Zinc in PDB 6h0f: Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2)
Protein crystallography data
The structure of Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2), PDB code: 6h0f
was solved by
G.Petzold,
R.D.Bunker,
N.H.Thoma,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.85 /
3.25
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
161.450,
177.860,
242.470,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.2 /
23.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2)
(pdb code 6h0f). 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 DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2), PDB code: 6h0f:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 6h0f
Go back to
Zinc Binding Sites List in 6h0f
Zinc binding site 1 out
of 8 in the Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:35.3
occ:1.00
|
SG
|
B:CYS323
|
2.2
|
48.5
|
1.0
|
SG
|
B:CYS394
|
2.2
|
41.7
|
1.0
|
SG
|
B:CYS391
|
2.3
|
38.1
|
1.0
|
SG
|
B:CYS326
|
2.5
|
44.6
|
1.0
|
HB3
|
B:CYS326
|
2.7
|
36.5
|
0.0
|
H
|
B:CYS326
|
2.8
|
47.3
|
0.0
|
H
|
B:CYS394
|
2.8
|
36.9
|
0.0
|
HB3
|
B:CYS323
|
3.0
|
43.3
|
0.0
|
CB
|
B:CYS323
|
3.1
|
45.0
|
1.0
|
HB3
|
B:CYS391
|
3.1
|
31.4
|
0.0
|
CB
|
B:CYS391
|
3.1
|
33.1
|
1.0
|
HB2
|
B:CYS391
|
3.1
|
32.3
|
0.0
|
CB
|
B:CYS326
|
3.1
|
40.1
|
1.0
|
HB2
|
B:CYS323
|
3.2
|
43.9
|
0.0
|
HB3
|
B:CYS394
|
3.4
|
40.0
|
0.0
|
CB
|
B:CYS394
|
3.4
|
37.1
|
1.0
|
N
|
B:CYS326
|
3.6
|
42.7
|
1.0
|
N
|
B:CYS394
|
3.7
|
36.3
|
1.0
|
HB
|
B:ILE393
|
3.8
|
31.6
|
0.0
|
HB3
|
B:GLN325
|
3.8
|
53.5
|
0.0
|
HB
|
B:THR329
|
3.9
|
50.3
|
0.0
|
CA
|
B:CYS326
|
3.9
|
41.0
|
1.0
|
HB2
|
B:SER396
|
4.0
|
33.8
|
0.0
|
HG
|
B:SER396
|
4.0
|
35.6
|
0.0
|
HB2
|
B:CYS326
|
4.0
|
37.1
|
0.0
|
HG22
|
B:ILE393
|
4.1
|
47.4
|
0.0
|
H
|
B:SER396
|
4.1
|
32.5
|
0.0
|
CA
|
B:CYS394
|
4.1
|
35.6
|
1.0
|
H
|
B:GLN327
|
4.2
|
41.3
|
0.0
|
HB2
|
B:CYS394
|
4.3
|
39.1
|
0.0
|
H
|
B:ILE393
|
4.3
|
32.2
|
0.0
|
HD11
|
B:ILE398
|
4.3
|
36.2
|
0.0
|
HG1
|
B:THR329
|
4.4
|
73.1
|
0.0
|
CA
|
B:CYS323
|
4.5
|
44.9
|
1.0
|
CA
|
B:CYS391
|
4.6
|
32.2
|
1.0
|
H
|
B:GLU328
|
4.6
|
42.5
|
0.0
|
CB
|
B:ILE393
|
4.7
|
38.7
|
1.0
|
H
|
B:ALA395
|
4.7
|
31.9
|
0.0
|
HG22
|
B:THR329
|
4.7
|
48.1
|
0.0
|
CB
|
B:GLN325
|
4.7
|
48.3
|
1.0
|
H
|
B:GLN325
|
4.7
|
39.9
|
0.0
|
C
|
B:GLN325
|
4.7
|
48.1
|
1.0
|
HA
|
B:CYS326
|
4.8
|
41.1
|
0.0
|
N
|
B:GLN327
|
4.8
|
41.3
|
1.0
|
HG21
|
B:THR329
|
4.8
|
48.4
|
0.0
|
HB2
|
B:GLN325
|
4.8
|
53.8
|
0.0
|
C
|
B:CYS394
|
4.8
|
38.1
|
1.0
|
C
|
B:CYS326
|
4.8
|
45.7
|
1.0
|
CB
|
B:THR329
|
4.8
|
55.3
|
1.0
|
C
|
B:ILE393
|
4.8
|
39.6
|
1.0
|
CG2
|
B:ILE393
|
4.8
|
44.5
|
1.0
|
OG
|
B:SER396
|
4.9
|
39.4
|
1.0
|
CB
|
B:SER396
|
4.9
|
33.8
|
1.0
|
HA
|
B:CYS391
|
4.9
|
28.0
|
0.0
|
O
|
B:CYS323
|
4.9
|
46.3
|
1.0
|
HA
|
B:CYS323
|
4.9
|
43.3
|
0.0
|
C
|
B:CYS323
|
5.0
|
47.3
|
1.0
|
N
|
B:ALA395
|
5.0
|
33.7
|
1.0
|
|
Zinc binding site 2 out
of 8 in 6h0f
Go back to
Zinc Binding Sites List in 6h0f
Zinc binding site 2 out
of 8 in the Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn201
b:49.2
occ:1.00
|
NE2
|
C:HIS167
|
1.9
|
59.2
|
1.0
|
NE2
|
C:HIS163
|
2.0
|
43.1
|
1.0
|
SG
|
C:CYS150
|
2.2
|
44.6
|
1.0
|
SG
|
C:CYS147
|
2.3
|
38.7
|
1.0
|
H
|
C:CYS150
|
2.9
|
43.1
|
0.0
|
CD2
|
C:HIS167
|
2.9
|
58.9
|
1.0
|
CD2
|
C:HIS163
|
2.9
|
42.1
|
1.0
|
CE1
|
C:HIS167
|
3.0
|
60.0
|
1.0
|
CE1
|
C:HIS163
|
3.0
|
43.6
|
1.0
|
HB3
|
C:CYS147
|
3.1
|
38.2
|
0.0
|
HD2
|
C:HIS167
|
3.1
|
50.7
|
0.0
|
HB3
|
C:GLN149
|
3.2
|
41.8
|
0.0
|
HD2
|
C:HIS163
|
3.2
|
33.5
|
0.0
|
CB
|
C:CYS147
|
3.2
|
34.9
|
1.0
|
HE1
|
C:HIS167
|
3.2
|
59.3
|
0.0
|
HE1
|
C:HIS163
|
3.3
|
49.3
|
0.0
|
HB3
|
C:CYS150
|
3.3
|
37.4
|
0.0
|
CB
|
C:CYS150
|
3.4
|
41.4
|
1.0
|
HB2
|
C:CYS147
|
3.5
|
37.2
|
0.0
|
N
|
C:CYS150
|
3.5
|
42.0
|
1.0
|
HB3
|
C:ALA152
|
3.6
|
37.4
|
0.0
|
H
|
C:ALA152
|
3.8
|
34.0
|
0.0
|
CA
|
C:CYS150
|
4.0
|
42.1
|
1.0
|
CG
|
C:HIS167
|
4.0
|
58.8
|
1.0
|
ND1
|
C:HIS167
|
4.1
|
61.3
|
1.0
|
CG
|
C:HIS163
|
4.1
|
40.5
|
1.0
|
HB2
|
C:ALA152
|
4.1
|
39.1
|
0.0
|
ND1
|
C:HIS163
|
4.1
|
43.8
|
1.0
|
H
|
C:GLN149
|
4.2
|
48.3
|
0.0
|
CB
|
C:GLN149
|
4.2
|
42.4
|
1.0
|
HB2
|
C:CYS150
|
4.3
|
38.5
|
0.0
|
CB
|
C:ALA152
|
4.4
|
38.7
|
1.0
|
HG22
|
C:ILE164
|
4.4
|
21.4
|
0.0
|
C
|
C:GLN149
|
4.4
|
46.6
|
1.0
|
H
|
C:GLY151
|
4.4
