Zinc in PDB 2vje: Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer

The structure of Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer, PDB code: 2vje was solved by P.D.Mace, K.Linke, C.A.Smith, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.92 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.562, 40.769, 77.514, 90.00, 109.06, 90.00
R / Rfree (%)	19.6 / 22.3

The binding sites of Zinc atom in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer (pdb code 2vje). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer, PDB code: 2vje:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer


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 the MDM2-Mdmx Ring Domain Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1492 b:57.2 occ:1.00 SG A:CYS438 2.3 41.9 1.0 SG A:CYS464 2.3 47.6 1.0 SG A:CYS461 2.4 41.2 1.0 SG A:CYS441 2.4 46.4 1.0 CB A:CYS438 3.0 42.0 1.0 CB A:CYS441 3.2 46.2 1.0 CB A:CYS464 3.2 48.6 1.0 CB A:CYS461 3.6 41.9 1.0 N A:CYS441 3.7 45.8 1.0 N A:CYS461 3.9 42.1 1.0 CA A:CYS441 4.0 46.1 1.0 CA A:CYS461 4.3 42.3 1.0 N A:CYS464 4.3 47.9 1.0 CA A:CYS464 4.4 48.7 1.0 NH2 A:ARG444 4.5 62.5 1.0 CA A:CYS438 4.5 42.3 1.0 NE A:ARG444 4.6 58.7 1.0 CB A:ILE440 4.7 44.6 1.0 C A:ILE440 4.7 45.3 1.0 C A:CYS441 4.8 46.4 1.0 CB A:ARG444 4.9 49.9 1.0 N A:GLN442 4.9 46.6 1.0 CG2 A:ILE440 4.9 44.8 1.0 C A:CYS461 4.9 43.0 1.0 CA A:ILE440 5.0 44.6 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer


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 the MDM2-Mdmx Ring Domain Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1493 b:62.1 occ:1.00 ND1 A:HIS457 2.1 43.4 1.0 NE2 A:HIS452 2.2 45.6 1.0 SG A:CYS475 2.3 50.0 1.0 SG A:CYS478 2.3 55.1 1.0 CE1 A:HIS452 3.0 44.1 1.0 CE1 A:HIS457 3.0 43.1 1.0 CG A:HIS457 3.0 43.5 1.0 CB A:CYS475 3.2 51.6 1.0 CD2 A:HIS452 3.2 44.7 1.0 CB A:HIS457 3.4 43.9 1.0 CB A:CYS478 3.5 54.8 1.0 N A:CYS478 3.8 54.4 1.0 NE2 A:HIS457 4.1 42.6 1.0 ND1 A:HIS452 4.1 44.5 1.0 CD2 A:HIS457 4.2 44.0 1.0 CA A:CYS478 4.2 54.9 1.0 CG A:HIS452 4.3 44.9 1.0 CB A:VAL477 4.4 53.2 1.0 N A:HIS457 4.6 44.2 1.0 CA A:HIS457 4.6 44.2 1.0 O A:HOH2015 4.6 55.0 1.0 CA A:CYS475 4.6 52.0 1.0 C A:VAL477 4.8 53.7 1.0 CG2 A:ILE450 4.8 42.5 1.0 CG1 A:VAL477 4.9 54.1 1.0 C A:CYS478 4.9 55.5 1.0 CA A:VAL477 4.9 53.3 1.0 N A:ARG479 4.9 55.9 1.0 N A:VAL477 5.0 52.8 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer


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 the MDM2-Mdmx Ring Domain Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1491 b:52.1 occ:1.00 SG B:CYS460 2.2 38.9 1.0 SG B:CYS463 2.4 40.1 1.0 SG B:CYS437 2.4 38.9 1.0 SG B:CYS440 2.4 44.2 1.0 CB B:CYS437 3.1 40.0 1.0 CB B:CYS463 3.2 39.5 1.0 CB B:CYS440 3.3 44.7 1.0 CB B:CYS460 3.4 38.8 1.0 N B:CYS440 3.7 44.2 1.0 N B:CYS460 3.9 38.7 1.0 NE B:ARG443 4.0 55.5 1.0 CA B:CYS440 4.1 45.6 1.0 CA B:CYS460 4.2 38.8 1.0 N B:CYS463 4.3 39.9 1.0 CA B:CYS463 4.4 39.5 1.0 NH2 B:ARG443 4.4 56.1 1.0 CB B:ARG443 4.5 47.8 1.0 CA B:CYS437 4.6 40.4 1.0 CB B:LEU439 4.6 42.1 1.0 CZ B:ARG443 4.7 55.3 1.0 C B:LEU439 4.8 43.1 1.0 C B:CYS460 4.8 39.5 1.0 O B:CYS460 4.9 39.3 1.0 N B:GLU441 4.9 48.1 1.0 C B:CYS440 4.9 46.8 1.0 CD B:ARG443 5.0 49.5 1.0 C B:THR459 5.0 38.3 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer


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 the MDM2-Mdmx Ring Domain Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1492 b:49.6 occ:1.00 NE2 B:HIS451 2.1 37.8 1.0 ND1 B:HIS456 2.3 36.8 1.0 SG B:CYS474 2.3 35.8 1.0 SG B:CYS477 2.4 38.6 1.0 CD2 B:HIS451 3.0 36.0 1.0 CE1 B:HIS451 3.1 37.4 1.0 CE1 B:HIS456 3.2 37.3 1.0 CB B:CYS474 3.2 37.1 1.0 CG B:HIS456 3.2 36.5 1.0 CB B:HIS456 3.6 37.6 1.0 CB B:CYS477 3.6 39.0 1.0 N B:CYS477 3.9 38.5 1.0 CG B:HIS451 4.1 37.9 1.0 ND1 B:HIS451 4.1 36.7 1.0 NE2 B:HIS456 4.2 36.5 1.0 CD2 B:HIS456 4.3 37.6 1.0 CA B:CYS477 4.3 39.0 1.0 N B:HIS456 4.4 37.9 1.0 O B:HOH2027 4.4 59.0 1.0 CB B:ILE476 4.5 37.6 1.0 CA B:HIS456 4.6 37.7 1.0 CA B:CYS474 4.6 37.4 1.0 O B:ILE449 4.9 37.9 1.0 C B:ILE476 4.9 38.4 1.0 N B:ILE476 4.9 37.6 1.0 C B:CYS477 5.0 39.3 1.0 C B:GLY455 5.0 38.6 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1492 b:53.3 occ:1.00 SG C:CYS461 2.3 38.6 1.0 SG C:CYS464 2.3 38.4 1.0 SG C:CYS441 2.4 42.5 1.0 SG C:CYS438 2.5 37.8 1.0 CB C:CYS464 3.1 39.7 1.0 CB C:CYS438 3.2 39.9 1.0 CB C:CYS441 3.3 42.7 1.0 CB C:CYS461 3.5 37.1 1.0 N C:CYS441 3.8 43.3 1.0 NH2 C:ARG444 3.9 57.8 1.0 N C:CYS461 4.0 37.7 1.0 CA C:CYS441 4.1 43.3 1.0 NE C:ARG444 4.2 55.5 1.0 N C:CYS464 4.2 39.6 1.0 CA C:CYS464 4.2 39.5 1.0 CA C:CYS461 4.3 37.4 1.0 CZ C:ARG444 4.5 57.7 1.0 CB C:ILE440 4.7 41.8 1.0 CA C:CYS438 4.7 40.0 1.0 C C:ILE440 4.7 42.5 1.0 O C:CYS461 4.8 37.0 1.0 C C:CYS461 4.8 36.9 1.0 CB C:ARG444 4.9 47.8 1.0 C C:CYS441 4.9 43.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1493 b:58.9 occ:1.00 NE2 C:HIS452 2.0 40.9 1.0 ND1 C:HIS457 2.1 45.0 1.0 SG C:CYS475 2.2 47.2 1.0 SG C:CYS478 2.4 52.5 1.0 CD2 C:HIS452 2.9 40.2 1.0 CE1 C:HIS457 3.0 46.0 1.0 CB C:CYS475 3.1 49.1 1.0 CE1 C:HIS452 3.1 38.7 1.0 CG C:HIS457 3.1 44.5 1.0 CB C:CYS478 3.5 52.4 1.0 CB C:HIS457 3.5 42.8 1.0 N C:CYS478 3.8 51.7 1.0 CG C:HIS452 4.1 41.3 1.0 NE2 C:HIS457 4.1 47.5 1.0 ND1 C:HIS452 4.1 39.9 1.0 CD2 C:HIS457 4.2 46.6 1.0 CA C:CYS478 4.3 52.2 1.0 CB C:VAL477 4.4 50.1 1.0 CA C:CYS475 4.5 49.0 1.0 N C:HIS457 4.6 42.4 1.0 CA C:HIS457 4.7 42.8 1.0 C C:VAL477 4.8 51.1 1.0 CG2 C:ILE450 4.8 40.4 1.0 C C:CYS478 4.9 52.6 1.0 OE1 C:GLN480 4.9 55.8 0.8 N C:VAL477 4.9 49.7 1.0 N C:ARG479 4.9 53.2 1.0 C C:CYS475 4.9 48.8 1.0 CA C:VAL477 5.0 50.