Zinc in PDB 5f7t: TRIM5 B-BOX2 and Coiled-Coil Chimera
Enzymatic activity of TRIM5 B-BOX2 and Coiled-Coil Chimera
All present enzymatic activity of TRIM5 B-BOX2 and Coiled-Coil Chimera:
6.1.1.11;
Protein crystallography data
The structure of TRIM5 B-BOX2 and Coiled-Coil Chimera, PDB code: 5f7t
was solved by
J.M.Wagner,
G.Doss,
O.Pornillos,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
35.05 /
2.29
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.802,
52.329,
69.691,
94.77,
105.54,
103.02
|
|
R / Rfree (%)
|
22.4 /
25.6
|
Zinc Binding Sites:
The binding sites of Zinc atom in the TRIM5 B-BOX2 and Coiled-Coil Chimera
(pdb code 5f7t). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
TRIM5 B-BOX2 and Coiled-Coil Chimera, PDB code: 5f7t:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5f7t
Go back to
Zinc Binding Sites List in 5f7t
Zinc binding site 1 out
of 8 in the TRIM5 B-BOX2 and Coiled-Coil Chimera
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of TRIM5 B-BOX2 and Coiled-Coil Chimera within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn701
b:38.2
occ:1.00
|
OD2
|
E:ASP111
|
2.0
|
63.2
|
1.0
|
|
ND1
|
E:HIS125
|
2.0
|
40.0
|
1.0
|
|
ND1
|
E:HIS128
|
2.0
|
43.0
|
1.0
|
|
SG
|
E:CYS108
|
2.3
|
40.9
|
1.0
|
|
CG
|
E:ASP111
|
2.8
|
66.7
|
1.0
|
|
CE1
|
E:HIS125
|
2.9
|
40.8
|
1.0
|
|
CE1
|
E:HIS128
|
2.9
|
44.4
|
1.0
|
|
HE1
|
E:HIS125
|
3.0
|
48.9
|
1.0
|
|
HE1
|
E:HIS128
|
3.1
|
53.3
|
1.0
|
|
CG
|
E:HIS128
|
3.1
|
43.9
|
1.0
|
|
HA
|
E:HIS125
|
3.1
|
57.9
|
1.0
|
|
CG
|
E:HIS125
|
3.1
|
40.3
|
1.0
|
|
HB2
|
E:ASP111
|
3.2
|
71.5
|
1.0
|
|
HB3
|
E:HIS125
|
3.3
|
49.4
|
1.0
|
|
HB3
|
E:HIS128
|
3.3
|
52.2
|
1.0
|
|
CB
|
E:CYS108
|
3.4
|
38.6
|
1.0
|
|
HB2
|
E:CYS108
|
3.4
|
46.3
|
1.0
|
|
HB2
|
E:HIS128
|
3.4
|
52.2
|
1.0
|
|
CB
|
E:HIS128
|
3.5
|
43.5
|
1.0
|
|
OD1
|
E:ASP111
|
3.5
|
74.5
|
1.0
|
|
CB
|
E:HIS125
|
3.5
|
41.2
|
1.0
|
|
HB3
|
E:CYS108
|
3.5
|
46.3
|
1.0
|
|
CB
|
E:ASP111
|
3.6
|
59.6
|
1.0
|
|
H
|
E:ASP111
|
3.7
|
56.2
|
1.0
|
|
CA
|
E:HIS125
|
3.8
|
48.3
|
1.0
|
|
HB2
|
E:GLU110
|
3.9
|
65.6
|
1.0
|
|
NE2
|
E:HIS125
|
4.1
|
39.4
|
1.0
|
|
NE2
|
E:HIS128
|
4.1
|
46.1
|
1.0
|
|
CD2
|
E:HIS128
|
4.2
|
45.8
|
1.0
|
|
CD2
|
E:HIS125
|
4.2
|
39.9
|
1.0
|
|
HB3
|
E:ASP111
|
4.2
|
71.5
|
1.0
|
|
N
|
E:ASP111
|
4.3
|
46.9
|
1.0
|
|
O
|
E:GLU124
|
4.4
|
44.8
|
1.0
|
|
HB2
|
