Zinc in PDB 7tfg: Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
Enzymatic activity of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
All present enzymatic activity of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242:
2.3.2.27;
Protein crystallography data
The structure of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242, PDB code: 7tfg
was solved by
M.Luo,
J.R.Terrell,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.03 /
1.68
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
29.351,
39.794,
52.095,
84.44,
85.88,
89.98
|
R / Rfree (%)
|
16.8 /
20.1
|
Other elements in 7tfg:
The structure of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
(pdb code 7tfg). 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 Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242, PDB code: 7tfg:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 7tfg
Go back to
Zinc Binding Sites List in 7tfg
Zinc binding site 1 out
of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:21.1
occ:1.00
|
SG
|
A:CYS441
|
2.3
|
23.4
|
1.0
|
SG
|
A:CYS464
|
2.3
|
23.1
|
1.0
|
SG
|
A:CYS461
|
2.4
|
18.8
|
1.0
|
SG
|
A:CYS438
|
2.4
|
18.2
|
1.0
|
CB
|
A:CYS438
|
3.1
|
18.2
|
1.0
|
CB
|
A:CYS441
|
3.1
|
30.4
|
1.0
|
CB
|
A:CYS464
|
3.2
|
19.6
|
1.0
|
CB
|
A:CYS461
|
3.5
|
17.8
|
1.0
|
N
|
A:CYS441
|
3.7
|
23.6
|
1.0
|
N
|
A:CYS461
|
3.9
|
14.5
|
1.0
|
O
|
A:HOH647
|
4.0
|
41.4
|
1.0
|
CA
|
A:CYS441
|
4.0
|
24.5
|
1.0
|
CA
|
A:CYS461
|
4.3
|
16.9
|
1.0
|
O
|
A:HOH642
|
4.3
|
37.1
|
1.0
|
N
|
A:CYS464
|
4.3
|
19.8
|
1.0
|
CA
|
A:CYS464
|
4.4
|
17.4
|
1.0
|
CB
|
A:ARG444
|
4.5
|
21.6
|
1.0
|
CA
|
A:CYS438
|
4.6
|
15.3
|
1.0
|
CB
|
A:ILE440
|
4.6
|
21.5
|
1.0
|
C
|
A:ILE440
|
4.7
|
22.0
|
1.0
|
C
|
A:CYS441
|
4.9
|
24.3
|
1.0
|
O
|
A:CYS461
|
4.9
|
16.3
|
1.0
|
C
|
A:CYS461
|
4.9
|
16.1
|
1.0
|
CG
|
A:ARG444
|
4.9
|
27.6
|
1.0
|
N
|
A:GLN442
|
5.0
|
20.7
|
1.0
|
|
Zinc binding site 2 out
of 8 in 7tfg
Go back to
Zinc Binding Sites List in 7tfg
Zinc binding site 2 out
of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:17.8
