Magnesium in PDB 4x6z: Yeast 20S Proteasome in Complex with Pr-VI Modulator

All present enzymatic activity of Yeast 20S Proteasome in Complex with Pr-VI Modulator:
3.4.25.1;

The structure of Yeast 20S Proteasome in Complex with Pr-VI Modulator, PDB code: 4x6z was solved by R.Rostankowski, J.Witkowska, D.Borek, Z.Otwinowski, E.Jankowska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.46 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	133.350, 300.790, 144.580, 90.00, 112.11, 90.00
R / Rfree (%)	17.7 / 22.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 56;

Binding sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Pr-VI Modulator (pdb code 4x6z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 56 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with Pr-VI Modulator, PDB code: 4x6z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 56 in the Yeast 20S Proteasome in Complex with Pr-VI Modulator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast 20S Proteasome in Complex with Pr-VI Modulator within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg304 b:35.2 occ:1.00 ND2 1:ASN-6 4.2 29.1 1.0 OH 1:TYR97 4.4 71.8 1.0 CB 1:TYR-4 4.5 22.8 1.0 O 1:TYR-4 4.8 26.6 1.0 CZ 1:TYR97 4.8 66.7 1.0 C 1:TYR-4 4.8 24.5 1.0 CE1 1:TYR97 4.8 62.9 1.0 N 1:GLY-3 4.9 25.2 1.0 CA 1:GLY-3 4.9 27.5 1.0

Magnesium binding site 2 out of 56 in the Yeast 20S Proteasome in Complex with Pr-VI Modulator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast 20S Proteasome in Complex with Pr-VI Modulator within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg304 b:22.5 occ:1.00 CD1 2:TRP103 4.1 21.2 1.0 NE1 2:TRP103 4.3 21.1 1.0 CA 2:GLY47 4.5 22.6 1.0 C 2:ASN104 4.5 20.5 1.0 O 2:TRP103 4.6 20.4 1.0 N 2:ALA105 4.7 21.9 1.0 O 2:ASN104 4.7 20.4 1.0 CA 2:ASN104 4.7 20.2 1.0 N 2:ASN104 4.7 20.6 1.0 C 2:TRP103 4.8 21.1 1.0 CB 2:ALA105 4.8 22.2 1.0

Magnesium binding site 3 out of 56 in the Yeast 20S Proteasome in Complex with Pr-VI Modulator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast 20S Proteasome in Complex with Pr-VI Modulator within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg305 b:39.1 occ:1.00 CZ T:PHE99 4.4 28.1 1.0 CB 2:GLU65 4.5 36.8 1.0 CE2 T:PHE99 4.6 28.4 1.0 CD1 2:LEU62 4.7 41.3 1.0 O 2:GLU65 4.9 35.9 1.0 NH2 T:ARG107 4.9 78.9 1.0 C 2:GLU65 4.9 34.0 1.0 CZ T:ARG107 4.9 80.8 1.0 N 2:ASN66 5.0 31.6 1.0 NH1 T:ARG107 5.0 80.2 1.0

Magnesium binding site 4 out of 56 in the Yeast 20S Proteasome in Complex with Pr-VI Modulator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast 20S Proteasome in Complex with Pr-VI Modulator within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg306 b:44.0 occ:1.00 OD2 2:ASP152 3.4 62.3 1.0 CE2 I:TRP164 3.9 34.1 1.0 CD2 I:TRP164 4.0 33.9 1.0 CZ2 I:TRP164 4.1 35.2 1.0 NE 1:ARG212 4.1 49.4 1.0 CE3 I:TRP164 4.3 34.8 1.0 CH2 I:TRP164 4.3 35.3 1.0 CG 2:ASP152 4.3 58.7 1.0 NE1 I:TRP164 4.3 33.8 1.0 CZ3 I:TRP164 4.4 35.0 1.0 CD 1:ARG212 4.5 48.0 1.0 CG I:TRP164 4.5 33.0 1.0 OD1 2:ASP152 4.6 65.0 1.0 CD1 I:TRP164 4.7 32.9 1.0 NH1 2:ARG153 4.7 53.3 1.0