E:HIS125
|
4.5
|
49.4
|
1.0
|
|
HD13
|
E:ILE115
|
4.5
|
44.5
|
1.0
|
|
CA
|
E:ASP111
|
4.5
|
51.8
|
1.0
|
|
C
|
E:HIS125
|
4.7
|
44.9
|
1.0
|
|
CA
|
E:CYS108
|
4.8
|
41.5
|
1.0
|
|
N
|
E:HIS125
|
4.8
|
43.9
|
1.0
|
|
H
|
E:GLU110
|
4.8
|
60.0
|
1.0
|
|
O
|
E:HIS125
|
4.8
|
45.6
|
1.0
|
|
HE2
|
E:HIS125
|
4.8
|
47.3
|
1.0
|
|
CB
|
E:GLU110
|
4.8
|
54.6
|
1.0
|
|
HE2
|
E:HIS128
|
4.8
|
55.4
|
1.0
|
|
OE1
|
E:GLU110
|
4.9
|
62.9
|
1.0
|
|
C
|
E:GLU124
|
5.0
|
44.9
|
1.0
|
|
HA
|
E:CYS108
|
5.0
|
49.8
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5f7t
Go back to
Zinc Binding Sites List in 5f7t
Zinc binding site 2 out
of 8 in the TRIM5 B-BOX2 and Coiled-Coil Chimera
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of TRIM5 B-BOX2 and Coiled-Coil Chimera within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn702
b:40.8
occ:1.00
|
ND1
|
E:HIS100
|
2.0
|
41.5
|
1.0
|
|
SG
|
E:CYS119
|
2.3
|
41.4
|
1.0
|
|
SG
|
E:CYS116
|
2.3
|
40.3
|
1.0
|
|
SG
|
E:CYS97
|
2.3
|
54.4
|
1.0
|
|
HB2
|
E:HIS100
|
2.8
|
55.2
|
1.0
|
|
CE1
|
E:HIS100
|
3.0
|
41.0
|
1.0
|
|
CG
|
E:HIS100
|
3.1
|
41.5
|
1.0
|
|
HB2
|
E:CYS97
|
3.1
|
47.7
|
1.0
|
|
CB
|
E:CYS97
|
3.1
|
39.8
|
1.0
|
|
HE1
|
E:HIS100
|
3.1
|
49.2
|
1.0
|
|
HB3
|
E:CYS97
|
3.2
|
47.7
|
1.0
|
|
H
|
E:CYS119
|
3.3
|
50.0
|
1.0
|
|
HB3
|
E:CYS116
|
3.3
|
45.5
|
1.0
|
|
H
|
E:CYS116
|
3.4
|
51.2
|
1.0
|
|
CB
|
E:HIS100
|
3.4
|
46.0
|
1.0
|
|
CB
|
E:CYS116
|
3.5
|
37.9
|
1.0
|
|
HB2
|
E:ARG99
|
3.5
|
70.1
|
1.0
|
|
H
|
E:HIS100
|
3.7
|
60.0
|
1.0
|
|
CB
|
E:CYS119
|
3.7
|
39.4
|
1.0
|
|
N
|
E:CYS119
|
3.8
|
41.7
|
1.0
|
|
HB2
|
E:LEU118
|
3.8
|
51.8
|
1.0
|
|
HB2
|
E:CYS119
|
4.0
|
47.2
|
1.0
|
|
HB3
|
E:HIS100
|
4.1
|
55.2
|
1.0
|
|
NE2
|
E:HIS100
|
4.1
|
42.8
|
1.0
|
|
N
|
E:CYS116
|
4.1
|
42.7
|
1.0
|
|
CD2
|
E:HIS100
|
4.2
|
44.8
|
1.0
|
|
N
|
E:HIS100
|
4.2
|
50.0
|
1.0
|
|
CA
|
E:CYS119
|
4.2
|
42.7
|
1.0
|
|
HB2
|
E:CYS116
|
4.2
|
45.5
|
1.0
|
|
CA
|
E:CYS116
|
4.3
|
40.3
|
1.0
|
|
HA
|
E:CYS119
|
4.3
|
51.3
|
1.0
|
|
HD2
|
E:ARG99
|
4.4
|
97.5
|
1.0
|
|
CA
|
E:HIS100
|
4.4
|
47.4
|
1.0
|
|
H
|
E:LEU118
|
4.5
|
46.6
|
1.0
|
|
HB3
|
E:CYS119
|
4.5
|
47.2
|
1.0
|
|
CB
|
E:ARG99
|
4.5
|
58.4
|
1.0
|
|
HB2
|
E:GLU102
|
4.6
|
62.1
|
1.0
|
|
H
|
E:ARG99
|
4.6
|
55.5
|
1.0
|
|
CA
|
E:CYS97
|
4.6
|
41.9
|
1.0
|
|
CB
|
E:LEU118
|
4.6
|
43.2
|
1.0
|
|
C
|
E:LEU118
|
4.6
|
