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

The structure of Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer, PDB code: 2vjf 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)	25.17 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.216, 41.784, 76.939, 90.00, 109.03, 90.00
R / Rfree (%)	20.8 / 23.4

The binding sites of Zinc atom in the Crystal Structure of the MDM2-Mdmx Ring Domain Heterodimer (pdb code 2vjf). 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: 2vjf:
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:55.0 occ:1.00 SG A:CYS438 2.2 49.1 1.0 SG A:CYS464 2.3 55.1 1.0 SG A:CYS441 2.4 54.7 1.0 SG A:CYS461 2.4 54.3 1.0 CB A:CYS438 3.0 50.9 1.0 CB A:CYS441 3.2 54.2 1.0 CB A:CYS464 3.2 56.5 1.0 CB A:CYS461 3.4 53.7 1.0 N A:CYS441 3.6 53.6 1.0 N A:CYS461 3.8 53.3 1.0 CA A:CYS441 4.0 54.0 1.0 CA A:CYS461 4.2 53.6 1.0 NH2 A:ARG444 4.3 61.0 1.0 N A:CYS464 4.4 56.6 1.0 CA A:CYS464 4.4 56.8 1.0 CA A:CYS438 4.5 51.1 1.0 CB A:ILE440 4.5 53.2 1.0 NE A:ARG444 4.5 59.2 1.0 C A:ILE440 4.6 53.5 1.0 C A:CYS441 4.8 54.0 1.0 C A:CYS461 4.8 54.0 1.0 CZ A:ARG444 4.9 60.9 1.0 CA A:ILE440 4.9 53.3 1.0 N A:GLN442 4.9 54.3 1.0 C A:CYS438 4.9 51.5 1.0 N A:ILE440 4.9 53.1 1.0 O A:CYS461 4.9 54.0 1.0 CB A:ARG444 4.9 53.0 1.0 C A:ALA460 5.0 53.2 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:58.2 occ:1.00 ND1 A:HIS457 2.1 49.3 1.0 NE2 A:HIS452 2.2 52.9 1.0 SG A:CYS475 2.3 62.8 1.0 SG A:CYS478 2.4 61.6 1.0 CE1 A:HIS452 3.1 51.8 1.0 CE1 A:HIS457 3.1 49.0 1.0 CD2 A:HIS452 3.1 52.1 1.0 CG A:HIS457 3.1 50.0 1.0 CB A:CYS475 3.2 63.8 1.0 CB A:HIS457 3.4 51.0 1.0 CB A:CYS478 3.6 63.0 1.0 N A:CYS478 3.8 63.4 1.0 ND1 A:HIS452 4.1 52.1 1.0 CG A:HIS452 4.2 51.6 1.0 NE2 A:HIS457 4.2 49.3 1.0 CD2 A:HIS457 4.2 48.7 1.0 CA A:CYS478 4.3 63.3 1.0 CB A:VAL477 4.3 63.4 1.0 N A:HIS457 4.6 51.2 1.0 CA A:CYS475 4.6 63.9 1.0 CA A:HIS457 4.6 51.1 1.0 O A:HOH2008 4.7 64.5 1.0 O A:HOH2011 4.7 67.3 1.0 CG2 A:ILE450 4.8 47.6 1.0 C A:VAL477 4.8 63.4 1.0 CA A:VAL477 4.9 63.3 1.0 C A:CYS478 4.9 63.7 1.0 N A:VAL477 5.0 63.5 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:52.0 occ:1.00 SG B:CYS460 2.2 44.3 1.0 SG B:CYS440 2.3 54.4 1.0 SG B:CYS437 2.3 50.6 1.0 SG