Atomistry » Zinc » PDB 5evk-5f8g » 5eya
Atomistry »
  Zinc »
    PDB 5evk-5f8g »
      5eya »

Zinc in PDB 5eya: TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate

Enzymatic activity of TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate

All present enzymatic activity of TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate:
2.3.2.23;

Protein crystallography data

The structure of TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate, PDB code: 5eya was solved by O.Pornillos, J.G.Sanchez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.97 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.047, 75.779, 169.101, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.8

Zinc Binding Sites:

The binding sites of Zinc atom in the TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate (pdb code 5eya). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate, PDB code: 5eya:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5eya

Go back to Zinc Binding Sites List in 5eya
Zinc binding site 1 out of 4 in the TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:25.4
occ:1.00
ND1 F:HIS30 2.1 19.6 1.0
SG F:CYS53 2.1 26.3 1.0
SG F:CYS50 2.1 21.9 1.0
SG F:CYS28 2.1 23.8 1.0
HB2 F:CYS28 2.8 27.7 1.0
CE1 F:HIS30 2.9 19.5 1.0
HE1 F:HIS30 2.9 23.4 1.0
CB F:CYS50 3.0 18.0 1.0
HB3 F:CYS50 3.0 21.6 1.0
HB2 F:CYS50 3.0 21.6 1.0
CB F:CYS28 3.1 23.1 1.0
HB2 F:HIS30 3.2 26.2 1.0
CG F:HIS30 3.2 19.9 1.0
H F:CYS53 3.5 33.6 1.0
CB F:CYS53 3.6 26.7 1.0
HB3 F:CYS53 3.6 32.0 1.0
HB3 F:CYS28 3.6 27.7 1.0
CB F:HIS30 3.7 21.8 1.0
HB3 F:GLN52 3.7 45.4 1.0
HB3 F:ALA55 3.8 31.5 1.0
N F:CYS53 4.0 28.0 1.0
HB2 F:ALA55 4.0 31.5 1.0
HG1 F:THR26 4.0 27.6 1.0
NE2 F:HIS30 4.0 19.5 1.0
OG1 F:THR26 4.1 23.0 1.0
H F:ALA55 4.2 34.7 1.0
CD2 F:HIS30 4.2 18.8 1.0
HB3 F:HIS30 4.3 26.2 1.0
HB2 F:CYS53 4.3 32.0 1.0
CA F:CYS28 4.3 21.0 1.0
O F:CYS28 4.3 21.3 1.0
H F:GLN52 4.3 32.0 1.0
CA F:CYS53 4.3 26.7 1.0
C F:CYS28 4.4 20.9 1.0
CB F:ALA55 4.4 26.3 1.0
H F:HIS30 4.4 28.2 1.0
HH F:TYR57 4.4 30.9 1.0
CA F:CYS50 4.4 18.8 1.0
CB F:GLN52 4.6 37.8 1.0
H F:CYS28 4.7 25.1 1.0
O D:HOH113 4.7 42.6 1.0
N F:HIS30 4.7 23.5 1.0
HA F:CYS50 4.8 22.6 1.0
HE2 F:HIS30 4.8 23.4 1.0
C F:GLN52 4.8 29.7 1.0
CA F:HIS30 4.9 21.5 1.0
HB2 F:GLN52 4.9 45.4 1.0
HE1 F:PHE32 4.9 29.5 1.0
C F:CYS53 5.0 25.6 1.0
C F:CYS50 5.0 19.5 1.0
N F:ALA55 5.0 28.9 1.0
HA F:CYS28 5.0 25.2 1.0
N F:GLN52 5.0 26.6 1.0

