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Zinc in PDB 5mnj: Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex

Enzymatic activity of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex

All present enzymatic activity of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex:
2.3.2.23; 2.3.2.24;

Protein crystallography data

The structure of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex, PDB code: 5mnj was solved by M.Klejnot, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.49 / 2.16
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.240, 62.760, 66.350, 69.83, 69.22, 78.21
R / Rfree (%) 19 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex (pdb code 5mnj). 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 MDM2-Mdmx-UBCH5B-Ubiquitin Complex, PDB code: 5mnj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5mnj

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Zinc binding site 1 out of 8 in the Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:52.8
occ:1.00
 SG C:CYS464 2.3 54.1 1.0
SG C:CYS438 2.4 48.0 1.0
SG C:CYS441 2.5 54.1 1.0
SG C:CYS461 2.5 51.6 1.0
CB C:CYS438 3.1 46.6 1.0
CB C:CYS441 3.1 53.7 1.0
CB C:CYS464 3.3 49.0 1.0
CB C:CYS461 3.5 50.1 1.0
N C:CYS441 3.6 58.6 1.0
N C:CYS461 3.9 43.1 1.0
CA C:CYS441 3.9 54.0 1.0
CA C:CYS461 4.3 47.6 1.0
NE C:ARG444 4.4 66.5 1.0
N C:CYS464 4.4 52.3 1.0
CA C:CYS464 4.5 49.9 1.0
NH2 C:ARG444 4.5 73.3 1.0
CA C:CYS438 4.6 44.2 1.0
CB C:ILE440 4.7 53.3 1.0
C C:ILE440 4.7 55.0 1.0
C C:CYS441 4.7 48.9 1.0
N C:GLN442 4.8 51.0 1.0
CB C:ARG444 4.9 53.9 1.0
CZ C:ARG444 4.9 74.5 1.0
C C:CYS461 5.0 48.6 1.0

Zinc binding site 2 out of 8 in 5mnj

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Zinc binding site 2 out of 8 in the Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:48.6
occ:1.00
 ND1 C:HIS457 2.0 42.2 1.0
SG C:CYS478 2.2 45.5 1.0
SG C:CYS475 2.2 45.7 1.0
NE2 C:HIS452 2.3 48.9 1.0
CE1 C:HIS457 2.9 40.1 1.0
CE1 C:HIS452 3.0 51.5 1.0
CG C:HIS457 3.1 38.3 1.0
CB C:CYS475 3.3 46.5 1.0
CD2 C:HIS452 3.4 50.3 1.0
CB C:CYS478 3.5 48.6 1.0
CB C:HIS457 3.5 36.8 1.0
N C:CYS478 3.7 48.5 1.0
NE2 C:HIS457 4.0 40.4 1.0
CD2 C:HIS457 4.1 35.6 1.0
CA C:CYS478 4.2 48.4 1.0
ND1 C:HIS452 4.2 51.5 1.0
N C:HIS457 4.4 43.7 1.0
CG C:HIS452 4.4 54.0 1.0
CB C:VAL477 4.5 50.6 1.0
CA C:HIS457 4.6 39.0 1.0
CA C:CYS475 4.7 46.6 1.0
C C:VAL477 4.7 53.0 1.0
CG1 C:VAL477 4.9 46.7 1.0
N C:VAL477 4.9 45.4 1.0
CA C:VAL477 4.9 46.1 1.0
OE1 C:GLN480 4.9 64.7 1.0
C C:GLY456 5.0 45.0 1.0
C C:CYS478 5.0 49.1 1.0
CG2 C:ILE450 5.0 46.7 1.0

Zinc binding site 3 out of 8 in 5mnj

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Zinc binding site 3 out of 8 in the Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:43.2
occ:1.00
 SG D:CYS437 2.2 40.8 1.0
SG D:CYS460 2.3 40.3 1.0
SG D:CYS440 2.4 47.0 1.0
SG D:CYS463 2.5 46.3 1.0
CB D:CYS437 3.0 44.2 1.0
CB D:CYS463 3.3 39.1 1.0
CB D:CYS440 3.3 47.3 1.0
CB D:CYS460 3.4 41.6 1.0
N D:CYS440 3.8 45.9 1.0
NH2 D:ARG443 3.8 58.9 1.0
N D:CYS460 3.9 37.5 1.0
CA D:CYS440 4.1 45.8 1.0
NE D:ARG443 4.1 55.3 1.0
CA D:CYS460 4.2 41.1 1.0
N D:CYS463 4.3 41.5 1.0
CZ D:ARG443 4.4 57.6 1.0
CA D:CYS463 4.4 41.3 1.0
CA D:CYS437 4.5 41.4 1.0
N D:GLU441 4.5 51.3 1.0
C D:CYS440 4.8 51.4 1.0
CB D:LEU439 4.8 39.6 1.0
C D:CYS460 4.9 41.3 1.0
C D:LEU439 4.9 49.9 1.0
CB D:ARG443 4.9 45.7 1.0
C D:CYS437 5.0 41.4 1.0
O D:CYS460 5.0 44.3 1.0