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1491 b:54.5 occ:1.00 SG D:CYS460 2.2 38.0 1.0 SG D:CYS437 2.3 42.8 1.0 SG D:CYS463 2.4 41.1 1.0 SG D:CYS440 2.5 46.3 1.0 CB D:CYS437 3.0 42.9 1.0 CB D:CYS463 3.2 39.5 1.0 CB D:CYS440 3.4 47.3 1.0 CB D:CYS460 3.4 38.2 1.0 N D:CYS460 3.8 37.8 1.0 NH1 D:ARG443 3.8 55.2 1.0 N D:CYS440 3.8 46.8 1.0 CA D:CYS460 4.1 38.4 1.0 CA D:CYS440 4.2 47.8 1.0 N D:CYS463 4.2 40.3 1.0 CA D:CYS463 4.3 39.7 1.0 CA D:CYS437 4.5 43.3 1.0 CB D:ARG443 4.5 46.6 1.0 CB D:LEU439 4.6 45.2 1.0 CD D:ARG443 4.7 48.5 1.0 C D:CYS460 4.8 38.5 1.0 O D:CYS460 4.8 38.6 1.0 C D:LEU439 4.9 45.6 1.0 C D:THR459 4.9 37.2 1.0 N D:GLU441 4.9 49.5 1.0 CZ D:ARG443 5.0 53.5 1.0 C D:CYS437 5.0 43.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1492 b:54.7 occ:1.00 NE2 D:HIS451 2.0 38.0 1.0 ND1 D:HIS456 2.2 40.0 1.0 SG D:CYS474 2.4 40.8 1.0 SG D:CYS477 2.5 43.9 1.0 CE1 D:HIS451 2.9 40.2 1.0 CD2 D:HIS451 3.0 39.1 1.0 CB D:CYS474 3.1 40.6 1.0 CE1 D:HIS456 3.1 39.1 1.0 CG D:HIS456 3.2 38.7 1.0 CB D:HIS456 3.5 38.7 1.0 CB D:CYS477 3.7 45.4 1.0 N D:CYS477 4.0 45.1 1.0 ND1 D:HIS451 4.0 41.6 1.0 CG D:HIS451 4.1 40.4 1.0 NE2 D:HIS456 4.2 40.4 1.0 CD2 D:HIS456 4.3 37.8 1.0 N D:HIS456 4.3 39.0 1.0 CA D:CYS477 4.4 46.0 1.0 CB D:ILE476 4.5 43.7 1.0 CA D:HIS456 4.5 38.6 1.0 CA D:CYS474 4.6 41.1 1.0 O D:ILE449 4.9 38.2 1.0 C D:GLY455 4.9 39.5 1.0 C D:ILE476 4.9 44.7 1.0 N D:ILE476 5.0 43.9 1.0 C D:CYS477 5.0 46.9 1.0

K.Linke, P.D.Mace, C.A.Smith, D.L.Vaux, J.Silke, C.L.Day. Structure of the MDM2/Mdmx Ring Domain Heterodimer Reveals Dimerization Is Required For Their Ubiquitylation in Trans. Cell Death Differ. V. 15 841 2008.
ISSN: ISSN 1350-9047
PubMed: 18219319
DOI: 10.1038/SJ.CDD.4402309