occ:1.00
|
NE2
|
A:HIS452
|
2.1
|
16.9
|
1.0
|
ND1
|
A:HIS457
|
2.1
|
20.2
|
1.0
|
SG
|
A:CYS475
|
2.2
|
17.3
|
1.0
|
SG
|
A:CYS478
|
2.3
|
17.6
|
1.0
|
CE1
|
A:HIS457
|
2.9
|
22.9
|
1.0
|
CE1
|
A:HIS452
|
3.0
|
16.6
|
1.0
|
CD2
|
A:HIS452
|
3.0
|
19.1
|
1.0
|
CB
|
A:CYS475
|
3.1
|
17.2
|
1.0
|
CG
|
A:HIS457
|
3.2
|
18.8
|
1.0
|
CB
|
A:CYS478
|
3.5
|
19.4
|
1.0
|
CB
|
A:HIS457
|
3.6
|
23.4
|
1.0
|
N
|
A:CYS478
|
3.8
|
16.1
|
1.0
|
ND1
|
A:HIS452
|
4.1
|
17.3
|
1.0
|
NE2
|
A:HIS457
|
4.1
|
35.1
|
1.0
|
CG
|
A:HIS452
|
4.1
|
16.7
|
1.0
|
CD2
|
A:HIS457
|
4.2
|
29.5
|
1.0
|
CA
|
A:CYS478
|
4.3
|
18.2
|
1.0
|
O
|
A:HOH644
|
4.3
|
26.1
|
1.0
|
CB
|
A:VAL477
|
4.4
|
16.9
|
1.0
|
CA
|
A:CYS475
|
4.6
|
14.0
|
1.0
|
CG1
|
A:VAL477
|
4.8
|
19.9
|
1.0
|
N
|
A:HIS457
|
4.8
|
16.2
|
1.0
|
C
|
A:VAL477
|
4.8
|
18.6
|
1.0
|
CA
|
A:HIS457
|
4.8
|
15.8
|
1.0
|
CG2
|
A:ILE450
|
4.9
|
17.7
|
1.0
|
N
|
A:VAL477
|
5.0
|
17.5
|
1.0
|
CA
|
A:VAL477
|
5.0
|
19.6
|
1.0
|
N
|
A:ARG479
|
5.0
|
17.0
|
1.0
|
C
|
A:CYS478
|
5.0
|
20.4
|
1.0
|
C
|
A:CYS475
|
5.0
|
13.9
|
1.0
|
|
Zinc binding site 3 out
of 8 in 7tfg
Go back to
Zinc Binding Sites List in 7tfg
Zinc binding site 3 out
of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:22.7
occ:1.00
|
SG
|
B:CYS464
|
2.3
|
24.1
|
1.0
|
SG
|
B:CYS438
|
2.3
|
18.0
|
1.0
|
SG
|
B:CYS441
|
2.4
|
25.2
|
1.0
|
SG
|
B:CYS461
|
2.4
|
20.4
|
1.0
|
CB
|
B:CYS438
|
3.1
|
20.5
|
1.0
|
CB
|
B:CYS441
|
3.1
|
25.5
|
1.0
|
CB
|
B:CYS464
|
3.3
|
21.4
|
1.0
|
CB
|
B:CYS461
|
3.6
|
16.9
|
1.0
|
N
|
B:CYS441
|
3.7
|
27.4
|
1.0
|
N
|
B:CYS461
|
3.9
|
16.2
|
1.0
|
CA
|
B:CYS441
|
4.0
|
26.0
|
1.0
|
CA
|
B:CYS461
|
4.3
|
18.7
|
1.0
|
N
|
B:CYS464
|
4.3
|
19.9
|
1.0
|
CB
|
B:ARG444
|
4.4
|
21.0
|
1.0
|
CA
|
B:CYS464
|
4.4
|
16.4
|
1.0
|
CA
|
B:CYS438
|
4.6
|
18.7
|
1.0
|
CB
|
B:ILE440
|
4.6
|
24.7
|
1.0
|
C
|
B:ILE440
|
4.7
|
26.2
|
1.0
|
CG
|
B:ARG444
|
4.7
|
27.4
|
1.0
|
O
|
B:CYS461
|
4.8
|
16.8
|
1.0
|
C
|
B:CYS461
|
4.9
|
17.7
|
1.0
|
C
|
B:CYS441
|
4.9
|
28.9
|
1.0