40.4
|
1.0
|
|
C
|
E:CYS116
|
4.6
|
39.5
|
1.0
|
|
O
|
E:CYS116
|
4.7
|
39.1
|
1.0
|
|
HB3
|
E:LEU118
|
4.8
|
51.8
|
1.0
|
|
H
|
E:GLU102
|
4.8
|
57.7
|
1.0
|
|
HB3
|
E:ARG99
|
4.8
|
70.1
|
1.0
|
|
HA
|
E:CYS97
|
4.8
|
50.2
|
1.0
|
|
HD21
|
E:LEU104
|
4.8
|
53.2
|
1.0
|
|
HB
|
E:ILE115
|
4.8
|
43.9
|
1.0
|
|
HE2
|
E:HIS100
|
4.9
|
51.4
|
1.0
|
|
HD23
|
E:LEU104
|
4.9
|
53.2
|
1.0
|
|
N
|
E:LEU118
|
5.0
|
38.9
|
1.0
|
|
H
|
E:GLY101
|
5.0
|
65.2
|
1.0
|
|
CA
|
E:LEU118
|
5.0
|
41.9
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5f7t
Go back to
Zinc Binding Sites List in 5f7t
Zinc binding site 3 out
of 8 in the TRIM5 B-BOX2 and Coiled-Coil Chimera
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of TRIM5 B-BOX2 and Coiled-Coil Chimera within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn701
b:41.3
occ:1.00
|
OD2
|
F:ASP111
|
2.0
|
78.9
|
1.0
|
|
ND1
|
F:HIS128
|
2.0
|
45.8
|
1.0
|
|
ND1
|
F:HIS125
|
2.0
|
38.5
|
1.0
|
|
SG
|
F:CYS108
|
2.3
|
54.5
|
1.0
|
|
CG
|
F:ASP111
|
2.7
|
79.1
|
1.0
|
|
CE1
|
F:HIS125
|
2.9
|
42.0
|
1.0
|
|
CE1
|
F:HIS128
|
2.9
|
48.4
|
1.0
|
|
HE1
|
F:HIS125
|
3.0
|
50.4
|
1.0
|
|
HE1
|
F:HIS128
|
3.0
|
58.1
|
1.0
|
|
HA
|
F:HIS125
|
3.1
|
52.2
|
1.0
|
|
CG
|
F:HIS128
|
3.1
|
47.0
|
1.0
|
|
CG
|
F:HIS125
|
3.1
|
37.6
|
1.0
|
|
HB2
|
F:ASP111
|
3.2
|
80.2
|
1.0
|
|
HB3
|
F:HIS125
|
3.3
|
49.7
|
1.0
|
|
HB3
|
F:HIS128
|
3.3
|
54.1
|
1.0
|
|
HB2
|
F:HIS128
|
3.4
|
54.1
|
1.0
|
|
OD1
|
F:ASP111
|
3.5
|
87.2
|
1.0
|
|
CB
|
F:CYS108
|
3.5
|
41.9
|
1.0
|
|
CB
|
F:HIS128
|
3.5
|
45.1
|
1.0
|
|
CB
|
F:HIS125
|
3.5
|
41.4
|
1.0
|
|
CB
|
F:ASP111
|
3.5
|
66.8
|
1.0
|
|
HB3
|
F:CYS108
|
3.5
|
50.3
|
1.0
|
|
HB2
|
F:CYS108
|
3.6
|
50.3
|
1.0
|
|
H
|
F:ASP111
|
3.7
|
62.0
|
1.0
|
|
CA
|
F:HIS125
|
3.8
|
43.5
|
1.0
|
|
HB2
|
F:GLU110
|
3.8
|
61.1
|
1.0
|
|
NE2
|
F:HIS125
|
4.1
|
35.7
|
1.0
|
|
NE2
|
F:HIS128
|
4.1
|
51.4
|
1.0
|
|
CD2
|
F:HIS128
|
4.2
|
50.5
|
1.0
|
|
CD2
|
F:HIS125
|
4.2
|
36.0
|
1.0
|
|
N
|
F:ASP111
|
4.2
|
51.7
|
1.0
|
|
O
|
F:GLU124
|
4.2
|
46.4
|
1.0
|
|
HB3
|
F:ASP111
|
4.2
|
80.2
|
1.0
|
|
HB2
|
F:HIS125
|
4.5
|
49.7
|
1.0
|
|
CA
|
F:ASP111
|
4.5
|
56.6
|
1.0
|
|
HD13
|
F:ILE115
|
4.6
|
41.2
|
1.0
|
|
N
|
F:HIS125
|
4.7
|
44.8
|
1.0
|
|
CB
|
F:GLU110
|
4.7
|
51.0
|
1.0
|
|
C
|
F:HIS125
|
4.8
|
51.9
|
1.0
|
|
H
|
F:GLU110
|
4.8
|
62.1
|
1.0
|
|
O
|
F:HIS125
|
4.8
|
50.5
|
1.0
|
|
HE2
|
F:HIS125
|
4.8
|
42.9
|
1.0
|
|
HE2
|
F:HIS128
|
4.8
|
61.6
|
1.0
|
|
CA
|
F:CYS108
|
4.9
|
44.2
|
1.0
|
|
C
|
F:GLU124
|
4.9
|
44.2
|
1.0
|
|
OE1
|
F:GLU110
|
4.9
|
58.6
|
1.0
|
|
HB3
|
F:GLU110
|
5.0
|
61.1
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5f7t
Go back to
Zinc Binding Sites List in 5f7t
Zinc binding site 4 out
of 8 in the TRIM5 B-BOX2 and Coiled-Coil Chimera
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of TRIM5 B-BOX2 and Coiled-Coil Chimera within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn702
b:67.3
occ:1.00
|
ND1
|
F:HIS100
|
2.0
|
40.1
|
1.0
|
|
SG
|
F:CYS119
|
2.3
|
42.1
|
1.0
|
|
SG
|
F:CYS97
|
2.3
|
48.8
|
1.0
|
|
SG
|
F:CYS116
|
2.3
|
42.4
|
1.0
|
|
HB2
|
F:HIS100
|
2.7
|
44.4
|
1.0
|
|
CE1
|
F:HIS100
|
3.0
|
39.3
|
1.0
|
|
CG
|
F:HIS100
|
3.0
|
37.4
|
1.0
|
|
HB2
|
F:CYS97
|
3.1
|
60.1
|
1.0
|
|
CB
|
F:CYS97
|
3.2
|
50.1
|
1.0
|
|
HE1
|
F:HIS100
|
3.2
|
47.1
|
1.0
|
|
HB3
|
F:CYS97
|
3.2
|
60.1
|
1.0
|
|
HB3
|
F:CYS116
|
3.2
|
40.0
|
1.0
|
|
CB
|
F:HIS100
|
3.3
|
37.0
|
1.0
|
|
H
|
F:CYS116
|
3.4
|
46.1
|
1.0
|
|
H
|
F:CYS119
|
3.4
|
49.5
|
1.0
|
|
CB
|
F:CYS116
|
3.4
|
33.4
|
1.0
|
|
HB2
|
F:ARG99
|
3.5
|
61.3
|
1.0
|
|
H
|
F:HIS100
|
3.6
|
54.7
|
1.0
|
|
CB
|
F:CYS119
|
3.8
|
39.3
|
1.0
|
|
HB2
|
F:LEU118
|
3.9
|
45.7
|
1.0
|
|
N
|
F:CYS119
|
3.9
|
41.2
|
1.0
|
|
HB3
|
F:HIS100
|
4.0
|
44.4
|
1.0
|
|
HB2
|
F:CYS119
|
4.0
|
47.1
|
1.0
|
|
N
|
F:CYS116
|
4.1
|
38.5
|
1.0
|
|
N
|
F:HIS100
|
4.1
|
45.6
|
1.0
|
|
NE2
|
F:HIS100
|
4.1
|
41.1
|
1.0
|
|
CD2
|
F:HIS100
|
4.1
|
41.3
|
1.0
|
|
HB2
|
F:CYS116
|
4.2
|
40.0
|
1.0
|
|
CA
|
F:CYS116
|
4.2
|
38.5
|
1.0
|
|
CA
|
F:CYS119
|
4.3
|
40.1
|
1.0
|
|
CA
|
F:HIS100
|
4.3
|
42.1
|
1.0
|
|
HA
|
F:CYS119
|
4.4
|
48.1
|
1.0
|
|
HB2
|
F:GLU102
|
4.4
|
66.9
|
1.0
|
|
HD3
|
F:ARG99
|
4.5
|
80.6
|
1.0
|
|
H
|
F:LEU118
|
4.5
|
44.9
|
1.0
|
|
CB
|
F:ARG99
|
4.5
|
51.1
|
1.0
|
|
HB3
|
F:CYS119
|
4.5
|
47.1
|
1.0
|
|
H
|
F:ARG99
|
4.6
|
57.7
|
1.0
|
|
CA
|
F:CYS97
|
4.6
|
49.4
|
1.0
|
|
C
|
F:CYS116
|
4.6
|
36.2
|
1.0
|
|
H
|
F:GLU102
|
4.7
|
60.2
|
1.0
|
|
O
|
F:CYS116
|
4.7
|
38.1
|
1.0
|
|
CB
|
F:LEU118
|
4.7
|
38.1
|
1.0
|
|
C
|
F:LEU118
|
4.8
|
40.3
|
1.0
|
|
HD21
|
F:LEU104
|
4.8
|
48.8
|
1.0
|
|
HB3
|
F:ARG99
|
4.8
|
61.3
|
1.0
|
|
HA
|
F:CYS97
|
4.8
|
59.3
|
1.0
|
|
HB
|
F:ILE115
|
4.8
|
38.1
|
1.0
|
|
HB3
|
F:LEU118
|
4.9
|
45.7
|
1.0
|
|
HD23
|
F:LEU104
|
4.9
|
48.8
|
1.0
|
|
HE2
|
F:HIS100
|
4.9
|
49.4
|
1.0
|
|
H
|
F:GLY101
|
4.9
|
65.2
|
1.0
|
|
C
|
F:ARG99
|
5.0
|
47.5
|
1.0
|
|
HD2
|
F:HIS100
|
5.0
|
49.6
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5f7t
Go back to
Zinc Binding Sites List in 5f7t
Zinc binding site 5 out
of 8 in the TRIM5 B-BOX2 and Coiled-Coil Chimera
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of TRIM5 B-BOX2 and Coiled-Coil Chimera within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn701
b:49.5
occ:1.00
|
OD2
|
H:ASP111
|
2.0
|
71.7
|
1.0
|
|
ND1
|
H:HIS125
|
2.0
|
41.1
|
1.0
|
|
ND1
|
H:HIS128
|
2.0
|
48.0
|
1.0
|
|
SG
|
H:CYS108
|
2.3
|
51.3
|
1.0
|
|
CG
|
H:ASP111
|
2.8
|
69.5
|
1.0
|
|
CE1
|
H:HIS125
|
2.9
|
44.0
|
1.0
|
|
CE1
|
H:HIS128
|
2.9
|
49.0
|
1.0
|
|
HE1
|
H:HIS125
|
3.0
|
52.8
|
1.0
|
|
HA
|
H:HIS125
|
3.0
|
47.6
|
1.0
|
|
HE1
|
H:HIS128
|
3.1
|
58.8
|
1.0
|
|
CG
|
H:HIS128
|
3.1
|
48.0
|
1.0
|
|
CG
|
H:HIS125
|
3.1
|
39.4
|
1.0
|
|
HB3
|
H:HIS128
|
3.2
|
60.9
|
1.0
|
|
HB3
|
H:HIS125
|
3.3
|
44.0
|
1.0
|
|
HB2
|
H:ASP111
|
3.3
|
76.3
|
1.0
|
|
HB2
|
H:HIS128
|
3.4
|
60.9
|
1.0
|
|
CB
|
H:CYS108
|
3.4
|
45.4
|
1.0
|
|
CB
|
H:HIS128
|
3.5
|
50.7
|
1.0
|
|
HB2
|
H:CYS108
|
3.5
|
54.5
|
1.0
|
|
CB
|
H:HIS125
|
3.5
|
36.7
|
1.0
|
|
OD1
|
H:ASP111
|
3.5
|
73.1
|
1.0
|
|
HB3
|
H:CYS108
|
3.5
|
54.5
|
1.0
|
|
CB
|
H:ASP111
|
3.6
|
63.6
|
1.0
|
|
CA
|
H:HIS125
|
3.7
|
39.7
|
1.0
|
|
H
|
H:ASP111
|
3.8
|
63.4
|
1.0
|
|
HB2
|
H:GLU110
|
4.0
|
72.3
|
1.0
|
|
NE2
|
H:HIS125
|
4.1
|
45.9
|
1.0
|
|
NE2
|
H:HIS128
|
4.1
|
49.2
|
1.0
|
|
CD2
|
H:HIS128
|
4.2
|
48.4
|
1.0
|
|
CD2
|
H:HIS125
|
4.2
|
39.7
|
1.0
|
|
O
|
H:GLU124
|
4.2
|
42.2
|
1.0
|
|
HB3
|
H:ASP111
|
4.3
|
76.3
|
1.0
|
|
N
|
H:ASP111
|
4.4
|
52.8
|
1.0
|
|
HD13
|
H:ILE115
|
4.5
|
45.2
|
1.0
|
|
O
|
H:HOH812
|
4.5
|
70.4
|
1.0
|
|
HB2
|
H:HIS125
|
4.5
|
44.0
|
1.0
|
|
CA
|
H:ASP111
|
4.6
|
58.0
|
1.0
|
|
C
|
H:HIS125
|
4.7
|
42.7
|
1.0
|
|
N
|
H:HIS125
|
4.7
|
37.4
|
1.0
|
|
O
|
H:HIS125
|
4.8
|
41.7
|
1.0
|
|
HE2
|
H:HIS125
|
4.8
|
55.0
|
1.0
|
|
CA
|
H:CYS108
|
4.8
|
47.7
|
1.0
|
|
HE2
|
H:HIS128
|
4.9
|
59.0
|
1.0
|
|
C
|
H:GLU124
|
4.9
|
41.0
|
1.0
|
|
H
|
H:GLU110
|
4.9
|
67.8
|
1.0
|
|
CB
|
H:GLU110
|
4.9
|
60.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5f7t
Go back to
