Zinc in PDB 4tzu: Crystal Structure of Murine Cereblon in Complex with Pomalidomide
Protein crystallography data
The structure of Crystal Structure of Murine Cereblon in Complex with Pomalidomide, PDB code: 4tzu
was solved by
P.P.Chamberlain,
B.Pagarigan,
S.Delker,
B.Leon,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.00
|
Space group
|
I 2 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
143.340,
143.340,
143.340,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
23.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Murine Cereblon in Complex with Pomalidomide
(pdb code 4tzu). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Murine Cereblon in Complex with Pomalidomide, PDB code: 4tzu:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4tzu
Go back to
Zinc Binding Sites List in 4tzu
Zinc binding site 1 out
of 4 in the Crystal Structure of Murine Cereblon in Complex with Pomalidomide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Murine Cereblon in Complex with Pomalidomide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:21.2
occ:1.00
|
SG
|
A:CYS328
|
2.3
|
21.7
|
1.0
|
SG
|
A:CYS393
|
2.3
|
19.6
|
1.0
|
SG
|
A:CYS396
|
2.4
|
22.6
|
1.0
|
SG
|
A:CYS325
|
2.4
|
23.6
|
1.0
|
CB
|
A:CYS325
|
3.1
|
22.3
|
1.0
|
CB
|
A:CYS393
|
3.2
|
20.3
|
1.0
|
CB
|
A:CYS328
|
3.2
|
19.2
|
1.0
|
CB
|
A:CYS396
|
3.4
|
23.4
|
1.0
|
N
|
A:CYS328
|
3.7
|
21.4
|
1.0
|
N
|
A:CYS396
|
3.8
|
22.1
|
1.0
|
CA
|
A:CYS328
|
4.0
|
21.4
|
1.0
|
CA
|
A:CYS396
|
4.1
|
22.7
|
1.0
|
CB
|
A:ILE395
|
4.5
|
22.4
|
1.0
|
CB
|
A:SER398
|
4.6
|
25.7
|
1.0
|
CB
|
A:THR331
|
4.6
|
22.3
|
1.0
|
CA
|
A:CYS325
|
4.6
|
19.5
|
1.0
|
OG1
|
A:THR331
|
4.6
|
22.9
|
1.0
|
CA
|
A:CYS393
|
4.6
|
21.5
|
1.0
|
C
|
A:ILE395
|
4.7
|
26.9
|
1.0
|
C
|
A:CYS396
|
4.8
|
23.2
|
1.0
|
CB
|
A:GLN327
|
4.8
|
25.4
|
1.0
|
C
|
A:GLN327
|
4.8
|
22.9
|
1.0
|
N
|
A:ALA397
|
4.9
|
21.4
|
1.0
|
C
|
A:CYS328
|
4.9
|
22.2
|
1.0
|
CA
|
A:ILE395
|
4.9
|
22.8
|
1.0
|
N
|
A:ILE395
|
5.0
|
21.3
|
1.0
|
N
|
A:SER398
|
5.0
|
20.7
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4tzu
Go back to
Zinc Binding Sites List in 4tzu
Zinc binding site 2 out
of 4 in the Crystal Structure of Murine Cereblon in Complex with Pomalidomide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Murine Cereblon in Complex with Pomalidomide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn504
b:34.7
occ:1.00
|
SG
|
B:CYS328
|
2.3
|
39.4
|
1.0
|
SG
|
B:CYS396
|
2.3
|
33.0
|
1.0
|
SG
|
B:CYS393
|
2.4
|
37.0
|
1.0
|
SG
|
B:CYS325
|
2.4
|
36.2
|
1.0
|
CB
|
B:CYS393
|
3.1
|
34.9
|
1.0
|
CB
|
B:CYS325
|
3.2
|
30.6
|
1.0
|
CB
|
B:CYS328
|
3.2
|
36.5
|
1.0
|
CB
|
B:CYS396
|
3.4
|
37.8
|
1.0
|
N
|
B:CYS328
|
3.7
|
34.9
|
1.0
|
N
|
B:CYS396
|
3.8
|
38.5
|
1.0
|
CA
|
B:CYS328
|
4.0
|
40.7
|
1.0
|
CA
|
B:CYS396
|
4.1
|
37.0
|
1.0
|
CA
|
B:CYS393
|
4.6
|
33.6
|
1.0
|
CB
|
B:ILE395
|
4.6
|
37.7
|
1.0
|
CB
|
B:GLN327
|
4.6
|
36.1
|
1.0
|
OG1
|
B:THR331
|
4.6
|
35.3
|
1.0
|
CA
|
B:CYS325
|
4.7
|
34.7
|
1.0
|
CB
|
B:SER398
|
4.7
|
38.8
|
1.0
|
CB
|
B:THR331
|
4.7
|
38.0
|
1.0
|
C
|
B:GLN327
|
4.8