Zinc binding site 2 out of 4 in 5eya

Go back to Zinc Binding Sites List in 5eya
Zinc binding site 2 out of 4 in the TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn102

b:27.8
occ:1.00
SG F:CYS16 2.1 26.8 1.0
SG F:CYS36 2.1 24.7 1.0
SG F:CYS13 2.1 19.6 1.0
SG F:CYS33 2.2 22.2 1.0
HB3 F:CYS13 2.7 22.7 1.0
HB2 F:CYS33 2.9 31.2 1.0
CB F:CYS13 2.9 18.9 1.0
HB3 F:CYS16 2.9 33.4 1.0
HB2 F:CYS13 3.0 22.7 1.0
H F:CYS16 3.1 35.1 1.0
CB F:CYS33 3.1 26.0 1.0
CB F:CYS16 3.1 27.8 1.0
H F:CYS33 3.3 28.4 1.0
HB2 F:CYS36 3.3 33.5 1.0
CB F:CYS36 3.4 27.9 1.0
HB3 F:CYS36 3.7 33.5 1.0
N F:CYS16 3.7 29.3 1.0
HB F:ILE15 3.8 26.7 1.0
HB3 F:CYS33 3.8 31.2 1.0
HZ2 F:LYS21 3.9 55.6 1.0
HB2 F:CYS16 3.9 33.4 1.0
N F:CYS33 4.0 23.6 1.0
CA F:CYS16 4.0 29.0 1.0
HZ1 F:LYS21 4.1 55.6 1.0
CA F:CYS33 4.2 24.0 1.0
H F:ILE15 4.3 31.4 1.0
H F:CYS36 4.4 33.2 1.0
CA F:CYS13 4.4 21.5 1.0
NZ F:LYS21 4.4 46.3 1.0
H F:LEU17 4.6 35.2 1.0
H F:GLU18 4.6 42.4 1.0
HA F:PHE20 4.7 23.0 1.0
CB F:ILE15 4.7 22.3 1.0
CA F:CYS36 4.7 27.3 1.0
H F:LYS21 4.7 23.6 1.0
HE2 F:LYS21 4.8 56.3 1.0
HA F:CYS16 4.8 34.8 1.0
C F:ILE15 4.8 28.1 1.0
HA F:CYS13 4.8 25.8 1.0
HA F:CYS33 4.8 28.8 1.0
H F:CYS13 4.8 27.1 1.0
C F:CYS16 4.9 30.8 1.0
C F:CYS13 4.9 22.9 1.0
N F:CYS36 4.9 27.6 1.0
HG22 F:ILE15 5.0 26.5 1.0
HD1 F:PHE20 5.0 24.4 1.0
N F:ILE15 5.0 26.2 1.0

Zinc binding site 3 out of 4 in 5eya

Go back to Zinc Binding Sites List in 5eya
Zinc binding site 3 out of 4 in the TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn101

b:26.5
occ:1.00
ND1 G:HIS30 2.1 16.6 1.0
SG G:CYS53 2.1 22.6 1.0
SG G:CYS50 2.1 16.1 1.0
SG G:CYS28 2.1 27.9 1.0
CE1 G:HIS30 2.9 16.9 1.0
HE1 G:HIS30 2.9 20.3 1.0
HB3 G:CYS50 3.0 19.9 1.0
CB G:CYS50 3.0 16.6 1.0
HB2 G:CYS28 3.0 28.6 1.0
HB2 G:CYS50 3.1 19.9 1.0
HB2 G:HIS30 3.1 23.4 1.0
CG G:HIS30 3.2 16.9 1.0
CB G:CYS28 3.2 23.8 1.0
H G:CYS53 3.4 26.2 1.0
CB G:CYS53 3.6 24.3 1.0
HB3 G:GLN52 3.6 37.7 1.0
HB3 G:CYS53 3.6 29.1 1.0
CB G:HIS30 3.7 19.5 1.0
HB3 G:CYS28 3.8 28.6 1.0
N G:CYS53 3.9 21.8 1.0
HB3 G:ALA55 4.0 33.4 1.0
HG1 G:THR26 4.0 30.4 1.0
OG1 G:THR26 4.0 25.3 1.0
NE2 G:HIS30 4.1 16.8 1.0
HB2 G:ALA55 4.2 33.4 1.0
H G:GLN52 4.2 27.9 1.0
H G:ALA55 4.2 35.5 1.0
CD2 G:HIS30 4.2 16.4 1.0
O G:CYS28 4.3 27.4 1.0
HB2 G:CYS53 4.3 29.1 1.0
HB3 G:HIS30 4.3 23.4 1.0
CA G:CYS53 4.3 21.3 1.0
H G:HIS30 4.3 25.7 1.0
C G:CYS28 4.3 25.6 1.0
CA G:CYS28 4.4 23.0 1.0
HH G:TYR57 4.4 21.8 1.0
CA G:CYS50 4.5 19.9 1.0
CB G:GLN52 4.5 31.4 1.0
CB G:ALA55 4.5 27.9 1.0
N G:HIS30 4.7 21.4 1.0
H G:CYS28 4.7 26.2 1.0
HB2 G:GLN52 4.7 37.7 1.0
C G:GLN52 4.8 22.6 1.0
HE2 G:HIS30 4.8 20.2 1.0
HA G:CYS50 4.8 23.9 1.0
H G:ARG54 4.8 23.9 1.0
CA G:HIS30 4.8 17.7 1.0
C G:CYS53 4.9 20.5 1.0
N G:GLN52 4.9 23.2 1.0
HB G:THR26 4.9 27.8 1.0
HG21 G:THR26 4.9 26.3 1.0
CA G:GLN52 5.0 25.6 1.0
HE1 G:PHE32 5.0 25.5 1.0
C G:CYS50 5.0 18.9 1.0