Zinc Binding Sites List in 5f7t
Zinc binding site 6 out
of 8 in the TRIM5 B-BOX2 and Coiled-Coil Chimera
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of TRIM5 B-BOX2 and Coiled-Coil Chimera within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn702
b:40.4
occ:1.00
|
ND1
|
H:HIS100
|
2.0
|
39.0
|
1.0
|
|
SG
|
H:CYS97
|
2.3
|
53.5
|
1.0
|
|
SG
|
H:CYS119
|
2.3
|
42.4
|
1.0
|
|
SG
|
H:CYS116
|
2.3
|
38.5
|
1.0
|
|
HB2
|
H:HIS100
|
2.8
|
51.8
|
1.0
|
|
CE1
|
H:HIS100
|
3.0
|
35.8
|
1.0
|
|
CG
|
H:HIS100
|
3.1
|
40.4
|
1.0
|
|
HE1
|
H:HIS100
|
3.2
|
43.0
|
1.0
|
|
HB2
|
H:CYS97
|
3.3
|
69.1
|
1.0
|
|
HB3
|
H:CYS116
|
3.3
|
40.8
|
1.0
|
|
CB
|
H:CYS97
|
3.3
|
57.6
|
1.0
|
|
H
|
H:CYS119
|
3.3
|
56.1
|
1.0
|
|
HB3
|
H:CYS97
|
3.4
|
69.1
|
1.0
|
|
H
|
H:CYS116
|
3.4
|
49.5
|
1.0
|
|
CB
|
H:HIS100
|
3.4
|
43.2
|
1.0
|
|
CB
|
H:CYS116
|
3.4
|
34.0
|
1.0
|
|
HB2
|
H:ARG99
|
3.5
|
63.7
|
1.0
|
|
H
|
H:HIS100
|
3.7
|
55.6
|
1.0
|
|
CB
|
H:CYS119
|
3.7
|
39.2
|
1.0
|
|
N
|
H:CYS119
|
3.8
|
46.7
|
1.0
|
|
HB2
|
H:LEU118
|
3.9
|
47.0
|
1.0
|
|
HB2
|
H:CYS119
|
4.0
|
47.0
|
1.0
|
|
HB3
|
H:HIS100
|
4.1
|
51.8
|
1.0
|
|
N
|
H:CYS116
|
4.1
|
41.2
|
1.0
|
|
NE2
|
H:HIS100
|
4.1
|
37.8
|
1.0
|
|
N
|
H:HIS100
|
4.1
|
46.4
|
1.0
|
|
CD2
|
H:HIS100
|
4.2
|
41.1
|
1.0
|
|
HB2
|
H:CYS116
|
4.2
|
40.8
|
1.0
|
|
CA
|
H:CYS119
|
4.2
|
44.5
|
1.0
|
|
CA
|
H:CYS116
|
4.2
|
36.9
|
1.0
|
|
HA
|
H:CYS119
|
4.3
|
53.3
|
1.0
|
|
HD3
|
H:ARG99
|
4.4
|
74.9
|
1.0
|
|
CA
|
H:HIS100
|
4.4
|
47.6
|
1.0
|
|
CB
|
H:ARG99
|
4.4
|
53.1
|
1.0
|
|
HB3
|
H:CYS119
|
4.5
|
47.0
|
1.0
|
|
H
|
H:LEU118
|
4.5
|
43.8
|
1.0
|
|
H
|
H:ARG99
|
4.6
|
60.4
|
1.0
|
|
HB2
|
H:GLU102
|
4.6
|
56.6
|
1.0
|
|
C
|
H:CYS116
|
4.7
|
34.4
|
1.0
|
|
HD21
|
H:LEU104
|
4.7
|
53.5
|
1.0
|
|
CB
|
H:LEU118
|
4.7
|
39.1
|
1.0
|
|
C
|
H:LEU118
|
4.7
|
44.1
|
1.0
|
|
O
|
H:CYS116
|
4.7
|
35.3
|
1.0
|
|
CA
|
H:CYS97
|
4.7
|
58.7
|
1.0
|
|
HB3
|
H:ARG99
|
4.7
|
63.7
|
1.0
|
|
H
|
H:GLU102
|
4.8
|
61.2
|
1.0
|
|
HD23
|
H:LEU104
|
4.8
|
53.5
|
1.0
|
|
HB3
|
H:LEU118
|
4.8
|
47.0
|
1.0
|
|
HB
|
H:ILE115
|
4.9
|
45.7
|
1.0
|
|
HE2
|
H:HIS100
|
4.9
|
45.3
|
1.0
|
|
HA
|
H:CYS97
|
4.9
|
70.5
|
1.0
|
|
H
|
H:GLY101
|
5.0
|
64.5
|
1.0
|
|
C
|
H:ARG99
|
5.0
|
51.6
|
1.0
|
|
N
|
H:LEU118
|
5.0
|
36.5
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5f7t
Go back to
Zinc Binding Sites List in 5f7t
Zinc binding site 7 out
of 8 in the TRIM5 B-BOX2 and Coiled-Coil Chimera
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of TRIM5 B-BOX2 and Coiled-Coil Chimera within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn701
b:53.9
occ:1.00
|
OD2
|
L:ASP111
|
2.0
|
88.8
|
1.0
|
|
ND1
|
L:HIS128
|
2.0
|
52.7
|
1.0
|
|
ND1
|
L:HIS125
|
2.0
|
49.3
|
1.0
|
|
SG
|
L:CYS108
|
2.3
|
55.4
|
1.0
|
|
CG
|
L:ASP111
|
2.7
|
88.6
|
1.0
|
|
CE1
|
L:HIS125
|
2.9
|
50.3
|
1.0
|
|
CE1
|
L:HIS128
|
2.9
|
55.4
|
1.0
|
|
HE1
|
L:HIS125
|
3.0
|
60.3
|
1.0
|
|
HE1
|
L:HIS128
|
3.0
|
66.4
|
1.0
|
|
HA
|
L:HIS125
|
3.1
|
61.7
|
1.0
|
|
CG
|
L:HIS128
|
3.1
|
55.8
|
1.0
|
|
CG
|
L:HIS125
|
3.1
|
45.1
|
1.0
|
|
HB2
|
L:ASP111
|
3.2
|
97.6
|
1.0
|
|
HB3
|
L:HIS128
|
3.3
|
64.2
|
1.0
|
|
HB3
|
L:HIS125
|
3.3
|
55.4
|
1.0
|
|
OD1
|
L:ASP111
|
3.5
|
94.4
|
1.0
|
|
HB2
|
L:HIS128
|
3.5
|
64.2
|
1.0
|
|
CB
|
L:CYS108
|
3.5
|
50.1
|
1.0
|
|
CB
|
L:ASP111
|
3.5
|
81.3
|
1.0
|
|
CB
|
L:HIS128
|
3.5
|
53.5
|
1.0
|
|
HB2
|
L:CYS108
|
3.6
|
60.2
|
1.0
|
|
CB
|
L:HIS125
|
3.6
|
46.2
|
1.0
|
|
HB3
|
L:CYS108
|
3.6
|
60.2
|
1.0
|
|
H
|
L:ASP111
|
3.6
|
91.3
|
1.0
|
|
CA
|
L:HIS125
|
3.8
|
51.4
|
1.0
|
|
HB2
|
L:GLU110
|
3.8
|
84.2
|
1.0
|
|
NE2
|
L:HIS125
|
4.1
|
44.5
|
1.0
|
|
NE2
|
L:HIS128
|
4.1
|
58.2
|
1.0
|
|
N
|
L:ASP111
|
4.2
|
76.1
|
1.0
|
|
CD2
|
L:HIS128
|
4.2
|
57.1
|
1.0
|
|
CD2
|
L:HIS125
|
4.2
|
43.8
|
1.0
|
|
HB3
|
L:ASP111
|
4.2
|
97.6
|
1.0
|
|
O
|
L:GLU124
|
4.3
|
56.0
|
1.0
|
|
CA
|
L:ASP111
|
4.5
|
75.4
|
1.0
|
|
HB2
|
L:HIS125
|
4.5
|
55.4
|
1.0
|
|
HD13
|
L:ILE115
|
4.7
|
50.3
|
1.0
|
|
H
|
L:GLU110
|
4.7
|
66.0
|
1.0
|
|
CB
|
L:GLU110
|
4.8
|
70.1
|
1.0
|
|
N
|
L:HIS125
|
4.8
|
54.9
|
1.0
|
|
C
|
L:HIS125
|
4.8
|
52.9
|
1.0
|
|
HE2
|
L:HIS125
|
4.8
|
53.4
|
1.0
|
|
HE2
|
L:HIS128
|
4.8
|
69.8
|
1.0
|
|
CA
|
L:CYS108
|
4.8
|
52.4
|
1.0
|
|
OE1
|
L:GLU110
|
4.9
|
80.6
|
1.0
|
|
C
|
L:GLU124
|
4.9
|
54.5
|
1.0
|
|
O
|
L:HIS125
|
4.9
|
53.1
|
1.0
|
|
HA
|
L:ASP111
|
5.0
|
90.5
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5f7t
Go back to
Zinc Binding Sites List in 5f7t
Zinc binding site 8 out
of 8 in the TRIM5 B-BOX2 and Coiled-Coil Chimera
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of TRIM5 B-BOX2 and Coiled-Coil Chimera within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn702
b:40.0
occ:1.00
|
ND1
