.8 1.0
CG B:ASP127 3.0 24.2 1.0
CE1 E:HIS12 3.0 23.7 1.0
CD2 E:HIS12 3.1 23.0 1.0
OD1 B:ASP127 3.2 24.9 1.0
O B:HOH332 3.8 40.1 1.0
ND1 E:HIS12 4.1 23.0 1.0
CG E:HIS12 4.2 23.4 1.0
CB C:ASP127 4.2 27.6 1.0
O A:HOH370 4.3 29.4 1.0
CB A:ASP127 4.3 27.4 1.0
CB B:ASP127 4.4 22.1 1.0
O B:HOH414 4.6 32.7 1.0

Zinc binding site 3 out of 8 in 5ojj

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Zinc binding site 3 out of 8 in the Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T


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 the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:21.0
occ:1.00
 O B:ACT200 2.0 19.4 1.0
NZ B:LYS91 2.2 24.8 1.0
ND1 A:HIS150 2.2 24.8 1.0
SG B:CYS86 2.3 20.0 1.0
C B:ACT200 2.9 21.3 1.0
CE1 A:HIS150 3.0 25.4 1.0
CE B:LYS91 3.1 25.8 1.0
OXT B:ACT200 3.1 24.2 1.0
CB B:CYS86 3.2 18.4 1.0
CG A:HIS150 3.4 24.4 1.0
CA B:CYS86 3.6 17.9 1.0
CB A:HIS150 3.9 24.7 1.0
O B:HOH346 3.9 24.6 1.0
O A:LYS149 3.9 25.4 1.0
CA A:HIS150 4.1 26.5 1.0
NE2 A:HIS150 4.1 25.4 1.0
CH3 B:ACT200 4.3 22.7 1.0
CD2 A:HIS150 4.3 23.4 1.0
C A:LYS149 4.4 29.1 1.0
CD B:LYS91 4.5 25.9 1.0
C B:CYS86 4.6 17.8 1.0
N A:HIS150 4.6 27.1 1.0
N B:CYS86 4.7 16.1 1.0
CD2 B:LEU124 4.7 17.9 1.0
N B:LEU87 4.8 18.1 1.0
O B:HOH390 4.8 31.2 1.0

Zinc binding site 4 out of 8 in 5ojj

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Zinc binding site 4 out of 8 in the Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T


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 the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:21.7
occ:1.00
 O C:ACT200 2.1 19.6 1.0
ND1 B:HIS150 2.1 24.2 1.0
NZ C:LYS91 2.3 23.2 1.0
SG C:CYS86 2.3 21.1 1.0
CE1 B:HIS150 2.9 25.6 1.0
C C:ACT200 2.9 21.5 1.0
CE C:LYS91 3.0 24.1 1.0
OXT C:ACT200 3.0 24.8 1.0
CB C:CYS86 3.2 18.7 1.0
CG B:HIS150 3.2 23.5 1.0
CA C:CYS86 3.7 18.4 1.0
CB B:HIS150 3.7 23.0 1.0
O C:HOH375 3.9 23.1 1.0
O B:LYS149 3.9 23.5 1.0
CA B:HIS150 4.0 23.3 1.0
NE2 B:HIS150 4.1 24.8 1.0
CD2 B:HIS150 4.3 24.1 1.0
CH3 C:ACT200 4.4 21.9 1.0
C B:LYS149 4.4 23.8 1.0
CG B:LYS149 4.5 32.0 1.0
CD C:LYS91 4.5 23.1 1.0
C C:CYS86 4.5 18.2 1.0
N B:HIS150 4.5 23.2 1.0
N C:LEU87 4.7 19.0 1.0
O C:HOH379 4.8 22.5 1.0
N C:CYS86 4.8 17.2 1.0
CD2 C:LEU124 4.8 24.6 1.0
CG C:LEU124 5.0 25.9 1.0

Zinc binding site 5 out of 8 in 5ojj

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Zinc binding site 5 out of 8 in the Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T


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 the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:17.6
occ:1.00
 O D:ACT201 2.1 16.5 1.0
ND1 E:HIS150 2.2 20.1 1.0
NZ D:LYS91 2.2 20.7 1.0
SG D:CYS86 2.3 18.0 1.0
C D:ACT201 2.9 19.8 1.0
CE1 E:HIS150 2.9 21.0 1.0
OXT D:ACT201 3.0 21.0 1.0
CE D:LYS91 3.1 20.8 1.0
CB D:CYS86 3.2 17.1 1.0
CG E:HIS150 3.4 20.0 1.0
CA D:CYS86 3.7 17.0 1.0
O D:HOH378 3.8 18.9 1.0
CB E:HIS150 3.9 20.4 1.0
O E:LYS149 3.9 23.0 1.0
CA E:HIS150 4.0 21.3 1.0
NE2 E:HIS150 4.1 21.5 1.0
CG E:LYS149 4.3 29.9 1.0
CH3 D:ACT201 4.3 18.4 1.0
C E:LYS149 4.3 23.7 1.0
CD2 E:HIS150 4.4 20.8 1.0
N E:HIS150 4.5 21.1 1.0
CD D:LYS91 4.5 19.9 1.0
C D:CYS86 4.6 17.4 1.0
CD2 D:LEU124 4.7 18.7 1.0
N D:CYS86 4.8 16.2 1.0
N D:LEU87 4.8 17.7 1.0
O D:HOH388 4.8 21.4 1.0
CD E:LYS149 5.0 32.2 1.0