|
N
|
B:GLN442
|
5.0
|
19.1
|
1.0
|
|
Zinc binding site 4 out
of 8 in 7tfg
Go back to
Zinc Binding Sites List in 7tfg
Zinc binding site 4 out
of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:18.9
occ:1.00
|
ND1
|
B:HIS457
|
2.0
|
19.5
|
1.0
|
NE2
|
B:HIS452
|
2.1
|
20.4
|
1.0
|
SG
|
B:CYS475
|
2.3
|
17.0
|
1.0
|
SG
|
B:CYS478
|
2.3
|
17.6
|
1.0
|
CE1
|
B:HIS457
|
2.9
|
18.2
|
1.0
|
CD2
|
B:HIS452
|
2.9
|
26.5
|
1.0
|
CB
|
B:CYS475
|
3.1
|
15.7
|
1.0
|
CG
|
B:HIS457
|
3.1
|
16.1
|
1.0
|
CE1
|
B:HIS452
|
3.2
|
28.3
|
1.0
|
CB
|
B:CYS478
|
3.5
|
20.1
|
1.0
|
CB
|
B:HIS457
|
3.5
|
20.1
|
1.0
|
N
|
B:CYS478
|
3.8
|
16.4
|
1.0
|
NE2
|
B:HIS457
|
4.1
|
24.8
|
1.0
|
CG
|
B:HIS452
|
4.1
|
21.1
|
1.0
|
CD2
|
B:HIS457
|
4.2
|
23.0
|
1.0
|
ND1
|
B:HIS452
|
4.2
|
41.0
|
1.0
|
CA
|
B:CYS478
|
4.3
|
14.1
|
1.0
|
CB
|
B:VAL477
|
4.4
|
15.9
|
1.0
|
CA
|
B:CYS475
|
4.6
|
15.4
|
1.0
|
N
|
B:HIS457
|
4.7
|
16.2
|
1.0
|
CA
|
B:HIS457
|
4.8
|
16.5
|
1.0
|
CG1
|
B:VAL477
|
4.8
|
21.7
|
1.0
|
C
|
B:VAL477
|
4.8
|
17.5
|
1.0
|
N
|
B:VAL477
|
4.9
|
14.8
|
1.0
|
CA
|
B:VAL477
|
4.9
|
14.9
|
1.0
|
N
|
B:ARG479
|
5.0
|
16.2
|
1.0
|
C
|
B:CYS475
|
5.0
|
16.8
|
1.0
|
C
|
B:CYS478
|
5.0
|
17.8
|
1.0
|
CG2
|
B:ILE450
|
5.0
|
16.4
|
1.0
|
|
Zinc binding site 5 out
of 8 in 7tfg
Go back to
Zinc Binding Sites List in 7tfg
Zinc binding site 5 out
of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn502
b:23.3
occ:1.00
|
ND1
|
C:HIS457
|
2.0
|
19.6
|
1.0
|
SG
|
C:CYS475
|
2.2
|
23.7
|
1.0
|
SG
|
C:CYS478
|
2.4
|
25.6
|
1.0
|
NE2
|
C:HIS452
|
2.6
|
44.9
|
1.0
|
CE1
|
C:HIS452
|
2.8
|
30.4
|
1.0
|
CE1
|
C:HIS457
|
2.8
|
23.7
|
1.0
|
CB
|
C:CYS475
|
3.1
|
24.8
|
1.0
|
CG
|
C:HIS457
|
3.2
|
21.0
|
1.0
|
CB
|
C:CYS478
|
3.6
|
27.3
|
1.0
|
CD2
|
C:HIS452
|
3.6
|
50.8
|
1.0
|
CB
|
C:HIS457
|
3.7
|
19.6
|
1.0
|
ND1
|
C:HIS452
|
3.7
|
51.9
|
1.0
|
N
|
C:CYS478
|
3.9
|
26.3
|
1.0
|
NE2
|
C:HIS457
|
4.0
|
27.1
|
1.0
|
CD2
|
C:HIS457
|
4.2
|
22.1
|
1.0
|
CG
|
C:HIS452
|
4.2
|
21.1
|
1.0
|
CA
|
C:CYS478
|
4.3
|
26.1
|
1.0
|
CA
|
C:CYS475