|
L:HIS100
|
2.0
|
35.8
|
1.0
|
|
SG
|
L:CYS119
|
2.3
|
45.6
|
1.0
|
|
SG
|
L:CYS97
|
2.3
|
45.5
|
1.0
|
|
SG
|
L:CYS116
|
2.3
|
36.3
|
1.0
|
|
HB2
|
L:HIS100
|
2.8
|
50.2
|
1.0
|
|
CE1
|
L:HIS100
|
3.0
|
36.6
|
1.0
|
|
CG
|
L:HIS100
|
3.1
|
42.4
|
1.0
|
|
HE1
|
L:HIS100
|
3.1
|
44.0
|
1.0
|
|
HB2
|
L:CYS97
|
3.2
|
67.8
|
1.0
|
|
HB3
|
L:CYS116
|
3.2
|
45.4
|
1.0
|
|
H
|
L:CYS119
|
3.2
|
53.9
|
1.0
|
|
H
|
L:CYS116
|
3.2
|
46.2
|
1.0
|
|
CB
|
L:CYS97
|
3.2
|
56.5
|
1.0
|
|
HB3
|
L:CYS97
|
3.4
|
67.8
|
1.0
|
|
CB
|
L:CYS116
|
3.4
|
37.8
|
1.0
|
|
CB
|
L:HIS100
|
3.4
|
41.8
|
1.0
|
|
HB2
|
L:ARG99
|
3.5
|
65.4
|
1.0
|
|
CB
|
L:CYS119
|
3.7
|
45.3
|
1.0
|
|
H
|
L:HIS100
|
3.7
|
63.8
|
1.0
|
|
N
|
L:CYS119
|
3.8
|
44.9
|
1.0
|
|
HB2
|
L:LEU118
|
3.8
|
53.8
|
1.0
|
|
HB2
|
L:CYS119
|
3.9
|
54.4
|
1.0
|
|
N
|
L:CYS116
|
3.9
|
38.5
|
1.0
|
|
HB3
|
L:HIS100
|
4.1
|
50.2
|
1.0
|
|
NE2
|
L:HIS100
|
4.1
|
37.1
|
1.0
|
|
CA
|
L:CYS116
|
4.1
|
37.4
|
1.0
|
|
HB2
|
L:CYS116
|
4.1
|
45.4
|
1.0
|
|
CA
|
L:CYS119
|
4.2
|
39.1
|
1.0
|
|
CD2
|
L:HIS100
|
4.2
|
36.6
|
1.0
|
|
N
|
L:HIS100
|
4.2
|
53.2
|
1.0
|
|
HA
|
L:CYS119
|
4.3
|
46.9
|
1.0
|
|
H
|
L:LEU118
|
4.4
|
48.7
|
1.0
|
|
HD3
|
L:ARG99
|
4.4
|
87.6
|
1.0
|
|
CA
|
L:HIS100
|
4.4
|
51.2
|
1.0
|
|
HB3
|
L:CYS119
|
4.5
|
54.4
|
1.0
|
|
CB
|
L:ARG99
|
4.5
|
54.5
|
1.0
|
|
C
|
L:CYS116
|
4.5
|
37.2
|
1.0
|
|
HB2
|
L:GLU102
|
4.5
|
76.7
|
1.0
|
|
O
|
L:CYS116
|
4.6
|
37.7
|
1.0
|
|
C
|
L:LEU118
|
4.6
|
44.9
|
1.0
|
|
CB
|
L:LEU118
|
4.6
|
44.8
|
1.0
|
|
H
|
L:ARG99
|
4.7
|
57.5
|
1.0
|
|
HB
|
L:ILE115
|
4.7
|
49.7
|
1.0
|
|
CA
|
L:CYS97
|
4.7
|
57.2
|
1.0
|
|
HB3
|
L:ARG99
|
4.7
|
65.4
|
1.0
|
|
HB3
|
L:LEU118
|
4.8
|
53.8
|
1.0
|
|
H
|
L:GLU102
|
4.8
|
67.3
|
1.0
|
|
HA
|
L:CYS97
|
4.9
|
68.6
|
1.0
|
|
HE2
|
L:HIS100
|
4.9
|
44.6
|
1.0
|
|
N
|
L:LEU118
|
4.9
|
40.6
|
1.0
|
|
HD23
|
L:LEU104
|
4.9
|
64.3
|
1.0
|
|
HD21
|
L:LEU104
|
4.9
|
64.3
|
1.0
|
|
CA
|
L:LEU118
|
5.0
|
44.5
|
1.0
|
|
Reference:
J.M.Wagner,
M.D.Roganowicz,
K.Skorupka,
S.L.Alam,
D.E.Christensen,
G.L.Doss,
Y.Wan,
G.A.Frank,
B.K.Ganser-Pornillos,
W.I.Sundquist,
O.Pornillos.
Mechanism of B-Box 2 Domain-Mediated Higher-Order Assembly of the Retroviral Restriction Factor TRIM5 Alpha. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27253059
DOI: 10.7554/ELIFE.16309
Page generated: Wed Dec 16 06:13:13 2020
|
