Atomistry » Zinc » PDB 7zdp-7zn7 » 7zj3
Atomistry »
  Zinc »
    PDB 7zdp-7zn7 »
      7zj3 »

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

Go back to Zinc Binding Sites List in 7zj3
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

Go back to Zinc Binding Sites List in 7zj3
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

Go back to Zinc Binding Sites List in 7zj3
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

Go back to Zinc Binding Sites List in 7zj3
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

Go back to Zinc Binding Sites List in 7zj3
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

Go back to Zinc Binding Sites List in 7zj3
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

Go back to Zinc Binding Sites List in 7zj3
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

Go back to Zinc Binding Sites List in 7zj3
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy