Magnesium in PDB 3fdo: Structure of Human Mdmx in Complex with High Affinity Peptide

The structure of Structure of Human Mdmx in Complex with High Affinity Peptide, PDB code: 3fdo was solved by A.L.Czarna, G.M.Popowicz, T.A.Holak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.230, 30.950, 50.420, 90.00, 124.41, 90.00
R / Rfree (%)	17.9 / 24.7

The binding sites of Magnesium atom in the Structure of Human Mdmx in Complex with High Affinity Peptide (pdb code 3fdo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Human Mdmx in Complex with High Affinity Peptide, PDB code: 3fdo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of Human Mdmx in Complex with High Affinity Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Mdmx in Complex with High Affinity Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4 b:24.2 occ:1.00 OH A:TYR55 3.1 24.4 1.0 O A:HOH133 3.1 33.5 1.0 O A:HOH12 3.1 30.7 1.0 O A:HOH217 3.1 38.1 1.0 N A:GLN43 3.2 16.8 1.0 O A:GLN43 3.7 17.9 1.0 CZ A:TYR55 3.7 20.5 1.0 CE2 A:TYR55 3.8 19.5 1.0 CA A:ALA42 3.9 17.0 1.0 CB A:GLN43 4.0 17.4 1.0 CA A:GLN43 4.0 16.8 1.0 C A:ALA42 4.1 16.6 1.0 CE1 A:PHE47 4.3 12.7 1.0 O A:HOH223 4.3 33.1 1.0 C A:GLN43 4.3 16.8 1.0 CB A:ALA42 4.4 16.4 1.0 O A:GLY41 4.7 17.8 1.0 O A:HOH136 4.7 44.6 1.0 CE1 A:TYR55 4.8 20.0 1.0 NE2 A:GLN43 4.9 20.5 1.0 O A:HOH125 4.9 25.2 1.0 CD2 A:TYR55 4.9 17.1 1.0 CD1 A:PHE47 5.0 12.6 1.0

Magnesium binding site 2 out of 5 in the Structure of Human Mdmx in Complex with High Affinity Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Mdmx in Complex with High Affinity Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5 b:17.2 occ:1.00 NH1 A:ARG103 3.3 23.1 1.0 NH2 A:ARG103 3.4 20.8 1.0 CD1 A:TYR99 3.8 13.8 1.0 CZ A:ARG103 3.8 20.4 1.0 CB A:TYR99 4.0 13.0 1.0 CB A:SER96 4.1 17.7 1.0 CA A:SER96 4.2 16.8 1.0 CG A:TYR99 4.4 12.8 1.0 O A:HOH126 4.6 43.3 1.0 CE1 A:TYR99 4.8 13.8 1.0 O A:SER96 4.8 16.1 1.0

Magnesium binding site 3 out of 5 in the Structure of Human Mdmx in Complex with High Affinity Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human Mdmx in Complex with High Affinity Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg6 b:25.7 occ:1.00 O A:HOH185 3.1 37.1 1.0 N A:GLU45 3.1 15.0 1.0 N A:MET46 3.3 12.3 1.0 O A:HOH125 3.8 25.2 1.0 CA A:GLU45 3.9 14.9 1.0 CB A:GLU45 3.9 16.5 1.0 CA A:GLY44 4.0 15.5 1.0 C A:GLY44 4.0 15.1 1.0 O A:HOH192 4.0 22.0 1.0 C A:GLU45 4.1 13.5 1.0 CB A:MET46 4.1 13.4 1.0 O A:MET46 4.1 12.1 1.0 CG A:GLU45 4.2 19.6 1.0 CA A:MET46 4.2 12.2 1.0 CE A:MET46 4.2 17.2 1.0 CG A:MET46 4.6 14.2 1.0 C A:MET46 4.7 11.6 1.0

Magnesium binding site 4 out of 5 in the Structure of Human Mdmx in Complex with High Affinity Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human Mdmx in Complex with High Affinity Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2 b:15.5 occ:1.00 O A:HOH224 2.8 21.1 1.0 O B:HOH34 3.1 14.2 1.0 O B:HOH30 3.1 23.8 1.0 O A:HOH210 3.1 33.3 1.0 NE1 B:TRP23 3.5 10.1 1.0 CA A:HIS54 3.5 11.0 1.0 CD1 B:TRP23 3.6 9.7 1.0 N A:HIS54 3.6 10.3 1.0 O A:MET53 3.7 10.3 1.0 C A:MET53 3.7 10.3 1.0 O A:HOH10 3.8 21.4 1.0 O B:HOH58 4.0 25.8 1.0 CB A:MET53 4.2 9.8 1.0 CB A:HIS54 4.3 11.2 1.0 OG1 B:THR27 4.3 13.3 1.0 O A:HOH156 4.4 44.0 1.0 O B:HOH51 4.5 22.8 1.0 CA A:MET53 4.6 9.8 1.0 C A:HIS54 4.7 10.9 1.0 O A:LYS50 4.8 12.5 1.0 O B:HOH14 4.8 26.7 1.0 CE2 B:TRP23 4.8 9.0 1.0 CG B:TRP23 4.9 8.7 1.0 O A:HIS54 4.9 11.5 1.0 ND1 A:HIS54 4.9 15.7 1.0 CG2 B:THR27 5.0 15.1 1.0

Magnesium binding site 5 out of 5 in the Structure of Human Mdmx in Complex with High Affinity Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Human Mdmx in Complex with High Affinity Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3 b:23.6 occ:1.00 O A:HOH197 2.9 26.8 1.0 O A:HOH113 2.9 41.8 1.0 N B:GLU20 3.1 12.3 1.0 CB B:GLU20 3.6 14.1 1.0 N B:PHE19 3.7 12.2 1.0 CB B:PHE19 3.7 12.3 1.0 CA B:GLU20 3.9 13.1 1.0 CA B:PHE19 4.0 12.2 1.0 C B:PHE19 4.0 12.1 1.0 CB B:THR18 4.1 14.2 1.0 SD A:MET61 4.3 28.0 1.0 CG A:MET61 4.3 20.2 1.0 OE1 A:GLN71 4.3 11.7 1.0 C B:THR18 4.4 12.6 1.0 CD2 B:PHE19 4.5 12.2 1.0 CE A:MET61 4.5 26.4 1.0 OG1 B:THR18 4.6 14.1 1.0 CG B:PHE19 4.6 10.8 1.0 O A:HOH118 4.6 34.0 1.0 CA B:THR18 4.7 13.3 1.0 OH A:TYR66 4.8 16.3 1.0 CZ A:TYR66 4.9 13.0 1.0 CG2 B:THR18 5.0 15.0 1.0

A.Czarna, G.M.Popowicz, A.Pecak, S.Wolf, G.Dubin, T.A.Holak. High Affinity Interaction of the P53 Peptide-Analogue with Human MDM2 and Mdmx. Cell Cycle V. 8 1176 2009.
ISSN: ESSN 1551-4005
PubMed: 19305137
DOI: 10.4161/CC.8.8.8185