Zinc in PDB 7zj3: Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate

Enzymatic activity of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate

All present enzymatic activity of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate:
2.3.2.23; 2.3.2.24; 2.3.2.27;

Protein crystallography data

The structure of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate, PDB code: 7zj3 was solved by D.Esposito, A.Garza-Garcia, J.Dudley-Fraser, K.Rittinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.97 / 2.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.319, 123.662, 112.471, 90, 102.8, 90
R / Rfree (%) 21.1 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate (pdb code 7zj3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate, PDB code: 7zj3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7zj3

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Zinc binding site 1 out of 8 in the Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:55.7
occ:1.00
 SG D:CYS46 2.3 41.4 1.0
SG D:CYS26 2.3 46.0 1.0
SG D:CYS23 2.3 44.6 1.0
SG D:CYS43 2.4 44.8 1.0
CB D:CYS23 2.9 39.1 1.0
CB D:CYS43 3.1 37.4 1.0
CB D:CYS26 3.4 46.0 1.0
CB D:CYS46 3.5 42.6 1.0
N D:CYS26 3.8 39.3 1.0
N D:CYS43 4.0 44.7 1.0
CA D:CYS43 4.2 35.6 1.0
CA D:CYS26 4.2 50.1 1.0
CA D:CYS23 4.4 41.0 1.0
CB D:ILE25 4.7 38.1 1.0
CA D:CYS46 4.8 52.0 1.0
C D:CYS23 4.9 37.2 1.0
C D:ILE25 4.9 43.1 1.0
N D:ILE25 4.9 37.5 1.0

Zinc binding site 2 out of 8 in 7zj3

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Zinc binding site 2 out of 8 in the Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn102

b:53.2
occ:1.00
 ND1 D:HIS40 2.1 43.2 1.0
SG D:CYS60 2.3 36.9 1.0
SG D:CYS38 2.3 32.4 1.0
SG D:CYS63 2.3 39.8 1.0
CE1 D:HIS40 3.0 40.6 1.0
CB D:CYS60 3.0 35.3 1.0
CG D:HIS40 3.2 44.3 1.0
CB D:CYS38 3.5 34.4 1.0
CB D:CYS63 3.5 42.7 1.0
CB D:HIS40 3.6 44.5 1.0
N D:CYS63 3.8 39.4 1.0
NE2 D:HIS40 4.1 30.9 1.0
CA D:CYS63 4.2 35.3 1.0
CD2 D:HIS40 4.2 38.5 1.0
CA D:CYS60 4.5 40.9 1.0
CB D:VAL62 4.5 32.8 1.0
C D:VAL62 4.7 43.7 1.0
N D:HIS40 4.7 28.6 1.0
O D:CYS38 4.7 45.3 1.0
CA D:HIS40 4.8 36.0 1.0
CA D:CYS38 4.8 39.1 1.0
C D:CYS63 4.8 36.3 1.0
N D:VAL62 4.9 39.7 1.0
N D:ARG64 4.9 30.6 1.0
C D:CYS38 4.9 40.2 1.0
CG1 D:VAL62 4.9 34.1 1.0
CA D:VAL62 4.9 40.6 1.0
CB D:GLN65 4.9 38.8 1.0
C D:CYS60 4.9 36.0 1.0

Zinc binding site 3 out of 8 in 7zj3

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Zinc binding site 3 out of 8 in the Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn101

b:45.7
occ:1.00
 SG G:CYS46 2.3 36.7 1.0
SG G:CYS26 2.3 40.6 1.0
SG G:CYS43 2.3 42.4 1.0
SG G:CYS23 2.4 30.1 1.0
CB G:CYS23 2.9 29.0 1.0
CB G:CYS43 3.1 37.0 1.0
CB G:CYS26 3.3 36.5 1.0
CB G:CYS46 3.5 35.5 1.0
N G:CYS26 3.7 28.3 1.0
N G:CYS43 4.0 26.7 1.0
CA G:CYS26 4.1 32.6 1.0
CA G:CYS43 4.1 33.0 1.0
CA G:CYS23 4.4 30.8 1.0
CB G:ILE25 4.6 33.9 1.0
C G:ILE25 4.7 33.4 1.0
N G:ILE25 4.8 27.2 1.0
CA G:CYS46 4.8 32.0 1.0
C G:CYS23 4.8 33.1 1.0
C G:CYS26 5.0 36.3 1.0
CA G:ILE25 5.0 31.4 1.0
N G:CYS46 5.0 44.0 1.0