|
4.5
|
22.4
|
1.0
|
CB
|
C:VAL477
|
4.5
|
27.6
|
1.0
|
N
|
C:HIS457
|
4.6
|
18.7
|
1.0
|
CA
|
C:HIS457
|
4.8
|
17.0
|
1.0
|
CG2
|
C:ILE450
|
4.8
|
21.1
|
1.0
|
O
|
C:HOH632
|
4.8
|
44.5
|
1.0
|
C
|
C:VAL477
|
4.9
|
30.5
|
1.0
|
C
|
C:CYS475
|
4.9
|
22.8
|
1.0
|
N
|
C:VAL477
|
5.0
|
25.7
|
1.0
|
C
|
C:CYS478
|
5.0
|
25.4
|
1.0
|
|
Zinc binding site 6 out
of 8 in 7tfg
Go back to
Zinc Binding Sites List in 7tfg
Zinc binding site 6 out
of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn503
b:35.9
occ:1.00
|
SG
|
C:CYS441
|
2.3
|
36.5
|
1.0
|
SG
|
C:CYS464
|
2.3
|
33.4
|
1.0
|
SG
|
C:CYS461
|
2.3
|
33.4
|
1.0
|
SG
|
C:CYS438
|
2.4
|
32.0
|
1.0
|
CB
|
C:CYS438
|
3.1
|
30.7
|
1.0
|
CB
|
C:CYS441
|
3.2
|
39.2
|
1.0
|
CB
|
C:CYS464
|
3.2
|
34.5
|
1.0
|
CB
|
C:CYS461
|
3.5
|
31.9
|
1.0
|
N
|
C:CYS441
|
3.6
|
41.0
|
1.0
|
NH2
|
C:ARG444
|
3.8
|
51.2
|
1.0
|
N
|
C:CYS461
|
3.9
|
26.2
|
1.0
|
CA
|
C:CYS441
|
4.0
|
37.9
|
1.0
|
CZ
|
C:ARG444
|
4.2
|
59.8
|
1.0
|
N
|
C:CYS464
|
4.3
|
27.8
|
1.0
|
CA
|
C:CYS461
|
4.3
|
24.1
|
1.0
|
CA
|
C:CYS464
|
4.3
|
32.7
|
1.0
|
NE
|
C:ARG444
|
4.3
|
46.6
|
1.0
|
CB
|
C:ILE440
|
4.5
|
39.1
|
1.0
|
CA
|
C:CYS438
|
4.6
|
28.7
|
1.0
|
CB
|
C:ARG444
|
4.6
|
44.0
|
1.0
|
C
|
C:ILE440
|
4.7
|
43.4
|
1.0
|
C
|
C:CYS441
|
4.8
|
45.8
|
1.0
|
O
|
C:CYS461
|
4.9
|
26.2
|
1.0
|
C
|
C:CYS461
|
4.9
|
27.4
|
1.0
|
N
|
C:GLN442
|
4.9
|
43.0
|
1.0
|
N
|
C:ILE440
|
5.0
|
37.9
|
1.0
|
C
|
C:CYS438
|
5.0
|
33.4
|
1.0
|
CA
|
C:ILE440
|
5.0
|
37.8
|
1.0
|
|
Zinc binding site 7 out
of 8 in 7tfg
Go back to
Zinc Binding Sites List in 7tfg
Zinc binding site 7 out
of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn501
b:29.9
occ:1.00
|
SG
|
D:CYS438
|
2.3
|
25.0
|
1.0
|
SG
|
D:CYS441
|
2.3
|
30.5
|
1.0
|
SG
|
D:CYS464
|
2.4
|
31.3
|
1.0
|
SG
|
D:CYS461
|
2.4
|
29.9
|
1.0
|
CB
|
D:CYS438
|
3.1
|
27.0
|
1.0
|
CB
|
D:CYS441
|
3.2
|
30.4
|
1.0
|
CB
|
D:CYS464
|
3.2
|
26.7
|
1.0
|
CB
|
D:CYS461
|
3.5
|
25.8
|
1.0
|
N
|
D:CYS441
|
3.7
|
29.8
|
1.0
|
NH2
|
D:ARG444
|
3.8
|
46.9
|
1.0
|
N
|
