Zinc in PDB 7thl: Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A

Enzymatic activity of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A

All present enzymatic activity of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A:
2.3.2.27;

Protein crystallography data

The structure of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A, PDB code: 7thl 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) 29.07 / 1.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 29.145, 39.618, 102.656, 90, 94.11, 90
R / Rfree (%) 16.6 / 20.6

Other elements in 7thl:

The structure of Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A (pdb code 7thl). 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 Inulanolide A, PDB code: 7thl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7thl

Go back to Zinc Binding Sites List in 7thl
Zinc binding site 1 out of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A


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 Inulanolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:12.6
occ:1.00
 SG A:CYS438 2.3 10.2 1.0
SG A:CYS441 2.3 13.4 1.0
SG A:CYS464 2.3 13.7 1.0
SG A:CYS461 2.4 12.0 1.0
CB A:CYS438 3.1 10.5 1.0
CB A:CYS441 3.2 18.8 1.0
CB A:CYS464 3.2 11.7 1.0
CB A:CYS461 3.5 11.9 1.0
N A:CYS441 3.7 13.3 1.0
N A:CYS461 3.9 8.6 1.0
CA A:CYS441 4.0 12.8 1.0
N A:CYS464 4.3 11.3 1.0
CA A:CYS461 4.3 12.2 1.0
CA A:CYS464 4.3 11.4 1.0
CB A:ILE440 4.5 13.8 1.0
CB A:ARG444 4.5 12.4 1.0
CA A:CYS438 4.6 9.5 1.0
C A:ILE440 4.7 14.6 1.0
O A:CYS461 4.9 11.4 1.0
C A:CYS441 4.9 16.5 1.0
C A:CYS461 4.9 13.0 1.0
CG A:ARG444 5.0 19.6 1.0
CA A:ILE440 5.0 9.9 1.0
N A:GLN442 5.0 13.5 1.0

Zinc binding site 2 out of 8 in 7thl

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Zinc binding site 2 out of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A


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 Inulanolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:10.7
occ:1.00
 ND1 A:HIS457 2.0 8.4 1.0
NE2 A:HIS452 2.1 9.7 1.0
SG A:CYS475 2.3 9.9 1.0
SG A:CYS478 2.3 10.6 1.0
CE1 A:HIS457 2.9 13.2 1.0
CD2 A:HIS452 3.0 11.7 1.0
CE1 A:HIS452 3.1 9.8 1.0
CB A:CYS475 3.1 8.0 1.0
CG A:HIS457 3.2 9.6 1.0
CB A:CYS478 3.5 9.0 1.0
CB A:HIS457 3.6 11.7 1.0
N A:CYS478 3.7 9.9 1.0
NE2 A:HIS457 4.1 12.4 1.0
CG A:HIS452 4.1 8.2 1.0
ND1 A:HIS452 4.1 9.9 1.0
CA A:CYS478 4.2 9.8 1.0
CD2 A:HIS457 4.2 11.7 1.0
O B:HOH615 4.4 25.5 1.0
CB A:VAL477 4.4 10.4 1.0
CA A:CYS475 4.6 8.9 1.0
C A:VAL477 4.7 10.5 1.0
N A:HIS457 4.8 12.0 1.0
CA A:HIS457 4.8 9.8 1.0
CG1 A:VAL477 4.8 13.2 1.0
N A:VAL477 4.9 10.9 1.0
N A:ARG479 4.9 9.1 1.0
C A:CYS478 4.9 10.6 1.0
CA A:VAL477 4.9 11.2 1.0
CG2 A:ILE450 4.9 8.7 1.0
C A:CYS475 5.0 9.6 1.0

Zinc binding site 3 out of 8 in 7thl

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Zinc binding site 3 out of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A