Magnesium binding site 5 out of 56 in the Yeast 20S Proteasome in Complex with Pr-VI Modulator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast 20S Proteasome in Complex with Pr-VI Modulator within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg307 b:53.6 occ:1.00 CB 2:ASP212 3.8 44.6 1.0 N 2:PHE213 3.9 40.0 1.0 CB 2:LYS210 3.9 42.7 1.0 CD1 2:PHE213 4.0 40.2 1.0 OE1 I:GLN144 4.0 73.7 1.0 N 2:ASP212 4.1 38.8 1.0 CZ3 I:TRP142 4.4 35.5 1.0 CB 2:PHE213 4.4 40.4 1.0 CE 2:LYS210 4.4 54.4 1.0 CA 2:ASP212 4.4 41.0 1.0 CA 2:LYS210 4.5 39.0 1.0 CG 2:LYS210 4.5 46.2 1.0 N 2:TRP211 4.6 35.0 1.0 C 2:ASP212 4.6 40.2 1.0 CG 2:PHE213 4.7 39.2 1.0 CA 2:PHE213 4.7 40.5 1.0 C 2:LYS210 4.8 35.9 1.0 C 2:TRP211 4.8 36.2 1.0 CE1 2:PHE213 4.9 38.9 1.0

Magnesium binding site 6 out of 56 in the Yeast 20S Proteasome in Complex with Pr-VI Modulator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast 20S Proteasome in Complex with Pr-VI Modulator within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg308 b:32.9 occ:1.00 OE1 2:GLN94 3.7 66.1 1.0 OH T:TYR94 4.2 46.1 1.0 NE2 2:GLN94 4.3 67.2 1.0 CD 2:GLN94 4.4 59.9 1.0 CG2 2:THR90 4.6 21.9 1.0 CE1 2:TYR87 4.7 28.8 1.0 CG2 2:VAL91 4.8 19.3 1.0 CG1 T:VAL98 4.9 28.2 1.0

Magnesium binding site 7 out of 56 in the Yeast 20S Proteasome in Complex with Pr-VI Modulator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast 20S Proteasome in Complex with Pr-VI Modulator within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:42.1 occ:1.00 CA B:GLY223 3.9 36.7 1.0 CE I:LYS40 4.1 50.3 1.0 NZ I:LYS40 4.2 53.4 1.0 OE2 I:GLU73 4.2 61.5 1.0 N B:GLY223 4.4 36.0 1.0 OE1 I:GLU73 4.5 64.1 1.0 CD I:GLU73 4.7 58.6 1.0 C B:LEU222 4.8 37.3 1.0 O B:LEU222 4.8 38.5 1.0 O B:LEU221 4.9 41.4 1.0

Magnesium binding site 8 out of 56 in the Yeast 20S Proteasome in Complex with Pr-VI Modulator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast 20S Proteasome in Complex with Pr-VI Modulator within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:20.2 occ:1.00 N C:TYR98 4.0 23.4 1.0 CA C:TYR98 4.1 23.1 1.0 C C:ASN97 4.1 23.5 1.0 O C:ASN97 4.1 24.2 1.0 OG1 C:THR101 4.2 28.0 1.0 CB C:ASN97 4.2 23.8 1.0 CE1 C:HIS94 4.4 53.2 1.0 CB C:THR101 4.6 27.2 1.0 CB C:TYR98 4.7 22.5 1.0 CE2 C:TYR102 4.7 22.6 1.0 ND1 C:HIS94 4.8 52.2 1.0 CA C:ASN97 4.8 23.3 1.0 CD2 C:TYR98 5.0 21.6 1.0

Magnesium binding site 9 out of 56 in the Yeast 20S Proteasome in Complex with Pr-VI Modulator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Yeast 20S Proteasome in Complex with Pr-VI Modulator within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:28.3 occ:1.00 CG2 C:THR90 4.1 27.2 1.0 CG2 C:ILE86 4.3 29.7 1.0 OH C:TYR122 4.4 33.0 1.0 CZ C:PHE131 4.6 27.1 1.0 CG2 C:ILE118 4.8 24.0 1.0

Magnesium binding site 10 out of 56 in the Yeast 20S Proteasome in Complex with Pr-VI Modulator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Yeast 20S Proteasome in Complex with Pr-VI Modulator within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:28.0 occ:1.00 CG1 D:VAL126 4.5 33.2 1.0 CZ D:TYR120 4.6 27.0 1.0 CE1 D:TYR120 4.6 26.4 1.0 OH D:TYR120 4.6 26.3 1.0 CB D:SER123 4.8 28.4 1.0 OG D:SER123 4.9 27.9 1.0

J.Witkowska, R.Rostankowski, G.Dubin, P.Grudnik, P.Golik, M.Gaczynska, P.Osmulski, D.Borek, Z.Otwinowski, E.Jankowska. Crystal Structures Revealed the Common Place of Binding of Low-Molecular Mass Activators with the 20S Proteasome To Be Published.