Zinc binding site 4 out of 8 in 5mnj

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Zinc binding site 4 out of 8 in the Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:45.2
occ:1.00
 NE2 D:HIS451 2.1 50.6 1.0
ND1 D:HIS456 2.2 47.6 1.0
SG D:CYS474 2.3 46.8 1.0
SG D:CYS477 2.4 48.0 1.0
CE1 D:HIS451 3.0 46.2 1.0
CD2 D:HIS451 3.1 52.3 1.0
CE1 D:HIS456 3.1 51.0 1.0
CG D:HIS456 3.2 46.9 1.0
CB D:CYS474 3.2 46.5 1.0
CB D:HIS456 3.5 44.5 1.0
CB D:CYS477 3.6 41.5 1.0
N D:CYS477 3.8 43.5 1.0
ND1 D:HIS451 4.1 48.0 1.0
CG D:HIS451 4.2 52.4 1.0
NE2 D:HIS456 4.2 51.7 1.0
CA D:CYS477 4.2 47.1 1.0
CD2 D:HIS456 4.3 49.2 1.0
CB D:ILE476 4.4 50.2 1.0
N D:HIS456 4.7 42.9 1.0
CA D:CYS474 4.7 45.8 1.0
CA D:HIS456 4.7 46.1 1.0
CG2 D:ILE476 4.9 45.9 1.0
C D:ILE476 4.9 46.5 1.0
C D:CYS477 4.9 42.8 1.0
O D:ILE449 5.0 41.5 1.0

Zinc binding site 5 out of 8 in 5mnj

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Zinc binding site 5 out of 8 in the Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn501

b:48.4
occ:1.00
 SG G:CYS438 2.3 44.7 1.0
SG G:CYS464 2.4 50.4 1.0
SG G:CYS441 2.4 48.0 1.0
SG G:CYS461 2.5 47.9 1.0
CB G:CYS438 3.1 42.9 1.0
CB G:CYS464 3.2 49.1 1.0
CB G:CYS441 3.2 49.1 1.0
CB G:CYS461 3.5 44.5 1.0
N G:CYS441 3.6 54.4 1.0
N G:CYS461 3.9 40.9 1.0
CA G:CYS441 4.0 48.9 1.0
N G:CYS464 4.2 45.3 1.0
CA G:CYS461 4.3 42.9 1.0
CA G:CYS464 4.3 47.7 1.0
NE G:ARG444 4.5 64.5 1.0
CA G:CYS438 4.5 40.6 1.0
CB G:ILE440 4.6 47.7 1.0
NH1 G:ARG444 4.7 64.2 1.0
C G:ILE440 4.7 52.6 1.0
N G:GLN442 4.7 50.6 1.0
O G:HOH609 4.8 52.9 1.0
C G:CYS441 4.8 52.5 1.0
O G:CYS461 4.9 43.5 1.0
C G:CYS461 4.9 40.7 1.0
C G:ALA460 5.0 43.5 1.0

Zinc binding site 6 out of 8 in 5mnj

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Zinc binding site 6 out of 8 in the Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn502