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 Inulanolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:21.7
occ:1.00
 SG B:CYS441 2.3 23.5 1.0
SG B:CYS464 2.3 21.0 1.0
SG B:CYS461 2.3 22.2 1.0
SG B:CYS438 2.4 17.3 1.0
CB B:CYS438 3.1 21.5 1.0
CB B:CYS441 3.2 22.1 1.0
CB B:CYS464 3.2 15.5 1.0
CB B:CYS461 3.5 20.8 1.0
N B:CYS441 3.6 22.8 1.0
NH2 B:ARG444 3.8 43.6 1.0
N B:CYS461 3.9 13.8 1.0
CA B:CYS441 4.0 26.9 1.0
NE B:ARG444 4.1 39.6 1.0
CZ B:ARG444 4.3 45.6 1.0
CA B:CYS461 4.3 14.8 1.0
N B:CYS464 4.3 19.5 1.0
CA B:CYS464 4.3 17.4 1.0
CA B:CYS438 4.6 17.2 1.0
CB B:ARG444 4.6 24.7 1.0
CB B:ILE440 4.6 17.3 1.0
C B:ILE440 4.7 28.4 1.0
C B:CYS441 4.8 35.8 1.0
C B:CYS461 4.9 19.0 1.0
O B:CYS461 4.9 16.2 1.0
N B:GLN442 4.9 25.3 1.0
C B:CYS438 5.0 20.7 1.0

Zinc binding site 4 out of 8 in 7thl

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Zinc binding site 4 out of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A


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 Inulanolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:13.4
occ:1.00
 NE2 B:HIS452 2.1 9.9 1.0
ND1 B:HIS457 2.1 14.2 1.0
SG B:CYS475 2.3 13.6 1.0
SG B:CYS478 2.4 14.6 1.0
CE1 B:HIS457 2.9 16.5 1.0
CE1 B:HIS452 3.0 12.0 1.0
CD2 B:HIS452 3.0 12.0 1.0
CB B:CYS475 3.1 12.5 1.0
CG B:HIS457 3.2 12.7 1.0
CB B:CYS478 3.5 15.7 1.0
CB B:HIS457 3.7 12.1 1.0
N B:CYS478 3.8 15.7 1.0
NE2 B:HIS457 4.0 14.5 1.0
ND1 B:HIS452 4.1 11.3 1.0
CG B:HIS452 4.1 13.2 1.0
CD2 B:HIS457 4.2 13.8 1.0
CA B:CYS478 4.2 16.4 1.0
N B:HIS457 4.5 8.8 1.0
CA B:CYS475 4.5 15.3 1.0
CB B:VAL477 4.6 17.1 1.0
NE2 B:GLN480 4.7 32.8 1.0
CG2 B:ILE450 4.7 11.6 1.0
CA B:HIS457 4.7 9.9 1.0
C B:VAL477 4.9 19.5 1.0
C B:CYS478 4.9 15.1 1.0
C B:CYS475 5.0 13.2 1.0

Zinc binding site 5 out of 8 in 7thl

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Zinc binding site 5 out of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A


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 Inulanolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:11.0
occ:1.00
 SG C:CYS461 2.3 9.6 1.0
SG C:CYS464 2.3 10.9 1.0
SG C:CYS441 2.3 12.1 1.0
SG C:CYS438 2.4 9.2 1.0
CB C:CYS438 3.1 8.1 1.0
CB C:CYS441 3.1 12.0 1.0
CB C:CYS464 3.2 9.3 1.0
CB C:CYS461 3.5 8.9 1.0
N C:CYS441 3.7 9.3 1.0
N C:CYS461 3.9 7.1 1.0
CA C:CYS441 4.0 12.7 1.0
N C:CYS464 4.2 8.9 1.0
CA C:CYS461 4.2 8.5 1.0
CA C:CYS464 4.3 8.1 1.0
CB C:ARG444 4.4 12.3 1.0
CB C:ILE440 4.6 11.2 1.0
CA C:CYS438 4.6 6.6 1.0
CG C:ARG444 4.6 20.8 1.0
C C:ILE440 4.7 9.2 1.0
O C:CYS461 4.8 9.8 1.0
C C:CYS461 4.9 9.0 1.0
C C:CYS441 4.9 12.5 1.0
N C:GLN442 5.0 11.2 1.0

Zinc binding site 6 out of 8 in 7thl

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Zinc binding site 6 out of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A