|
46.5
|
0.0
|
HB2
|
B:HIS397
|
4.6
|
33.2
|
0.0
|
CA
|
C:CYS147
|
4.6
|
34.2
|
1.0
|
C
|
C:CYS150
|
4.6
|
48.4
|
1.0
|
HA
|
C:ILE164
|
4.7
|
39.2
|
0.0
|
CA
|
C:GLN149
|
4.7
|
41.6
|
1.0
|
N
|
C:ALA152
|
4.7
|
40.0
|
1.0
|
N
|
C:GLY151
|
4.8
|
47.2
|
1.0
|
HB2
|
C:GLN149
|
4.8
|
41.6
|
0.0
|
HG2
|
C:GLN149
|
4.8
|
41.4
|
0.0
|
N
|
C:GLN149
|
4.8
|
42.8
|
1.0
|
HG11
|
B:VAL388
|
4.9
|
37.2
|
0.0
|
HA
|
C:CYS150
|
4.9
|
44.9
|
0.0
|
C
|
C:CYS147
|
5.0
|
42.5
|
1.0
|
|
Zinc binding site 3 out
of 8 in 6h0f
Go back to
Zinc Binding Sites List in 6h0f
Zinc binding site 3 out
of 8 in the Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn501
b:48.6
occ:1.00
|
SG
|
E:CYS394
|
2.2
|
45.2
|
1.0
|
SG
|
E:CYS323
|
2.3
|
52.2
|
1.0
|
SG
|
E:CYS326
|
2.5
|
54.6
|
1.0
|
SG
|
E:CYS391
|
2.5
|
45.2
|
1.0
|
HB3
|
E:CYS326
|
2.6
|
50.7
|
0.0
|
H
|
E:CYS326
|
2.6
|
50.8
|
0.0
|
H
|
E:CYS394
|
2.9
|
38.5
|
0.0
|
CB
|
E:CYS326
|
3.0
|
50.4
|
1.0
|
HB3
|
E:CYS323
|
3.2
|
44.2
|
0.0
|
HB3
|
E:CYS391
|
3.2
|
37.2
|
0.0
|
CB
|
E:CYS391
|
3.2
|
40.8
|
1.0
|
HB3
|
E:CYS394
|
3.3
|
43.9
|
0.0
|
CB
|
E:CYS323
|
3.3
|
48.4
|
1.0
|
HB2
|
E:CYS391
|
3.3
|
37.5
|
0.0
|
CB
|
E:CYS394
|
3.3
|
42.0
|
1.0
|
N
|
E:CYS326
|
3.4
|
49.8
|
1.0
|
HB2
|
E:CYS323
|
3.5
|
44.3
|
0.0
|
HB3
|
E:GLN325
|
3.7
|
59.9
|
0.0
|
N
|
E:CYS394
|
3.8
|
42.0
|
1.0
|
CA
|
E:CYS326
|
3.8
|
49.6
|
1.0
|
HB
|
E:ILE393
|
3.9
|
43.3
|
0.0
|
HG
|
E:SER396
|
3.9
|
58.3
|
0.0
|
HB2
|
E:CYS326
|
3.9
|
51.2
|
0.0
|
HB2
|
E:SER396
|
4.0
|
50.9
|
0.0
|
HG22
|
E:ILE393
|
4.1
|
43.6
|
0.0
|
HG1
|
E:THR329
|
4.1
|
55.1
|
0.0
|
CA
|
E:CYS394
|
4.1
|
42.0
|
1.0
|
H
|
E:GLN327
|
4.1
|
49.4
|
0.0
|
H
|
E:SER396
|
4.1
|
44.6
|
0.0
|
HB2
|
E:CYS394
|
4.2
|
43.3
|
0.0
|
HD11
|
E:ILE398
|
4.3
|
51.3
|
0.0
|
OG1
|
E:THR329
|
4.5
|
58.8
|
1.0
|
H
|
E:ILE393
|
4.5
|
46.0
|
0.0
|
CB
|
E:GLN325
|
4.5
|
52.7
|
1.0
|
C
|
E:GLN325
|
4.6
|
53.5
|
1.0
|
HG23
|
E:THR329
|
4.6
|
63.8
|
0.0
|
H
|
E:GLN325
|
4.6
|
42.3
|
0.0
|
H
|
E:GLU328
|
4.6
|
47.0
|
0.0
|
HA
|
E:CYS326
|
4.6
|
49.9
|
0.0
|
HB2
|
E:GLN325
|
4.6
|
59.6
|
0.0
|
CA
|
E:CYS323
|
4.7
|
49.2
|
1.0
|
N
|
E:GLN327
|
4.7
|
48.2
|
1.0
|
C
|
E:CYS326
|
4.7
|
52.3
|
1.0
|
CA
|
E:CYS391
|
4.7
|
41.2
|
1.0
|
CB
|
E:ILE393
|
4.7
|
46.5
|
1.0
|
H
|
E:ALA395
|
4.8
|
37.9
|
0.0
|
OG
|
E:SER396
|
4.8
|
58.7
|
1.0
|
C
|
E:CYS394
|
4.8
|
45.5
|
1.0
|
CB
|
E:SER396
|
4.9
|
50.0
|
1.0
|
CG2
|
E:ILE393
|
4.9
|
45.4
|
1.0
|
C
|
E:ILE393
|
4.9
|
46.4
|
1.0
|
HG21
|
E:THR329
|
4.9
|
63.9
|
0.0
|
CA
|
E:GLN325
|
4.9
|
49.3
|
1.0
|
|
Zinc binding site 4 out
of 8 in 6h0f
Go back to
Zinc Binding Sites List in 6h0f
Zinc binding site 4 out
of 8 in the Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn201
b:51.4
occ:1.00
|
NE2
|
F:HIS163
|
2.0
|
43.4
|
1.0
|
NE2
|
F:HIS167
|
2.0
|
63.6
|
1.0
|
SG
|
F:CYS150
|
2.2
|
50.5
|
1.0
|
SG
|
F:CYS147
|
2.3
|
43.7
|
1.0
|
H
|
F:CYS150
|
2.8
|
46.6
|
0.0
|
CD2
|
F:HIS163
|
3.0
|
43.2
|
1.0
|
HB3
|
F:CYS147
|
3.0
|
34.1
|
0.0
|
CD2
|
F:HIS167
|
3.0
|
63.2
|
1.0
|
CE1
|
F:HIS163
|
3.0
|
43.7
|
1.0
|
CE1
|
F:HIS167
|
3.0
|
64.5
|
1.0
|
CB
|
F:CYS147
|
3.2
|
38.9
|
1.0
|
HD2
|
F:HIS163
|
3.2
|
34.9
|
0.0
|
HB3
|
F:GLN149
|
3.2
|
58.6
|
0.0
|
HD2
|
F:HIS167
|
3.2
|
43.6
|
0.0
|
HE1
|
F:HIS167
|
3.3
|
62.6
|
0.0
|
HE1
|
F:HIS163
|
3.3
|
42.6
|
0.0
|
HB3
|
F:CYS150
|
3.3
|
44.9
|
0.0
|
CB
|
F:CYS150
|
3.3
|
47.1
|
1.0
|
HB2
|
F:CYS147
|
3.5
|
33.9
|
0.0
|
N
|
F:CYS150
|
3.5
|
48.0
|
1.0
|
HB3
|
F:ALA152
|
3.5
|
41.1
|
0.0
|
H
|
F:ALA152
|
3.7
|
37.2
|
0.0
|
CA
|
F:CYS150
|
3.9
|
47.7
|
1.0
|
HB2
|
F:ALA152
|
4.1
|
42.6
|
0.0
|
CG
|
F:HIS163
|
4.1
|
43.3
|
1.0
|
CG
|
F:HIS167
|
4.1
|
66.1
|
1.0
|
ND1
|
F:HIS163
|
4.1
|
44.8
|
1.0
|
H
|
F:GLN149
|
4.1
|
46.1
|
0.0
|
ND1
|
F:HIS167
|
4.2
|
67.1
|
1.0
|
HB2
|
F:CYS150
|
4.2
|
45.4
|
0.0
|
CB
|
F:GLN149
|
4.3
|
52.6
|
1.0
|
CB
|
F:ALA152
|
4.3
|
41.3
|
1.0
|
H
|
F:GLY151
|
4.4
|
40.1
|
0.0
|
C
|
F:GLN149
|
4.4
|
52.9
|
1.0
|
C
|
F:CYS150
|
4.6
|
49.7
|
1.0
|
CA
|
F:CYS147
|
4.6
|
39.1
|
1.0
|
N
|
F:ALA152
|
4.7
|
40.3
|
1.0
|
HB2
|
E:HIS397
|
4.7
|
51.0
|
0.0
|
N
|
F:GLY151
|
4.7
|
43.4
|
1.0
|
CA
|
F:GLN149
|
4.7
|
49.3
|
1.0
|
N
|
F:GLN149
|
4.8
|
47.6
|
1.0
|
HG2
|
F:GLN149
|
4.8
|
59.9
|
0.0
|
HB2
|
F:GLN149
|
4.8
|
59.1
|
0.0
|
HA
|
F:ILE164
|
4.8
|
43.7
|
0.0
|
HA
|
F:CYS150
|
4.9
|
54.6
|
0.0
|
HG11
|
E:VAL388
|
4.9
|
48.6
|
0.0
|
C
|
F:CYS147
|
4.9
|
44.5
|
1.0
|
O
|
F:CYS147
|
5.0
|
44.2
|
1.0
|
|
Zinc binding site 5 out
of 8 in 6h0f
Go back to
Zinc Binding Sites List in 6h0f
Zinc binding site 5 out
of 8 in the Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn501
b:38.2
occ:1.00
|
SG
|
H:CYS326
|
2.3
|
66.0
|
1.0
|
SG
|
H:CYS394
|
2.4
|
40.1
|
1.0
|
SG
|
H:CYS323
|
2.4
|
54.3
|
1.0
|
SG
|
H:CYS391
|
2.4
|
45.2
|
1.0
|
H
|
H:CYS326
|
2.6
|
33.9
|
0.0
|
HB3
|
H:CYS326
|
2.6
|
83.3
|
0.0
|
HB3
|
H:CYS323
|
2.8
|
69.6
|
0.0
|
CB
|
H:CYS326
|
2.9
|
61.5
|
1.0
|
H
|
H:CYS394
|
3.0
|
21.9
|
0.0
|
CB
|
H:CYS323
|
3.0
|
51.1
|
1.0
|
HB2
|
H:CYS323
|
3.2
|
70.3
|
0.0
|
CB
|
H:CYS391
|
3.3
|
41.0
|
1.0
|
HB2
|
H:CYS391
|
3.3
|
47.3
|
0.0
|
HB3
|
H:CYS391
|
3.3
|
46.2
|
0.0
|
HB3
|
H:CYS394
|
3.4
|
44.5
|
0.0
|
N
|
H:CYS326
|
3.4
|
49.2
|
1.0
|
CB
|
H:CYS394
|
3.5
|
35.8
|
1.0
|
CA
|
H:CYS326
|
3.7
|
54.3
|
1.0
|
HB
|
H:ILE393
|
3.8
|
35.7
|
0.0
|
HB3
|
H:GLN325
|
3.8
|
50.7
|
0.0
|
N
|
H:CYS394
|
3.8
|
31.2
|
1.0
|
HB2
|
H:CYS326
|
3.9
|
83.8
|
0.0
|
H
|
H:GLN327
|
3.9
|
49.2
|
0.0
|
HG22
|
H:ILE393
|
4.0
|
42.9
|
0.0
|
HG
|
H:SER396
|
4.2
|
35.9
|
0.0
|
HB2
|
H:SER396
|
4.2
|
28.2
|
0.0
|
OG1
|
H:THR329
|
4.2
|
44.3
|
1.0
|
CA
|
H:CYS394
|
4.2
|
33.0
|
1.0
|
H
|
H:SER396
|
4.3
|
30.9
|
0.0
|
H
|
H:GLU328
|
4.4
|
44.4
|
0.0
|
HB2
|
H:CYS394
|
4.4
|
43.8
|
0.0
|
H
|
H:ILE393
|
4.4
|
31.9
|
0.0
|
CA
|
H:CYS323
|
4.5
|
46.1
|
1.0
|
HD11
|
H:ILE398
|
4.5
|
36.4
|
0.0
|
N
|
H:GLN327
|
4.5
|
48.1
|
1.0
|
C
|
H:CYS326
|
4.6
|
54.5
|
1.0
|
C
|
H:GLN325
|
4.6
|
50.6
|
1.0
|
HA
|
H:CYS326
|
4.6
|
39.6
|
0.0
|
HG1
|
H:THR329
|
4.6
|
44.0
|
0.0
|
H
|
H:GLN325
|
4.6
|
38.0
|
0.0
|
CB
|
H:ILE393
|
4.7
|
38.6
|
1.0
|
CB
|
H:GLN325
|
4.7
|
47.5
|
1.0
|
HG23
|
H:THR329
|
4.7
|
44.4
|
0.0
|
CA
|
H:CYS391
|
4.8
|
38.8
|
1.0
|
HB2
|
H:GLN325
|
4.8
|
51.1
|
0.0
|
CG2
|
H:ILE393
|
4.8
|
41.8
|
1.0
|
HG21
|
H:THR329
|
4.9
|
44.8
|
0.0
|
H
|
H:ALA395
|
4.9
|
30.7
|
0.0
|
C
|
H:CYS323
|
4.9
|
44.7
|
1.0
|
O
|
H:CYS323
|
4.9
|
44.2
|
1.0
|
C
|
H:ILE393
|
4.9
|
35.3
|
1.0
|
HA
|
H:CYS323
|
5.0
|
34.6
|
0.0
|
C
|
H:CYS394
|
5.0
|
35.8
|
1.0
|
CA
|
H:GLN325
|
5.0
|
45.1
|
1.0
|
|
Zinc binding site 6 out
of 8 in 6h0f
Go back to
Zinc Binding Sites List in 6h0f
Zinc binding site 6 out
of 8 in the Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:43.7
occ:1.00
|
NE2
|
I:HIS167
|
2.0
|
56.4
|
1.0
|
NE2
|
I:HIS163
|
2.1
|
39.6
|
1.0
|
SG
|
I:CYS150
|
2.2
|
45.9
|
1.0
|
SG
|
I:CYS147
|
2.3
|
44.6
|
1.0
|
H
|
I:CYS150
|
2.8
|
42.1
|
0.0
|
HB3
|
I:CYS147
|
3.0
|
41.5
|
0.0
|
CD2
|
I:HIS167
|
3.0
|
57.3
|
1.0
|
CE1
|
I:HIS167
|
3.0
|
56.0
|
1.0
|
CD2
|
I:HIS163
|
3.0
|
39.8
|
1.0
|
CE1
|
I:HIS163
|
3.1
|
39.3
|
1.0
|
HB3
|
I:GLN149
|
3.1
|
48.1
|
0.0
|
CB
|
I:CYS147
|
3.2
|
40.6
|
1.0
|
HD2
|
I:HIS167
|
3.2
|
49.4
|
0.0
|
HD2
|
I:HIS163
|
3.2
|
36.6
|
0.0
|
HB3
|
I:CYS150
|
3.3
|
38.6
|
0.0
|
HE1
|
I:HIS167
|
3.3
|
42.9
|
0.0
|
CB
|
I:CYS150
|
3.3
|
41.9
|
1.0
|
HE1
|
I:HIS163
|
3.3
|
35.0
|
0.0
|
N
|
I:CYS150
|
3.4
|
41.8
|
1.0
|
HB2
|
I:CYS147
|
3.5
|
40.6
|
0.0
|
HB3
|
I:ALA152
|
3.6
|
41.5
|
0.0
|
H
|
I:ALA152
|
3.7
|
41.9
|
0.0
|
CA
|
I:CYS150
|
3.9
|
41.9
|
1.0
|
H
|
I:GLN149
|
4.1
|
44.4
|
0.0
|
HB2
|
I:ALA152
|
4.1
|
42.7
|
0.0
|
CG
|
I:HIS167
|
4.1
|
58.9
|
1.0
|
ND1
|
I:HIS167
|
4.1
|
58.8
|
1.0
|
CG
|
I:HIS163
|
4.2
|
38.8
|
1.0
|
CB
|
I:GLN149
|
4.2
|
45.4
|
1.0
|
HB2
|
I:CYS150
|
4.2
|
38.8
|
0.0
|
ND1
|
I:HIS163
|
4.2
|
40.8
|
1.0
|
H
|
I:GLY151
|
4.3
|
40.4
|
0.0
|
CB
|
I:ALA152
|
4.3
|
42.4
|
1.0
|
C
|
I:GLN149
|
4.3
|
46.3
|
1.0
|
HG22
|
I:ILE164
|
4.4
|
30.7
|
0.0
|
C
|
I:CYS150
|
4.5
|
46.9
|
1.0
|
CA
|
I:CYS147
|
4.6
|
40.4
|
1.0
|
HB2
|
H:HIS397
|
4.6
|
34.4
|
0.0
|
N
|
I:GLY151
|
4.6
|
43.4
|
1.0
|
CA
|
I:GLN149
|
4.6
|
43.1
|
1.0
|
N
|
I:ALA152
|
4.7
|
43.1
|
1.0
|
N
|
I:GLN149
|
4.7
|
43.8
|
1.0
|
HB2
|
I:GLN149
|
4.7
|
49.3
|
0.0
|
HA
|
I:ILE164
|
4.7
|
38.5
|
0.0
|
HG2
|
I:GLN149
|
4.7
|
54.2
|
0.0
|
HA
|
I:CYS150
|
4.8
|
39.5
|
0.0
|
HG11
|
H:VAL388
|
4.9
|
39.7
|
0.0
|
C
|
I:CYS147
|
4.9
|
45.6
|
1.0
|
O
|
I:CYS147
|
5.0
|
44.8
|
1.0
|
|
Zinc binding site 7 out
of 8 in 6h0f
Go back to
Zinc Binding Sites List in 6h0f
Zinc binding site 7 out
of 8 in the Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Zn501
b:45.7