Zinc binding site 4 out of 8 in 7zj3

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Zinc binding site 4 out of 8 in the Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn102

b:56.2
occ:1.00
 ND1 G:HIS40 2.1 39.7 1.0
SG G:CYS63 2.3 48.2 1.0
SG G:CYS38 2.3 35.9 1.0
SG G:CYS60 2.3 38.6 1.0
CE1 G:HIS40 2.9 38.8 1.0
CG G:HIS40 3.1 34.0 1.0
CB G:CYS60 3.2 38.3 1.0
CB G:CYS38 3.3 45.2 1.0
CB G:CYS63 3.4 52.1 1.0
CB G:HIS40 3.5 33.5 1.0
N G:CYS63 3.9 43.9 1.0
NE2 G:HIS40 4.1 31.7 1.0
CD2 G:HIS40 4.2 29.2 1.0
CA G:CYS63 4.2 42.3 1.0
CB G:VAL62 4.6 38.8 1.0
O G:CYS38 4.6 41.7 1.0
CA G:CYS38 4.6 41.1 1.0
N G:HIS40 4.6 32.9 1.0
CA G:CYS60 4.7 44.4 1.0
CA G:HIS40 4.7 36.8 1.0
C G:CYS38 4.8 40.4 1.0
C G:VAL62 4.8 47.7 1.0
C G:CYS63 4.9 50.5 1.0
O I:GLY35 5.0 62.5 1.0
CG1 G:VAL62 5.0 38.7 1.0

Zinc binding site 5 out of 8 in 7zj3

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Zinc binding site 5 out of 8 in the Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:70.3
occ:1.00
 SG J:CYS46 2.3 53.8 1.0
SG J:CYS23 2.3 43.4 1.0
SG J:CYS26 2.4 62.9 1.0
SG J:CYS43 2.4 56.2 1.0
CB J:CYS23 2.8 43.3 1.0
CB J:CYS43 3.0 54.6 1.0
CB J:CYS26 3.3 61.6 1.0
N J:CYS26 3.7 53.4 1.0
CB J:CYS46 3.7 57.2 1.0
N J:CYS43 3.9 36.8 1.0
CA J:CYS26 4.1 57.1 1.0
CA J:CYS43 4.1 48.2 1.0
CA J:CYS23 4.3 43.8 1.0
C J:ILE25 4.8 54.1 1.0
C J:CYS23 4.8 50.6 1.0
CB J:ILE25 4.8 43.5 1.0
N J:ILE25 4.9 55.1 1.0
C J:CYS26 4.9 52.2 1.0
CA J:CYS46 4.9 62.1 1.0

Zinc binding site 6 out of 8 in 7zj3

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Zinc binding site 6 out of 8 in the Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn102