Zinc binding site 4 out of 4 in 5eya

Go back to Zinc Binding Sites List in 5eya
Zinc binding site 4 out of 4 in the TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of TRIM25 Ring Domain in Complex with UBC13-Ub Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn102

b:27.0
occ:1.00
SG G:CYS16 2.1 25.9 1.0
SG G:CYS36 2.1 25.9 1.0
SG G:CYS13 2.1 23.9 1.0
SG G:CYS33 2.1 25.7 1.0
HB3 G:CYS13 2.7 25.4 1.0
CB G:CYS13 2.8 21.2 1.0
HB2 G:CYS33 2.9 25.4 1.0
HB2 G:CYS13 3.0 25.4 1.0
HB3 G:CYS16 3.1 23.8 1.0
CB G:CYS33 3.2 21.2 1.0
H G:CYS16 3.2 29.2 1.0
CB G:CYS16 3.2 19.8 1.0
HB2 G:CYS36 3.3 25.2 1.0
HZ2 G:LYS21 3.3 80.6 1.0
H G:CYS33 3.4 23.3 1.0
CB G:CYS36 3.4 21.0 1.0
HZ1 G:LYS21 3.5 80.6 1.0
HB3 G:CYS36 3.7 25.2 1.0
N G:CYS16 3.8 24.4 1.0
HB3 G:CYS33 3.8 25.4 1.0
HB G:ILE15 3.8 25.1 1.0
NZ G:LYS21 3.8 67.2 1.0
HB2 G:CYS16 4.0 23.8 1.0
N G:CYS33 4.1 19.4 1.0
CA G:CYS16 4.1 21.4 1.0
CA G:CYS33 4.2 20.5 1.0
CA G:CYS13 4.3 21.3 1.0
H G:ILE15 4.4 26.3 1.0
H G:CYS36 4.4 31.0 1.0
HZ3 G:LYS21 4.4 80.6 1.0
H G:GLU18 4.6 36.8 1.0
HE2 G:LYS21 4.6 77.0 1.0
H G:LEU17 4.7 32.0 1.0
HA G:PHE20 4.7 23.3 1.0
CA G:CYS36 4.7 24.1 1.0
CB G:ILE15 4.7 20.9 1.0
H G:LYS21 4.8 25.4 1.0
H G:CYS13 4.8 23.6 1.0
HA G:CYS13 4.8 25.6 1.0
C G:ILE15 4.8 26.3 1.0
C G:CYS13 4.9 23.6 1.0
HA G:CYS33 4.9 24.6 1.0
HA G:CYS16 4.9 25.7 1.0
CE G:LYS21 4.9 64.2 1.0
C G:CYS16 4.9 24.9 1.0
HG22 G:ILE15 4.9 22.5 1.0
N G:CYS36 5.0 25.8 1.0

Reference:

J.G.Sanchez, J.J.Chiang, K.M.Sparrer, S.L.Alam, M.Chi, M.D.Roganowicz, B.Sankaran, M.U.Gack, O.Pornillos. Mechanism of TRIM25 Catalytic Activation in the Antiviral Rig-I Pathway. Cell Rep V. 16 1315 2016.
ISSN: ESSN 2211-1247
PubMed: 27425606
DOI: 10.1016/J.CELREP.2016.06.070
Page generated: Sun Oct 27 15:35:19 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy