Zinc in PDB 5vzw: TRIM23 Ring Domain in Complex with UBCH5-Ub
Enzymatic activity of TRIM23 Ring Domain in Complex with UBCH5-Ub
All present enzymatic activity of TRIM23 Ring Domain in Complex with UBCH5-Ub:
2.3.2.23;
2.3.2.24;
Protein crystallography data
The structure of TRIM23 Ring Domain in Complex with UBCH5-Ub, PDB code: 5vzw
was solved by
O.Pornillos,
D.Dawidziak,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.57 /
2.28
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.830,
109.355,
122.963,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
20.8 /
23.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the TRIM23 Ring Domain in Complex with UBCH5-Ub
(pdb code 5vzw). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
TRIM23 Ring Domain in Complex with UBCH5-Ub, PDB code: 5vzw:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5vzw
Go back to
Zinc Binding Sites List in 5vzw
Zinc binding site 1 out
of 4 in the TRIM23 Ring Domain in Complex with UBCH5-Ub
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of TRIM23 Ring Domain in Complex with UBCH5-Ub within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn301
b:47.7
occ:1.00
|
OD2
|
F:ASP75
|
2.1
|
50.4
|
1.0
|
|
ND1
|
F:HIS53
|
2.1
|
48.8
|
1.0
|
|
SG
|
F:CYS51
|
2.3
|
44.8
|
1.0
|
|
SG
|
F:CYS72
|
2.3
|
44.3
|
1.0
|
|
CG
|
F:ASP75
|
2.8
|
45.7
|
1.0
|
|
HB2
|
F:HIS53
|
2.9
|
53.0
|
1.0
|
|
HB2
|
F:CYS51
|
2.9
|
60.8
|
1.0
|
|
CE1
|
F:HIS53
|
3.0
|
52.4
|
1.0
|
|
OD1
|
F:ASP75
|
3.0
|
51.3
|
1.0
|
|
HB2
|
F:CYS72
|
3.1
|
61.3
|
1.0
|
|
CB
|
F:CYS72
|
3.1
|
51.1
|
1.0
|
|
CG
|
F:HIS53
|
3.1
|
51.3
|
1.0
|
|
HB3
|
F:CYS72
|
3.1
|
61.3
|
1.0
|
|
CB
|
F:CYS51
|
3.1
|
50.7
|
1.0
|
|
HE1
|
F:HIS53
|
3.2
|
62.9
|
1.0
|
|
CB
|
F:HIS53
|
3.5
|
44.2
|
1.0
|
|
HB3
|
F:CYS51
|
3.5
|
60.8
|
1.0
|
|
HB2
|
F:PHE74
|
3.7
|
59.9
|
1.0
|
|
H
|
F:HIS53
|
3.8
|
55.8
|
1.0
|
|
HD2
|
F:PHE74
|
3.8
|
56.9
|
1.0
|
|
H
|
F:ASP75
|
4.0
|
55.6
|
1.0
|
|
HB3
|
F:HIS53
|
4.1
|
53.0
|
1.0
|
|
NE2
|
F:HIS53
|
4.2
|
49.7
|
1.0
|
|
CB
|
F:ASP75
|
4.2
|
50.0
|
1.0
|
|
CD2
|
F:HIS53
|
4.2
|
50.3
|
1.0
|
|
HB2
|
F:GLN77
|
4.3
|
53.2
|
1.0
|
|
HB3
|
F:ASP75
|
4.3
|
60.0
|
1.0
|
|
H
|
F:PHE74
|
4.3
|
57.9
|
1.0
|
|
N
|
F:ASP75
|
4.4
|
46.4
|
1.0
|
|
N
|
F:HIS53
|
4.4
|
46.5
|
1.0
|
|
CA
|
F:CYS51
|
4.5
|
47.7
|
1.0
|
|
HD12
|
F:LEU49
|
4.5
|
57.2
|
1.0
|
|
CA
|
F:CYS72
|
4.6
|
50.7
|
1.0
|
|
HB2
|
F:LEU49
|
4.6
|
58.0
|
1.0
|
|
CA
|
F:HIS53
|
4.6
|
49.2
|
1.0
|
|
CB
|
F:PHE74
|
4.6
|
49.9
|
1.0
|
|
C
|
F:CYS51
|
4.7
|
48.9
|
1.0
|
|
CD2
|
F:PHE74
|
4.7
|
47.4
|
1.0
|
|
H
|
F:CYS51
|
4.7
|
58.5
|
1.0
|
|
H
|
F:GLN77
|
4.8
|
60.0
|
1.0
|
|
O
|
F:HOH405
|
4.8
|
45.2
|
1.0
|
|
HB2
|
F:ASP75
|
4.8
|
60.0
|
1.0
|
|
O
|
F:CYS51
|
4.8
|
47.5
|
1.0
|
|
HA
|
F:CYS72
|
4.9
|
60.9
|
1.0
|
|
HD13
|
F:LEU49
|
4.9
|
57.2
|
1.0
|
|
CA
|
F:ASP75
|
4.9
|
47.8
|
1.0
|
|
HE2
|
F:HIS53
|
4.9
|
59.7
|
1.0
|
|
Zinc binding site 2 out
of 4 in 5vzw
Go back to
Zinc Binding Sites List in 5vzw
Zinc binding site 2 out
of 4 in the TRIM23 Ring Domain in Complex with UBCH5-Ub
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of TRIM23 Ring Domain in Complex with UBCH5-Ub within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn302
b:55.5
occ:1.00
|
SG
|
F:CYS59
|
2.3
|
51.6
|
1.0
|
|
SG
|
F:CYS56
|
2.4
|
57.7
|
1.0
|
|
SG
|
F:CYS31
|
2.4
|
49.8
|
1.0
|
|
SG
|
F:CYS34
|
2.4
|
59.0
|
1.0
|
|
H
|
F:CYS34
|
2.9
|
72.6
|
1.0
|
|
HB3
|
F:CYS31
|
2.9
|
73.0
|
1.0
|
|
HB3
|
F:CYS56
|
2.9
|
64.2
|
1.0
|
|
HB2
|
F:CYS59
|
3.0
|
62.9
|
1.0
|
|
CB
|
F:CYS31
|
3.1
|
60.9
|
1.0
|
|
HB3
|
F:CYS34
|
3.2
|
70.7
|
1.0
|
|
CB
|
F:CYS56
|
3.2
|
53.5
|
1.0
|
|
CB
|
F:CYS59
|
3.3
|
52.5
|
1.0
|
|
HB2
|
F:CYS31
|
3.3
|
73.0
|
1.0
|
|
CB
|
F:CYS34
|
3.4
|
58.9
|
1.0
|
|
H
|
F:CYS56
|
3.4
|
61.5
|
1.0
|
|
HZ2
|
F:LYS44
|
3.5
|
85.7
|
1.0
|
|
HB
|
F:VAL33
|
3.5
|
65.8
|
1.0
|
|
H
|
F:CYS59
|
3.6
|
62.9
|
1.0
|
|
N
|
F:CYS34
|
3.7
|
60.5
|
1.0
|
|
HB3
|
F:CYS59
|
3.9
|
62.9
|
1.0
|
|
HZ3
|
F:LYS44
|
3.9
|
85.7
|
1.0
|
|
HB2
|
F:CYS56
|
4.0
|
64.2
|
1.0
|
|
N
|
F:CYS56
|
4.1
|
51.2
|
1.0
|
|
CA
|
F:CYS34
|
4.1
|
60.0
|
1.0
|
|
NZ
|
F:LYS44
|
4.2
|
71.4
|
1.0
|
|
H
|
F:VAL33
|
4.2
|
63.9
|
1.0
|
|
HB2
|
F:CYS34
|
4.2
|
70.7
|
1.0
|
|
CA
|
F:CYS56
|
4.2
|
53.0
|
1.0
|
|
HG13
|
F:VAL55
|
4.2
|
61.6
|
1.0
|
|
N
|
F:CYS59
|
4.3
|
52.5
|
1.0
|
|
CA
|
F:CYS59
|
4.4
|
55.1
|
1.0
|
|
CB
|
F:VAL33
|
4.5
|
54.9
|
1.0
|
|
HG12
|
F:VAL55
|
4.5
|
61.6
|
1.0
|
|
HD2
|
F:LYS44
|
4.5
|
89.7
|
1.0
|
|
H
|
F:GLU35
|
4.5
|
79.7
|
1.0
|
|
CA
|
F:CYS31
|
4.6
|
61.6
|
1.0
|
|
HD3
|
F:LYS44
|
4.6
|
89.7
|
1.0
|
|
H
|
F:ASP36
|
4.6
|
83.5
|
1.0
|
|
O
|
F:CYS56
|
4.6
|
51.8
|
1.0
|
|
HZ1
|
F:LYS44
|
4.7
|
85.7
|
1.0
|
|
HB2
|
F:ASP36
|
4.7
|
83.7
|
1.0
|
|
C
|
F:CYS56
|
4.8
|
52.4
|
1.0
|
|
C
|
F:VAL33
|
4.8
|
56.0
|
1.0
|
|
HA
|
F:CYS59
|
4.8
|
66.1
|
1.0
|
|
CG1
|
F:VAL55
|
4.8
|
51.3
|
1.0
|
|
HG12
|
F:VAL33
|
4.8
|
65.5
|
1.0
|
|
N
|
F:VAL33
|
4.9
|
53.3
|
1.0
|
|
HB3
|
F:ASP58
|
4.9
|
73.2
|
1.0
|
|
HA
|
F:CYS34
|
4.9
|
72.0
|
1.0
|
|
C
|
F:CYS31
|
4.9
|
56.7
|
1.0
|
|
CD
|
F:LYS44
|
5.0
|
74.7
|
1.0
|
|
C
|
F:CYS34
|
5.0
|
69.7
|
1.0
|
|
CA
|
F:VAL33
|
5.0
|
58.1
|
1.0
|
|
N
|
F:GLU35
|
5.0
|
66.4
|
1.0
|
|
HE1
|
F:PHE38
|
5.0
|
74.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 5vzw
Go back to
Zinc Binding Sites List in 5vzw
Zinc binding site 3 out
of 4 in the TRIM23 Ring Domain in Complex with UBCH5-Ub
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of TRIM23 Ring Domain in Complex with UBCH5-Ub within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn301
b:44.9
occ:1.00
|
OD2
|
G:ASP75
|
1.9
|
53.3
|
1.0
|
|
ND1
|
G:HIS53
|
2.1
|
46.2
|
1.0
|
|
SG
|
G:CYS51
|
2.2
|
46.9
|
1.0
|
|
SG
|
G:CYS72
|
2.2
|
46.1
|
1.0
|
|
CG
|
G:ASP75
|
2.7
|
44.0
|
1.0
|
|
HB2
|
G:CYS51
|
2.9
|
51.6
|
1.0
|
|
OD1
|
G:ASP75
|
2.9
|
50.0
|
1.0
|
|
HB2
|
G:HIS53
|
2.9
|
51.5
|
1.0
|
|
CE1
|
G:HIS53
|
3.0
|
50.8
|
1.0
|
|
CB
|
G:CYS51
|
3.1
|
43.0
|
1.0
|
|
CB
|
G:CYS72
|
3.1
|
44.4
|
1.0
|
|
HB2
|
G:CYS72
|
3.1
|
53.3
|
1.0
|
|
HE1
|
G:HIS53
|
3.1
|
60.9
|
1.0
|
|
HB3
|
G:CYS72
|
3.1
|
53.3
|
1.0
|
|
CG
|
G:HIS53
|
3.2
|
50.4
|
1.0
|
|
HB3
|
G:CYS51
|
3.5
|
51.6
|
1.0
|
|
CB
|
G:HIS53
|
3.6
|
42.9
|
1.0
|
|
HB2
|
G:PHE74
|
3.7
|
53.7
|
1.0
|
|
H
|
G:HIS53
|
3.8
|
47.8
|
1.0
|
|
HD2
|
G:PHE74
|
3.9
|
60.8
|
1.0
|
|
H
|
G:ASP75
|
4.0
|
57.8
|
1.0
|
|
CB
|
G:ASP75
|
4.1
|
46.6
|
1.0
|
|
HB3
|
G:HIS53
|
4.2
|
51.5
|
1.0
|
|
NE2
|
G:HIS53
|
4.2
|
48.3
|
1.0
|
|
HB3
|
G:ASP75
|
4.2
|
55.9
|
1.0
|
|
HB2
|
G:GLN77
|
4.3
|
59.8
|
1.0
|
|
CD2
|
G:HIS53
|
4.3
|
43.3
|
1.0
|
|
HD12
|
G:LEU49
|
4.3
|
62.2
|
1.0
|
|
H
|
G:PHE74
|
4.3
|
58.2
|
1.0
|
|
N
|
G:ASP75
|
4.4
|
48.2
|
1.0
|
|
CA
|
G:CYS51
|
4.4
|
45.5
|
1.0
|
|
N
|
G:HIS53
|
4.5
|
39.8
|
1.0
|
|
HB2
|
G:LEU49
|
4.5
|
52.8
|
1.0
|
|
CA
|
G:CYS72
|
4.6
|
44.7
|
1.0
|
|
HD13
|
G:LEU49
|
4.6
|
62.2
|
1.0
|
|
CA
|
G:HIS53
|
4.6
|
45.8
|
1.0
|
|
C
|
G:CYS51
|
4.6
|
47.9
|
1.0
|
|
CB
|
G:PHE74
|
4.6
|
44.8
|
1.0
|
|
HB2
|
G:ASP75
|
4.7
|
55.9
|
1.0
|
|
H
|
G:CYS51
|
4.7
|
50.9
|
1.0
|
|
O
|
G:HOH403
|
4.7
|
49.8
|
1.0
|
|
H
|
G:GLN77
|
4.7
|
60.9
|
1.0
|
|
CD2
|
G:PHE74
|
4.7
|
50.7
|
1.0
|
|
O
|
G:CYS51
|
4.8
|
46.2
|
1.0
|
|
CA
|
G:ASP75
|
4.8
|
48.6
|
1.0
|
|
HA
|
G:CYS72
|
4.9
|
53.7
|
1.0
|
|
CD1
|
G:LEU49
|
4.9
|
51.8
|
1.0
|
|
HE2
|
G:HIS53
|
4.9
|
58.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 5vzw
Go back to
Zinc Binding Sites List in 5vzw
Zinc binding site 4 out
of 4 in the TRIM23 Ring Domain in Complex with UBCH5-Ub
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of TRIM23 Ring Domain in Complex with UBCH5-Ub within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn302
b:55.0
occ:1.00
|
SG
|
G:CYS59
|
2.2
|
50.7
|
1.0
|
|
SG
|
G:CYS31
|
2.3
|
52.8
|
1.0
|
|
SG
|
G:CYS56
|
2.4
|
52.6
|
1.0
|
|
SG
|
G:CYS34
|
2.4
|
57.9
|
1.0
|
|
HB3
|
G:CYS31
|
2.8
|
65.6
|
1.0
|
|
HB3
|
G:CYS56
|
2.9
|
63.2
|
1.0
|
|
H
|
G:CYS34
|
2.9
|
72.3
|
1.0
|
|
HB2
|
G:CYS59
|
2.9
|
62.0
|
1.0
|
|
CB
|
G:CYS31
|
3.0
|
54.6
|
1.0
|
|
HB2
|
G:CYS31
|
3.2
|