b:73.8
occ:1.00
 ND1 J:HIS40 2.1 63.6 1.0
SG J:CYS60 2.3 54.0 1.0
SG J:CYS38 2.3 61.8 1.0
SG J:CYS63 2.3 79.4 1.0
CE1 J:HIS40 3.0 57.8 1.0
CB J:CYS60 3.0 60.5 1.0
CG J:HIS40 3.1 52.1 1.0
CB J:CYS38 3.3 42.7 1.0
CB J:CYS63 3.5 67.9 1.0
CB J:HIS40 3.5 38.6 1.0
N J:CYS63 3.9 58.1 1.0
NE2 J:HIS40 4.1 54.8 1.0
CD2 J:HIS40 4.2 47.6 1.0
CA J:CYS63 4.2 64.2 1.0
CA J:CYS60 4.5 74.7 1.0
O J:CYS38 4.5 60.7 1.0
CB J:VAL62 4.6 55.5 1.0
N J:HIS40 4.6 50.4 1.0
CA J:CYS38 4.6 57.4 1.0
CA J:HIS40 4.7 48.8 1.0
C J:CYS38 4.7 56.2 1.0
C J:VAL62 4.8 63.9 1.0
C J:CYS63 4.9 68.7 1.0
CD1 J:LEU36 5.0 48.1 1.0
N J:VAL62 5.0 64.5 1.0
CG1 J:VAL62 5.0 50.2 1.0

Zinc binding site 7 out of 8 in 7zj3

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Zinc binding site 7 out of 8 in the Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:48.2
occ:1.00
 SG A:CYS46 2.3 39.3 1.0
SG A:CYS26 2.3 38.5 1.0
SG A:CYS23 2.4 31.2 1.0
SG A:CYS43 2.4 31.2 1.0
CB A:CYS23 2.9 29.9 1.0
CB A:CYS43 3.0 26.7 1.0
CB A:CYS26 3.2 27.2 1.0
CB A:CYS46 3.5 32.0 1.0
N A:CYS26 3.6 30.1 1.0
N A:CYS43 3.9 31.9 1.0
CA A:CYS26 4.0 32.5 1.0
CA A:CYS43 4.1 32.5 1.0
CA A:CYS23 4.4 37.4 1.0
CB A:ILE25 4.6 31.9 1.0
C A:ILE25 4.7 40.5 1.0
CA A:CYS46 4.9 35.8 1.0
N A:ILE25 4.9 31.6 1.0
C A:CYS26 4.9 37.0 1.0
C A:CYS23 4.9 38.3 1.0
CA A:ILE25 5.0 36.7 1.0

Zinc binding site 8 out of 8 in 7zj3

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Zinc binding site 8 out of 8 in the Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of TRIM2 Ring Domain in Complex with UBE2D1~Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:52.6
occ:1.00
 ND1 A:HIS40 2.1 27.8 1.0
SG A:CYS60 2.3 30.0 1.0
SG A:CYS63 2.3 34.4 1.0
SG A:CYS38 2.3 35.0 1.0
CE1 A:HIS40 3.0 28.9 1.0
CB A:CYS60 3.1 27.5 1.0
CG A:HIS40 3.1 23.6 1.0
CB A:CYS38 3.4 31.7 1.0
CB A:HIS40 3.5 26.5 1.0
CB A:CYS63 3.5 40.0 1.0
N A:CYS63 3.8 29.9 1.0
NE2 A:HIS40 4.2 22.7 1.0
CD2 A:HIS40 4.2 23.1 1.0
CA A:CYS63 4.2 36.5 1.0
O A:CYS38 4.5 37.3 1.0
CB A:VAL62 4.5 31.9 1.0
N A:HIS40 4.5 28.0 1.0
CA A:CYS60 4.6 34.1 1.0
CA A:CYS38 4.6 39.6 1.0
CA A:HIS40 4.7 31.9 1.0
C A:CYS38 4.7 37.0 1.0
C A:VAL62 4.8 35.8 1.0
C A:CYS63 4.9 33.8 1.0
CG1 A:VAL62 4.9 29.0 1.0
N A:VAL62 5.0 34.9 1.0
CA A:VAL62 5.0 30.0 1.0

Reference:

D.Esposito, J.Dudley-Fraser, A.Garza-Garcia, K.Rittinger. Divergent Self-Association Properties of Paralogous Proteins TRIM2 and TRIM3 Regulate Their E3 Ligase Activity. Nat Commun V. 13 7583 2022.
ISSN: ESSN 2041-1723
PubMed: 36481767
DOI: 10.1038/S41467-022-35300-7
Page generated: Wed Oct 30 17:08:51 2024

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