occ:1.00
|
SG
|
K:CYS391
|
2.3
|
52.0
|
1.0
|
SG
|
K:CYS394
|
2.3
|
54.4
|
1.0
|
SG
|
K:CYS323
|
2.3
|
60.2
|
1.0
|
SG
|
K:CYS326
|
2.5
|
67.0
|
1.0
|
H
|
K:CYS326
|
2.8
|
55.5
|
0.0
|
HB3
|
K:CYS326
|
2.8
|
66.1
|
0.0
|
H
|
K:CYS394
|
2.9
|
46.1
|
0.0
|
HB3
|
K:CYS323
|
3.0
|
53.7
|
0.0
|
CB
|
K:CYS391
|
3.1
|
48.0
|
1.0
|
HB3
|
K:CYS391
|
3.1
|
46.1
|
0.0
|
HB2
|
K:CYS391
|
3.1
|
46.8
|
0.0
|
CB
|
K:CYS326
|
3.1
|
62.2
|
1.0
|
CB
|
K:CYS323
|
3.1
|
57.4
|
1.0
|
HB2
|
K:CYS323
|
3.4
|
54.3
|
0.0
|
HB3
|
K:CYS394
|
3.4
|
56.1
|
0.0
|
CB
|
K:CYS394
|
3.5
|
50.2
|
1.0
|
N
|
K:CYS326
|
3.6
|
58.2
|
1.0
|
N
|
K:CYS394
|
3.8
|
48.5
|
1.0
|
HB
|
K:ILE393
|
3.8
|
58.3
|
0.0
|
HB3
|
K:GLN325
|
3.9
|
60.7
|
0.0
|
CA
|
K:CYS326
|
3.9
|
59.8
|
1.0
|
HB2
|
K:SER396
|
4.0
|
47.2
|
0.0
|
HB2
|
K:CYS326
|
4.0
|
66.7
|
0.0
|
HG
|
K:SER396
|
4.1
|
57.8
|
0.0
|
HG22
|
K:ILE393
|
4.1
|
56.8
|
0.0
|
H
|
K:SER396
|
4.2
|
49.2
|
0.0
|
H
|
K:GLN327
|
4.2
|
61.1
|
0.0
|
CA
|
K:CYS394
|
4.2
|
48.4
|
1.0
|
OG1
|
K:THR329
|
4.2
|
70.3
|
1.0
|
HG23
|
K:THR329
|
4.2
|
75.1
|
0.0
|
H
|
K:ILE393
|
4.3
|
55.0
|
0.0
|
HB2
|
K:CYS394
|
4.3
|
54.9
|
0.0
|
HD11
|
K:ILE398
|
4.3
|
51.9
|
0.0
|
H
|
K:GLU328
|
4.5
|
65.4
|
0.0
|
CA
|
K:CYS391
|
4.6
|
48.3
|
1.0
|
CA
|
K:CYS323
|
4.6
|
58.8
|
1.0
|
HG21
|
K:THR329
|
4.6
|
75.9
|
0.0
|
HG1
|
K:THR329
|
4.7
|
69.4
|
0.0
|
CB
|
K:ILE393
|
4.7
|
55.0
|
1.0
|
H
|
K:ALA395
|
4.7
|
52.5
|
0.0
|
H
|
K:GLN325
|
4.7
|
51.4
|
0.0
|
CB
|
K:GLN325
|
4.7
|
57.7
|
1.0
|
C
|
K:GLN325
|
4.8
|
60.4
|
1.0
|
N
|
K:GLN327
|
4.8
|
57.2
|
1.0
|
HA
|
K:CYS326
|
4.8
|
56.9
|
0.0
|
C
|
K:CYS326
|
4.8
|
62.5
|
1.0
|
HB2
|
K:GLN325
|
4.8
|
60.4
|
0.0
|
C
|
K:CYS394
|
4.8
|
50.5
|
1.0
|
CG2
|
K:ILE393
|
4.8
|
56.5
|
1.0
|
C
|
K:ILE393
|
4.8
|
52.1
|
1.0
|
CG2
|
K:THR329
|
4.9
|
75.0
|
1.0
|
HA
|
K:CYS391
|
4.9
|
42.8
|
0.0
|
OG
|
K:SER396
|
4.9
|
57.4
|
1.0
|
CB
|
K:SER396
|
4.9
|
48.9
|
1.0
|
|
Zinc binding site 8 out
of 8 in 6h0f
Go back to
Zinc Binding Sites List in 6h0f
Zinc binding site 8 out
of 8 in the Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of DDB1-Crbn-Pomalidomide Complex Bound to IKZF1(ZF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn201