65.6
|
1.0
|
|
CB
|
G:CYS59
|
3.2
|
51.7
|
1.0
|
|
CB
|
G:CYS56
|
3.2
|
52.6
|
1.0
|
|
HB3
|
G:CYS34
|
3.3
|
67.2
|
1.0
|
|
H
|
G:CYS56
|
3.4
|
61.4
|
1.0
|
|
CB
|
G:CYS34
|
3.4
|
56.0
|
1.0
|
|
HZ2
|
G:LYS44
|
3.5
|
86.0
|
1.0
|
|
HB
|
G:VAL33
|
3.6
|
67.7
|
1.0
|
|
H
|
G:CYS59
|
3.6
|
57.7
|
1.0
|
|
N
|
G:CYS34
|
3.7
|
60.3
|
1.0
|
|
HB3
|
G:CYS59
|
3.8
|
62.0
|
1.0
|
|
HZ3
|
G:LYS44
|
3.8
|
86.0
|
1.0
|
|
HB2
|
G:CYS56
|
3.9
|
63.2
|
1.0
|
|
N
|
G:CYS56
|
4.1
|
51.1
|
1.0
|
|
NZ
|
G:LYS44
|
4.1
|
71.7
|
1.0
|
|
H
|
G:VAL33
|
4.1
|
68.8
|
1.0
|
|
CA
|
G:CYS56
|
4.2
|
49.8
|
1.0
|
|
CA
|
G:CYS34
|
4.2
|
62.0
|
1.0
|
|
HG13
|
G:VAL55
|
4.2
|
62.3
|
1.0
|
|
HB2
|
G:CYS34
|
4.2
|
67.2
|
1.0
|
|
N
|
G:CYS59
|
4.3
|
48.1
|
1.0
|
|
CA
|
G:CYS59
|
4.3
|
53.7
|
1.0
|
|
HG12
|
G:VAL55
|
4.5
|
62.3
|
1.0
|
|
CA
|
G:CYS31
|
4.5
|
56.9
|
1.0
|
|
HD2
|
G:LYS44
|
4.5
|
88.2
|
1.0
|
|
CB
|
G:VAL33
|
4.5
|
56.4
|
1.0
|
|
H
|
G:GLU35
|
4.5
|
77.4
|
1.0
|
|
HZ1
|
G:LYS44
|
4.6
|
86.0
|
1.0
|
|
HD3
|
G:LYS44
|
4.6
|
88.2
|
1.0
|
|
O
|
G:CYS56
|
4.6
|
50.0
|
1.0
|
|
H
|
G:ASP36
|
4.7
|
87.1
|
1.0
|
|
HA
|
G:CYS59
|
4.7
|
64.5
|
1.0
|
|
C
|
G:CYS56
|
4.7
|
49.5
|
1.0
|
|
HE1
|
G:PHE38
|
4.8
|
70.5
|
1.0
|
|
C
|
G:VAL33
|
4.8
|
56.6
|
1.0
|
|
CG1
|
G:VAL55
|
4.8
|
51.9
|
1.0
|
|
N
|
G:VAL33
|
4.9
|
57.4
|
1.0
|
|
HB2
|
G:ASP36
|
4.9
|
84.9
|
1.0
|
|
C
|
G:CYS31
|
4.9
|
57.4
|
1.0
|
|
HG12
|
G:VAL33
|
4.9
|
61.6
|
1.0
|
|
HA
|
G:CYS31
|
4.9
|
68.3
|
1.0
|
|
CD
|
G:LYS44
|
4.9
|
73.5
|
1.0
|
|
HB3
|
G:ASP58
|
4.9
|
77.2
|
1.0
|
|
HA
|
G:CYS34
|
4.9
|
74.4
|
1.0
|
|
CA
|
G:VAL33
|
5.0
|
57.5
|
1.0
|
|
N
|
G:GLU35
|
5.0
|
64.5
|
1.0
|
|
C
|
G:CYS34
|
5.0
|
62.0
|
1.0
|
|
HA
|
G:CYS56
|
5.0
|
59.8
|
1.0
|
|
Reference:
D.M.Dawidziak,
J.G.Sanchez,
J.M.Wagner,
B.K.Ganser-Pornillos,
O.Pornillos.
Structure and Catalytic Activation of the TRIM23 Ring E3 Ubiquitin Ligase. Proteins V. 85 1957 2017.
ISSN: ESSN 1097-0134
PubMed: 28681414
DOI: 10.1002/PROT.25348
Page generated: Wed Dec 16 11:13:42 2020
|