Zinc binding site 6 out of 8 in 5ojj

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Zinc binding site 6 out of 8 in the Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T


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 the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:24.0
occ:1.00
 OD2 D:ASP127 1.9 19.8 1.0
OD2 E:ASP127 2.0 20.8 1.0
OD2 F:ASP127 2.1 19.5 1.0
CG D:ASP127 2.7 21.6 1.0
CG F:ASP127 2.9 20.5 1.0
CG E:ASP127 2.9 23.8 1.0
OD1 D:ASP127 2.9 20.5 1.0
OD1 F:ASP127 3.0 21.7 1.0
OD1 E:ASP127 3.0 22.6 1.0
O F:HOH358 3.9 32.7 1.0
O D:HOH409 4.0 32.0 1.0
O E:HOH368 4.0 27.9 1.0
CB D:ASP127 4.2 21.6 1.0
CB E:ASP127 4.3 22.1 1.0
CB F:ASP127 4.3 19.3 1.0
O E:HOH367 4.5 34.9 1.0
O F:HOH316 4.6 31.8 1.0

Zinc binding site 7 out of 8 in 5ojj

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Zinc binding site 7 out of 8 in the Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T


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 the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:19.2
occ:1.00
 O E:ACT200 1.9 21.8 1.0
ND1 F:HIS150 2.2 22.7 1.0
NZ E:LYS91 2.2 28.7 1.0
SG E:CYS86 2.3 17.9 1.0
C E:ACT200 2.9 23.1 1.0
CE1 F:HIS150 3.0 24.5 1.0
OXT E:ACT200 3.2 25.9 1.0
CB E:CYS86 3.2 16.6 1.0
CG F:HIS150 3.3 23.3 1.0
CE E:LYS91 3.3 29.5 1.0
CA E:CYS86 3.7 16.0 1.0
CB F:HIS150 3.8 24.1 1.0
CA F:HIS150 3.9 24.4 1.0
O F:LYS149 4.0 26.4 1.0
O E:HOH372 4.1 25.1 1.0
NE2 F:HIS150 4.2 24.5 1.0
CH3 E:ACT200 4.3 23.8 1.0
CD2 F:HIS150 4.3 24.7 1.0
C F:LYS149 4.5 28.5 1.0
C E:CYS86 4.6 17.4 1.0
O E:HOH418 4.6 31.7 1.0
N F:HIS150 4.6 26.8 1.0
CD E:LYS91 4.6 27.4 1.0
CG F:LYS149 4.6 37.1 1.0
N E:LEU87 4.7 17.1 1.0
CD2 E:LEU124 4.8 23.1 1.0
N E:CYS86 4.9 16.2 1.0

Zinc binding site 8 out of 8 in 5ojj

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Zinc binding site 8 out of 8 in the Crystal Structure of the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T


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 the Zn-Bound Ubiquitin-Conjugating Enzyme UBE2T within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:17.8
occ:1.00
 O F:ACT200 2.1 16.6 1.0
NZ F:LYS91 2.1 24.9 1.0
ND1 D:HIS150 2.2 17.8 1.0
SG F:CYS86 2.3 18.3 1.0
CE1 D:HIS150 2.9 18.3 1.0
C F:ACT200 3.0 19.5 1.0
CE F:LYS91 3.1 28.1 1.0
CB F:CYS86 3.2 15.3 1.0
OXT F:ACT200 3.2 20.4 1.0
CG D:HIS150 3.3 18.2 1.0
CA F:CYS86 3.6 15.2 1.0
CB D:HIS150 3.8 18.8 1.0
O F:HOH332 4.0 33.2 1.0
O D:LYS149 4.1 21.6 1.0
CA D:HIS150 4.1 20.4 1.0
NE2 D:HIS150 4.1 18.1 1.0
CD2 D:HIS150 4.3 18.6 1.0
CH3 F:ACT200 4.4 20.3 1.0
C D:LYS149 4.4 23.0 1.0
C F:CYS86 4.5 15.6 1.0
CD F:LYS91 4.5 28.0 1.0
N D:HIS150 4.6 20.3 1.0
CD2 F:LEU124 4.7 17.4 1.0
O F:HOH342 4.7 39.9 1.0
N F:LEU87 4.7 16.1 1.0
N F:CYS86 4.8 15.2 1.0
O F:HOH402 4.8 48.3 1.0
CB D:LYS149 5.0 25.6 1.0

Reference:

F.E.Morreale, A.Testa, V.K.Chaugule, A.Bortoluzzi, A.Ciulli, H.Walden. Mind the Metal: A Fragment Library-Derived Zinc Impurity Binds the E2 Ubiquitin-Conjugating Enzyme UBE2T and Induces Structural Rearrangements. J. Med. Chem. V. 60 8183 2017.
ISSN: ISSN 1520-4804
PubMed: 28933844
DOI: 10.1021/ACS.JMEDCHEM.7B01071
Page generated: Sun Oct 27 23:39:04 2024

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