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 Inulanolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:10.2
occ:1.00
 NE2 C:HIS452 2.1 11.1 1.0
ND1 C:HIS457 2.1 11.9 1.0
SG C:CYS478 2.3 10.2 1.0
SG C:CYS475 2.3 9.2 1.0
CE1 C:HIS457 3.0 12.8 1.0
CD2 C:HIS452 3.0 8.4 1.0
CE1 C:HIS452 3.0 9.3 1.0
CB C:CYS475 3.1 7.4 1.0
CG C:HIS457 3.1 13.2 1.0
CB C:CYS478 3.5 12.2 1.0
CB C:HIS457 3.5 10.8 1.0
N C:CYS478 3.8 10.1 1.0
ND1 C:HIS452 4.1 7.6 1.0
NE2 C:HIS457 4.1 14.2 1.0
CG C:HIS452 4.1 8.3 1.0
CA C:CYS478 4.2 10.9 1.0
CD2 C:HIS457 4.2 16.4 1.0
CB C:VAL477 4.5 11.3 1.0
CA C:CYS475 4.5 7.6 1.0
C C:VAL477 4.8 12.1 1.0
CA C:HIS457 4.8 10.6 1.0
N C:HIS457 4.8 10.3 1.0
N C:VAL477 4.9 8.2 1.0
C C:CYS478 4.9 12.5 1.0
N C:ARG479 4.9 9.2 1.0
CG1 C:VAL477 4.9 11.1 1.0
O C:HOH623 5.0 19.8 1.0
CA C:VAL477 5.0 11.5 1.0
C C:CYS475 5.0 9.9 1.0
CG2 C:ILE450 5.0 9.1 1.0

Zinc binding site 7 out of 8 in 7thl

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Zinc binding site 7 out of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A


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 Inulanolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:16.4
occ:1.00
 SG D:CYS441 2.3 15.8 1.0
SG D:CYS461 2.3 15.3 1.0
SG D:CYS464 2.3 17.1 1.0
SG D:CYS438 2.4 14.1 1.0
CB D:CYS438 3.1 15.2 1.0
CB D:CYS441 3.2 20.6 1.0
CB D:CYS464 3.2 18.2 1.0
CB D:CYS461 3.4 15.9 1.0
N D:CYS441 3.7 14.8 1.0
N D:CYS461 3.9 12.1 1.0
CA D:CYS441 4.0 16.3 1.0
CA D:CYS461 4.2 13.3 1.0
N D:CYS464 4.2 14.8 1.0
CA D:CYS464 4.3 13.5 1.0
CB D:ARG444 4.6 16.0 1.0
CA D:CYS438 4.6 14.6 1.0
CB D:ILE440 4.6 17.7 1.0
C D:ILE440 4.7 19.0 1.0
C D:CYS441 4.9 21.6 1.0
C D:CYS461 4.9 13.6 1.0
N D:GLN442 4.9 17.5 1.0
O D:CYS461 4.9 12.7 1.0
CG D:ARG444 5.0 21.6 1.0

Zinc binding site 8 out of 8 in 7thl

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Zinc binding site 8 out of 8 in the Structure of Mouse Double Minute 2 Homolog (MDM2) Ring Domain in Complex with Inulanolide A


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 Inulanolide A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:12.9
occ:1.00
 NE2 D:HIS452 2.1 9.5 1.0
ND1 D:HIS457 2.1 14.8 1.0
SG D:CYS475 2.2 14.1 1.0
SG D:CYS478 2.4 13.9 1.0
CE1 D:HIS457 2.9 11.0 1.0
CE1 D:HIS452 3.0 11.2 1.0
CD2 D:HIS452 3.1 11.3 1.0
CB D:CYS475 3.1 16.9 1.0
CG D:HIS457 3.2 9.9 1.0
CB D:CYS478 3.5 11.8 1.0
CB D:HIS457 3.7 9.4 1.0
N D:CYS478 3.8 16.9 1.0
ND1 D:HIS452 4.1 10.3 1.0
NE2 D:HIS457 4.1 11.3 1.0
CG D:HIS452 4.1 10.5 1.0
CA D:CYS478 4.2 15.3 1.0
CD2 D:HIS457 4.2 9.3 1.0
CB D:VAL477 4.5 18.0 1.0
N D:HIS457 4.6 8.9 1.0
CA D:CYS475 4.6 12.4 1.0
CG2 D:ILE450 4.7 10.2 1.0
CA D:HIS457 4.8 9.1 1.0
C D:VAL477 4.8 18.0 1.0
C D:CYS478 4.9 19.6 1.0
N D:ARG479 5.0 15.4 1.0
N D:VAL477 5.0 17.4 1.0
C D:CYS475 5.0 16.8 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 03:30:49 2023

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