b:53.4
occ:1.00
|
NE2
|
L:HIS167
|
2.0
|
58.5
|
1.0
|
NE2
|
L:HIS163
|
2.1
|
46.8
|
1.0
|
SG
|
L:CYS150
|
2.2
|
57.3
|
1.0
|
SG
|
L:CYS147
|
2.2
|
46.5
|
1.0
|
H
|
L:CYS150
|
2.7
|
47.9
|
0.0
|
CD2
|
L:HIS167
|
2.9
|
59.4
|
1.0
|
CE1
|
L:HIS167
|
3.0
|
58.1
|
1.0
|
HB3
|
L:CYS147
|
3.0
|
41.3
|
0.0
|
HB3
|
L:GLN149
|
3.0
|
48.1
|
0.0
|
CD2
|
L:HIS163
|
3.1
|
46.4
|
1.0
|
CE1
|
L:HIS163
|
3.2
|
47.1
|
1.0
|
CB
|
L:CYS147
|
3.2
|
42.4
|
1.0
|
HD2
|
L:HIS167
|
3.2
|
52.4
|
0.0
|
HB3
|
L:CYS150
|
3.2
|
54.0
|
0.0
|
CB
|
L:CYS150
|
3.2
|
54.0
|
1.0
|
HE1
|
L:HIS167
|
3.3
|
45.1
|
0.0
|
HD2
|
L:HIS163
|
3.3
|
38.5
|
0.0
|
N
|
L:CYS150
|
3.4
|
51.5
|
1.0
|
HE1
|
L:HIS163
|
3.4
|
47.1
|
0.0
|
HB2
|
L:CYS147
|
3.5
|
40.2
|
0.0
|
HB3
|
L:ALA152
|
3.7
|
46.1
|
0.0
|
H
|
L:ALA152
|
3.7
|
37.6
|
0.0
|
CA
|
L:CYS150
|
3.8
|
53.6
|
1.0
|
H
|
L:GLN149
|
4.0
|
50.3
|
0.0
|
CG
|
L:HIS167
|
4.1
|
61.1
|
1.0
|
CB
|
L:GLN149
|
4.1
|
47.6
|
1.0
|
ND1
|
L:HIS167
|
4.1
|
60.7
|
1.0
|
HB2
|
L:ALA152
|
4.2
|
47.7
|
0.0
|
HB2
|
L:CYS150
|
4.2
|
55.2
|
0.0
|
CG
|
L:HIS163
|
4.2
|
46.2
|
1.0
|
C
|
L:GLN149
|
4.3
|
52.4
|
1.0
|
H
|
L:GLY151
|
4.3
|
57.5
|
0.0
|
ND1
|
L:HIS163
|
4.3
|
48.5
|
1.0
|
CB
|
L:ALA152
|
4.4
|
47.3
|
1.0
|
C
|
L:CYS150
|
4.5
|
57.0
|
1.0
|
CA
|
L:GLN149
|
4.5
|
46.9
|
1.0
|
CA
|
L:CYS147
|
4.6
|
42.1
|
1.0
|
N
|
L:GLY151
|
4.6
|
52.6
|
1.0
|
N
|
L:GLN149
|
4.6
|
47.4
|
1.0
|
HB2
|
L:GLN149
|
4.6
|
48.1
|
0.0
|
HG2
|
L:GLN149
|
4.7
|
46.6
|
0.0
|
N
|
L:ALA152
|
4.7
|
46.9
|
1.0
|
HA
|
L:ILE164
|
4.7
|
39.8
|
0.0
|
HB2
|
K:HIS397
|
4.7
|
53.8
|
0.0
|
HA
|
L:CYS150
|
4.8
|
58.3
|
0.0
|
C
|
L:CYS147
|
4.9
|
46.0
|
1.0
|
HG11
|
K:VAL388
|
4.9
|
52.6
|
0.0
|
O
|
L:CYS147
|
4.9
|
46.4
|
1.0
|
CG
|
L:GLN149
|
4.9
|
48.9
|
1.0
|
|
Reference:
Q.L.Sievers,
G.Petzold,
R.D.Bunker,
A.Renneville,
M.Slabicki,
B.J.Liddicoat,
W.Abdulrahman,
T.Mikkelsen,
B.L.Ebert,
N.H.Thoma.
Defining the Human C2H2 Zinc Finger Degrome Targeted By Thalidomide Analogs Through Crbn. Science V. 362 T0572 2018.
ISSN: ESSN 1095-9203
PubMed: 30385546
DOI: 10.1126/SCIENCE.AAT0572
Page generated: Mon Oct 28 22:10:00 2024
|