|
38.7
|
1.0
|
C
|
B:ILE395
|
4.8
|
37.7
|
1.0
|
C
|
B:CYS396
|
4.8
|
34.2
|
1.0
|
C
|
B:CYS328
|
4.9
|
40.5
|
1.0
|
CG2
|
B:ILE395
|
5.0
|
41.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4tzu
Go back to
Zinc Binding Sites List in 4tzu
Zinc binding site 3 out
of 4 in the Crystal Structure of Murine Cereblon in Complex with Pomalidomide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Murine Cereblon in Complex with Pomalidomide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn503
b:39.6
occ:1.00
|
SG
|
C:CYS328
|
2.1
|
41.3
|
1.0
|
SG
|
C:CYS325
|
2.3
|
34.9
|
1.0
|
SG
|
C:CYS393
|
2.4
|
36.8
|
1.0
|
SG
|
C:CYS396
|
2.5
|
43.5
|
1.0
|
CB
|
C:CYS328
|
3.2
|
46.2
|
1.0
|
CB
|
C:CYS393
|
3.2
|
30.6
|
1.0
|
CB
|
C:CYS325
|
3.2
|
35.3
|
1.0
|
CB
|
C:CYS396
|
3.4
|
42.1
|
1.0
|
OG1
|
C:THR331
|
3.6
|
62.5
|
1.0
|
N
|
C:CYS328
|
3.7
|
36.3
|
1.0
|
N
|
C:CYS396
|
3.8
|
43.1
|
1.0
|
CA
|
C:CYS328
|
4.0
|
41.0
|
1.0
|
CA
|
C:CYS396
|
4.2
|
41.0
|
1.0
|
CB
|
C:ILE395
|
4.6
|
38.9
|
1.0
|
CB
|
C:GLN327
|
4.6
|
44.7
|
1.0
|
CA
|
C:CYS393
|
4.7
|
35.1
|
1.0
|
CA
|
C:CYS325
|
4.7
|
35.8
|
1.0
|
CB
|
C:SER398
|
4.7
|
39.6
|
1.0
|
C
|
C:CYS328
|
4.8
|
42.6
|
1.0
|
C
|
C:GLN327
|
4.8
|
43.2
|
1.0
|
C
|
C:ILE395
|
4.8
|
43.8
|
1.0
|
C
|
C:CYS396
|
4.9
|
40.5
|
1.0
|
N
|
C:GLN329
|
4.9
|
40.0
|
1.0
|
CB
|
C:THR331
|
4.9
|
43.5
|
1.0
|
N
|
C:ALA397
|
5.0
|
41.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4tzu
Go back to
Zinc Binding Sites List in 4tzu
Zinc binding site 4 out
of 4 in the Crystal Structure of Murine Cereblon in Complex with Pomalidomide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Murine Cereblon in Complex with Pomalidomide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn502
b:18.9
occ:1.00
|
SG
|
D:CYS328
|
2.3
|
18.3
|
1.0
|
SG
|
D:CYS396
|
2.4
|
20.0
|
1.0
|
SG
|
D:CYS393
|
2.4
|
19.4
|
1.0
|
SG
|
D:CYS325
|
2.4
|
18.9
|
1.0
|
CB
|
D:CYS325
|
3.1
|
16.4
|
1.0
|
CB
|
D:CYS393
|
3.1
|
16.4
|
1.0
|
CB
|
D:CYS328
|
3.3
|
17.5
|
1.0
|
CB
|
D:CYS396
|
3.5
|
21.5
|
1.0
|
N
|
D:CYS328
|
3.7
|
18.8
|
1.0
|
N
|
D:CYS396
|
3.8
|
19.0
|
1.0
|
CA
|
D:CYS328
|
4.1
|
20.3
|
1.0
|
CA
|
D:CYS396
|
4.2
|
19.9
|
1.0
|
CA
|
D:CYS325
|
4.6
|
17.3
|
1.0
|
OG1
|
D:THR331
|
4.6
|
23.0
|
1.0
|
CB
|
D:ILE395
|
4.6
|
22.7
|
1.0
|
CB
|
D:THR331
|
4.6
|
20.4
|
1.0
|
CA
|
D:CYS393
|
4.6
|
15.8
|
1.0
|
OG
|
D:SER398
|
4.7
|
23.9
|
1.0
|
CB
|
D:GLN327
|
4.7
|
21.1
|
1.0
|
C
|
D:ILE395
|
4.8
|
22.8
|
1.0
|
C
|
D:GLN327
|
4.9
|
19.5
|
1.0
|
CB
|
D:SER398
|
4.9
|
20.6
|
1.0
|
C
|
D:CYS396
|
5.0
|
21.4
|
1.0
|
C
|
D:CYS325
|
5.0
|
19.0
|
1.0
|
CG2
|
D:ILE395
|
5.0
|
20.7
|
1.0
|
C
|
D:CYS328
|
5.0
|
20.4
|
1.0
|
|
Reference:
P.P.Chamberlain,
M.Wang,
M.Riley,
S.Delker,
T.Ito,
A.Hideki,
T.Mori,
H.Handa,
T.Hakoshima,
T.O.Daniel,
B.E.Cathers,
A.Lopez-Girona,
K.Miller,
G.Carmel,
B.Pagarigan,
B.Leon,
E.Rychak,
L.Corral,
Y.Ren.
Structural Basis For Responsiveness to Thalidomide-Analog Drugs Defined By the Crystal Structure of the Human Cereblon:DDB1:Lenalidomide Complex To Be Published.
Page generated: Sun Oct 27 08:40:36 2024
|