b:41.1
occ:1.00
 ND1 G:HIS457 2.0 33.3 1.0
SG G:CYS475 2.2 44.5 1.0
NE2 G:HIS452 2.2 40.1 1.0
SG G:CYS478 2.5 42.6 1.0
CE1 G:HIS457 2.8 40.0 1.0
CG G:HIS457 3.0 39.5 1.0
CE1 G:HIS452 3.1 48.0 1.0
CB G:CYS475 3.1 42.4 1.0
CD2 G:HIS452 3.3 44.8 1.0
CB G:HIS457 3.5 34.3 1.0
CB G:CYS478 3.5 46.2 1.0
N G:CYS478 3.8 47.9 1.0
NE2 G:HIS457 4.0 39.6 1.0
CD2 G:HIS457 4.1 37.3 1.0
ND1 G:HIS452 4.2 44.2 1.0
CA G:CYS478 4.2 46.5 1.0
CG G:HIS452 4.3 45.7 1.0
NE2 G:GLN480 4.4 53.2 1.0
CA G:CYS475 4.6 45.9 1.0
N G:HIS457 4.6 40.4 1.0
CB G:VAL477 4.6 48.4 1.0
CA G:HIS457 4.7 37.7 1.0
C G:VAL477 4.8 44.3 1.0
C G:CYS478 4.9 42.7 1.0
N G:VAL477 5.0 43.9 1.0

Zinc binding site 7 out of 8 in 5mnj

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Zinc binding site 7 out of 8 in the Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn501

b:40.5
occ:1.00
 ND1 H:HIS456 2.1 39.3 1.0
NE2 H:HIS451 2.2 41.2 1.0
SG H:CYS474 2.3 39.0 1.0
SG H:CYS477 2.5 43.4 1.0
CE1 H:HIS456 2.8 43.4 1.0
CE1 H:HIS451 3.0 42.1 1.0
CD2 H:HIS451 3.1 38.5 1.0
CB H:CYS474 3.2 35.0 1.0
CG H:HIS456 3.2 41.8 1.0
CB H:CYS477 3.6 43.3 1.0
CB H:HIS456 3.7 38.1 1.0
N H:CYS477 3.7 42.5 1.0
NE2 H:HIS456 4.0 44.5 1.0
ND1 H:HIS451 4.1 38.6 1.0
CG H:HIS451 4.2 44.1 1.0
CA H:CYS477 4.2 46.3 1.0
CD2 H:HIS456 4.2 40.9 1.0
CB H:ILE476 4.4 46.2 1.0
CA H:CYS474 4.6 38.5 1.0
N H:HIS456 4.7 38.8 1.0
C H:ILE476 4.8 40.9 1.0
N H:ILE476 4.8 41.8 1.0
CA H:HIS456 4.8 38.4 1.0
CA H:ILE476 4.9 40.3 1.0
C H:CYS477 4.9 43.6 1.0
CG1 H:ILE476 4.9 44.3 1.0
C H:CYS474 5.0 37.3 1.0

Zinc binding site 8 out of 8 in 5mnj

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Zinc binding site 8 out of 8 in the Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of MDM2-Mdmx-UBCH5B-Ubiquitin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn502

b:44.3
occ:1.00
 SG H:CYS460 2.3 39.3 1.0
SG H:CYS440 2.4 47.0 1.0
SG H:CYS463 2.4 50.4 1.0
SG H:CYS437 2.4 41.4 1.0
CB H:CYS437 3.1 41.0 1.0
CB H:CYS440 3.3 46.5 1.0
CB H:CYS463 3.3 38.5 1.0
CB H:CYS460 3.4 43.6 1.0
N H:CYS440 3.7 52.4 1.0
N H:CYS460 3.9 39.9 1.0
CA H:CYS440 4.1 52.4 1.0
CA H:CYS460 4.2 39.3 1.0
NH2 H:ARG443 4.2 55.9 1.0
N H:CYS463 4.3 43.1 1.0
NE H:ARG443 4.3 49.5 1.0
CA H:CYS463 4.4 39.9 1.0
CA H:CYS437 4.6 43.8 1.0
N H:GLU441 4.6 54.9 1.0
CZ H:ARG443 4.7 56.5 1.0
CB H:LEU439 4.7 47.5 1.0
CB H:ARG443 4.7 42.8 1.0
C H:CYS440 4.8 54.8 1.0
C H:LEU439 4.8 55.5 1.0
C H:CYS460 4.9 41.1 1.0
O H:CYS460 4.9 38.2 1.0

Reference:

K.Nomura, M.Klejnot, D.Kowalczyk, A.K.Hock, G.J.Sibbet, K.H.Vousden, D.T.Huang. Structural Analysis of MDM2 Ring Separates Degradation From Regulation of P53 Transcription Activity. Nat. Struct. Mol. Biol. V. 24 578 2017.
ISSN: ESSN 1545-9985
PubMed: 28553961
DOI: 10.1038/NSMB.3414
Page generated: Sun Oct 27 22:12:39 2024

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