B:CYS463 2.4 48.0 1.0 CB B:CYS437 3.0 50.2 1.0 CB B:CYS463 3.2 47.0 1.0 CB B:CYS440 3.3 54.5 1.0 CB B:CYS460 3.4 44.3 1.0 N B:CYS440 3.7 54.2 1.0 N B:CYS460 3.8 43.9 1.0 NH2 B:ARG443 4.0 60.1 1.0 NE B:ARG443 4.1 59.6 1.0 CA B:CYS440 4.1 54.8 1.0 CA B:CYS460 4.2 44.1 1.0 N B:CYS463 4.3 47.4 1.0 CA B:CYS463 4.3 46.8 1.0 CZ B:ARG443 4.5 58.8 1.0 CA B:CYS437 4.5 50.6 1.0 CB B:ARG443 4.5 55.4 1.0 CB B:LEU439 4.5 53.4 1.0 C B:LEU439 4.8 53.8 1.0 C B:CYS460 4.9 44.6 1.0 N B:GLU441 4.9 56.0 1.0 C B:CYS440 4.9 55.5 1.0 O B:CYS460 5.0 45.0 1.0 C B:THR459 5.0 43.3 1.0 N B:LEU439 5.0 52.9 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:44.8 occ:1.00 NE2 B:HIS451 2.1 44.4 1.0 SG B:CYS477 2.2 41.8 1.0 ND1 B:HIS456 2.2 43.1 1.0 SG B:CYS474 2.3 41.1 1.0 CE1 B:HIS451 3.0 45.0 1.0 CE1 B:HIS456 3.1 43.1 1.0 CD2 B:HIS451 3.1 44.5 1.0 CB B:CYS474 3.1 41.6 1.0 CG B:HIS456 3.2 43.0 1.0 CB B:CYS477 3.6 43.4 1.0 CB B:HIS456 3.7 43.9 1.0 N B:CYS477 3.8 43.4 1.0 ND1 B:HIS451 4.1 45.0 1.0 NE2 B:HIS456 4.2 43.1 1.0 CG B:HIS451 4.2 45.7 1.0 CA B:CYS477 4.2 43.5 1.0 CD2 B:HIS456 4.3 42.7 1.0 CB B:ILE476 4.4 42.7 1.0 N B:HIS456 4.5 44.3 1.0 CA B:CYS474 4.6 41.6 1.0 CA B:HIS456 4.7 44.0 1.0 C B:ILE476 4.7 43.2 1.0 O B:ILE449 4.9 42.8 1.0 N B:ILE476 4.9 42.7 1.0 CA B:ILE476 4.9 42.5 1.0 C B:CYS477 5.0 43.9 1.0 CG2 B:ILE449 5.0 42.9 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:51.1 occ:1.00 SG C:CYS438 2.2 48.1 1.0 SG C:CYS461 2.3 48.7 1.0 SG C:CYS464 2.3 49.8 1.0 SG C:CYS441 2.4 51.4 1.0 CB C:CYS438 3.0 49.7 1.0 CB C:CYS464 3.2 49.7 1.0 CB C:CYS441 3.2 51.0 1.0 CB C:CYS461 3.5 47.3 1.0 N C:CYS441 3.6 51.0 1.0 N C:CYS461 3.9 47.7 1.0 CA C:CYS441 4.0 51.2 1.0 CA C:CYS461 4.2 47.6 1.0 NH2 C:ARG444 4.2 59.9 1.0 N C:CYS464 4.3 49.5 1.0 CA C:CYS464 4.4 49.8 1.0 NE C:ARG444 4.4 59.6 1.0 CA C:CYS438 4.5 49.8 1.0 CB C:ILE440 4.5 50.5 1.0 C C:ILE440 4.6 51.1 1.0 CZ C:ARG444 4.8 60.2 1.0 C C:CYS441 4.8 51.2 1.0 CB C:ARG444 4.9 53.2 1.0 C C:CYS461 4.9 47.5 1.0 O C:CYS461 4.9 47.6 1.0 CA C:ILE440 4.9 50.7 1.0 C C:CYS438 4.9 49.8 1.0 N C:ILE440 4.9 50.5 1.0 N C:GLN442 5.0 51.5 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:59.1 occ:1.00 ND1 C:HIS457 2.0 47.9 1.0 NE2 C:HIS452 2.1 46.9 1.0 