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
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