D:CYS461
|
3.9
|
24.3
|
1.0
|
CA
|
D:CYS441
|
4.0
|
30.4
|
1.0
|
NE
|
D:ARG444
|
4.1
|
50.5
|
1.0
|
CA
|
D:CYS461
|
4.2
|
22.2
|
1.0
|
N
|
D:CYS464
|
4.3
|
26.2
|
1.0
|
CZ
|
D:ARG444
|
4.3
|
47.5
|
1.0
|
CA
|
D:CYS464
|
4.4
|
22.6
|
1.0
|
CA
|
D:CYS438
|
4.5
|
25.8
|
1.0
|
CB
|
D:ILE440
|
4.6
|
38.1
|
1.0
|
CB
|
D:ARG444
|
4.6
|
41.5
|
1.0
|
C
|
D:ILE440
|
4.7
|
31.7
|
1.0
|
C
|
D:CYS441
|
4.8
|
32.6
|
1.0
|
N
|
D:GLN442
|
4.8
|
29.8
|
1.0
|
C
|
D:CYS461
|
4.9
|
26.1
|
1.0
|
O
|
D:CYS461
|
4.9
|
25.2
|
1.0
|
C
|
D:CYS438
|
5.0
|
32.0
|
1.0
|
|
Zinc binding site 8 out
of 8 in 7tfg
Go back to
Zinc Binding Sites List in 7tfg
Zinc binding site 8 out
of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with MA242 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn502
b:26.4
occ:1.00
|
ND1
|
D:HIS457
|
2.1
|
29.2
|
1.0
|
CE1
|
D:HIS452
|
2.2
|
40.8
|
1.0
|
SG
|
D:CYS475
|
2.2
|
32.6
|
1.0
|
SG
|
D:CYS478
|
2.4
|
31.6
|
1.0
|
NE2
|
D:HIS452
|
2.9
|
39.1
|
1.0
|
CE1
|
D:HIS457
|
2.9
|
28.0
|
1.0
|
CB
|
D:CYS475
|
3.1
|
35.3
|
1.0
|
ND1
|
D:HIS452
|
3.1
|
59.4
|
1.0
|
CG
|
D:HIS457
|
3.2
|
21.4
|
1.0
|
CB
|
D:CYS478
|
3.6
|
28.4
|
1.0
|
CB
|
D:HIS457
|
3.7
|
22.8
|
1.0
|
N
|
D:CYS478
|
3.9
|
35.9
|
1.0
|
CD2
|
D:HIS452
|
4.0
|
39.9
|
1.0
|
NE2
|
D:HIS457
|
4.1
|
22.7
|
1.0
|
CG
|
D:HIS452
|
4.2
|
27.5
|
1.0
|
CD2
|
D:HIS457
|
4.2
|
24.4
|
1.0
|
CA
|
D:CYS478
|
4.3
|
30.1
|
1.0
|
CB
|
D:VAL477
|
4.5
|
29.5
|
1.0
|
CA
|
D:CYS475
|
4.6
|
31.1
|
1.0
|
N
|
D:HIS457
|
4.6
|
19.2
|
1.0
|
CA
|
D:HIS457
|
4.8
|
21.3
|
1.0
|
C
|
D:VAL477
|
4.8
|
32.7
|
1.0
|
CG2
|
D:ILE450
|
4.9
|
23.9
|
1.0
|
N
|
D:VAL477
|
5.0
|
33.5
|
1.0
|
C
|
D:CYS475
|
5.0
|
32.1
|
1.0
|
C
|
D:CYS478
|
5.0
|
33.7
|
1.0
|
|
Reference:
J.R.Terrell,
S.Tang,
O.O.Faniyi,
I.H.Jeong,
J.Yin,
B.Nijampatnam,
S.E.Velu,
W.Wang,
R.Zhang,
M.Luo.
Structural Studies of Antitumor Compounds That Target the Ring Domain of MDM2. Protein Sci. V. 31 E4367 2022.
ISSN: ESSN 1469-896X
PubMed: 35900024
DOI: 10.1002/PRO.4367
Page generated: Sat Apr 8 03:28:39 2023
|