SG C:CYS475 2.3 57.7 1.0 SG C:CYS478 2.5 58.9 1.0 CE1 C:HIS457 2.9 47.2 1.0 CD2 C:HIS452 3.0 47.4 1.0 CG C:HIS457 3.0 48.1 1.0 CE1 C:HIS452 3.1 46.8 1.0 CB C:CYS475 3.1 58.7 1.0 CB C:HIS457 3.5 48.9 1.0 CB C:CYS478 3.6 58.8 1.0 N C:CYS478 3.9 59.0 1.0 NE2 C:HIS457 4.0 47.4 1.0 ND1 C:HIS452 4.1 47.2 1.0 CD2 C:HIS457 4.1 47.6 1.0 CG C:HIS452 4.1 47.8 1.0 CA C:CYS478 4.3 59.2 1.0 CB C:VAL477 4.4 58.5 1.0 CA C:CYS475 4.6 58.9 1.0 N C:HIS457 4.6 49.4 1.0 CA C:HIS457 4.7 49.2 1.0 CG2 C:ILE450 4.8 44.0 1.0 O C:HOH2007 4.8 60.8 1.0 C C:VAL477 4.9 58.8 1.0 OE1 C:GLN480 4.9 61.8 1.0 C C:CYS478 5.0 59.5 1.0 CA C:VAL477 5.0 58.4 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:53.5 occ:1.00 SG D:CYS460 2.3 44.4 1.0 SG D:CYS437 2.3 50.0 1.0 SG D:CYS463 2.5 50.1 1.0 SG D:CYS440 2.5 55.1 1.0 CB D:CYS437 3.1 49.9 1.0 CB D:CYS463 3.2 48.2 1.0 CB D:CYS440 3.3 54.8 1.0 CB D:CYS460 3.4 45.7 1.0 N D:CYS440 3.7 54.7 1.0 N D:CYS460 3.8 45.3 1.0 NH1 D:ARG443 3.9 58.6 1.0 CA D:CYS440 4.1 55.3 1.0 CA D:CYS460 4.2 45.3 1.0 N D:CYS463 4.2 48.8 1.0 CA D:CYS463 4.3 48.1 1.0 CB D:ARG443 4.5 55.4 1.0 CB D:LEU439 4.5 53.6 1.0 CA D:CYS437 4.5 50.5 1.0 CD D:ARG443 4.7 56.2 1.0 C D:LEU439 4.8 54.3 1.0 C D:CYS460 4.8 45.7 1.0 N D:GLU441 4.9 56.5 1.0 C D:CYS440 4.9 56.0 1.0 CG D:ARG443 4.9 55.8 1.0 C D:THR459 4.9 45.3 1.0 N D:LEU439 5.0 53.2 1.0 CA D:LEU439 5.0 54.0 1.0 O D:CYS460 5.0 45.7 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:45.9 occ:1.00 NE2 D:HIS451 2.1 46.1 1.0 ND1 D:HIS456 2.2 43.0 1.0 SG D:CYS477 2.2 46.4 1.0 SG D:CYS474 2.4 43.6 1.0 CE1 D:HIS456 3.0 41.7 1.0 CD2 D:HIS451 3.0 45.5 1.0 CE1 D:HIS451 3.1 46.3 1.0 CB D:CYS474 3.2 43.7 1.0 CG D:HIS456 3.2 43.0 1.0 CB D:CYS477 3.5 47.6 1.0 CB D:HIS456 3.6 44.8 1.0 N D:CYS477 3.8 47.6 1.0 ND1 D:HIS451 4.1 46.0 1.0 NE2 D:HIS456 4.1 42.2 1.0 CG D:HIS451 4.1 45.4 1.0 CA D:CYS477 4.2 47.9 1.0 CD2 D:HIS456 4.3 42.4 1.0 CB D:ILE476 4.5 46.6 1.0 O D:HOH2018 4.5 62.9 1.0 N D:HIS456 4.5 45.1 1.0 CA D:CYS474 4.6 43.8 1.0 CA D:HIS456 4.7 44.9 1.0 O D:ILE449 4.8 42.0 1.0 C D:ILE476 4.8 47.1 1.0 C D:CYS477 4.9 48.9 1.0 N D:ILE476 4.9 46.3 1.0 CA D:ILE476 4.9 46.5 1.0 CG2 D:ILE449 5.0 41.1 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