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Magnesium in PDB 4y69: Yeast 20S Proteasome in Complex with Ac-Pad-Ep

Enzymatic activity of Yeast 20S Proteasome in Complex with Ac-Pad-Ep

All present enzymatic activity of Yeast 20S Proteasome in Complex with Ac-Pad-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Pad-Ep, PDB code: 4y69 was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.680, 301.260, 145.940, 90.00, 113.23, 90.00
R / Rfree (%) 19.5 / 21.7

Other elements in 4y69:

The structure of Yeast 20S Proteasome in Complex with Ac-Pad-Ep also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Ac-Pad-Ep (pdb code 4y69). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with Ac-Pad-Ep, PDB code: 4y69:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y69

Go back to Magnesium Binding Sites List in 4y69
Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pad-Ep


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 Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:40.4
occ:1.00
 O G:MET125 2.1 47.7 1.0
O G:TYR119 2.3 33.0 1.0
O G:ARG122 2.5 35.8 1.0
OG1 G:THR8 2.6 40.1 1.0
CG2 G:THR8 3.2 39.4 1.0
C G:MET125 3.4 44.5 1.0
CB G:THR8 3.5 39.2 1.0
C G:TYR119 3.5 32.2 1.0
C G:ARG122 3.6 38.0 1.0
O G:ALA123 3.7 41.2 1.0
CA G:ALA123 3.9 39.8 1.0
C G:ALA123 3.9 40.9 1.0
CA G:ARG126 4.2 38.5 1.0
N G:ARG126 4.2 40.3 1.0
N G:ALA123 4.2 38.2 1.0
N G:MET125 4.3 44.6 1.0
CA G:TYR119 4.3 32.3 1.0
N G:THR8 4.4 41.7 1.0
CA G:MET125 4.4 47.1 1.0
CD G:PRO127 4.4 35.0 1.0
CA G:THR8 4.5 40.0 1.0
N G:THR120 4.5 31.9 1.0
CA G:THR120 4.7 32.6 1.0
C G:ARG126 4.7 37.2 1.0
C G:THR120 4.8 33.4 1.0
N G:ARG122 4.8 38.9 1.0
CA G:ARG122 4.8 40.3 1.0
N G:TYR124 4.8 42.1 1.0
CB G:MET125 4.8 52.2 1.0
CB G:TYR119 4.9 32.9 1.0
N G:PRO127 4.9 35.6 1.0

Magnesium binding site 2 out of 7 in 4y69

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pad-Ep


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 Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:59.7
occ:1.00
 O I:ASP177 2.6 41.0 1.0
O I:SER180 2.7 41.6 1.0
O I:ALA174 2.8 42.3 1.0
C I:ASP177 3.7 39.8 1.0
OXT I:ASP204 3.8 54.3 1.0
C I:ALA174 3.9 41.0 1.0
C I:SER180 3.9 41.7 1.0
CA I:ASP175 4.1 43.5 1.0
C I:ASP175 4.3 43.0 1.0
O I:ASP175 4.4 46.1 1.0
N I:ASP175 4.4 42.3 1.0
NH1 Y:ARG19 4.4 51.2 1.0
O I:ALA178 4.4 43.1 1.0
CA I:ALA178 4.5 39.6 1.0
N I:ASP177 4.5 40.1 1.0
N I:ALA178 4.5 38.6 1.0
C I:ALA178 4.6 40.9 1.0
O I:ASP204 4.6 52.6 1.0
NH2 Y:ARG19 4.6 52.6 1.0
C I:ASP204 4.6 51.3 1.0
CA I:ASP177 4.7 39.9 1.0
N I:SER180 4.7 39.1 1.0
CA I:GLY181 4.7 41.6 1.0
OD1 I:ASP175 4.8 47.1 1.0
N I:GLY181 4.8 41.3 1.0
CA I:SER180 4.9 41.0 1.0
CZ Y:ARG19 4.9 51.1 1.0

Magnesium binding site 3 out of 7 in 4y69

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pad-Ep


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 Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:48.2
occ:1.00
 O I:ASP204 2.3 52.6 1.0
O Y:ASP168 2.3 41.6 1.0
O Y:ALA165 2.6 39.0 1.0
O Y:SER171 2.7 40.1 1.0
C I:ASP204 3.1 51.3 1.0
C Y:ASP168 3.3 39.7 1.0
O Y:ALA169 3.5 39.5 1.0
CA Y:ALA169 3.5 39.2 1.0
NH1 Y:ARG19 3.5 51.2 1.0
C Y:ALA169 3.6 39.3 1.0
C Y:ALA165 3.8 37.5 1.0
CA I:ASP204 3.8 49.5 1.0
N Y:ALA169 3.8 39.8 1.0
C Y:SER171 3.9 39.0 1.0
OXT I:ASP204 3.9 54.3 1.0
CB I:ASP204 4.2 49.8 1.0
N Y:SER171 4.2 39.1 1.0
O Y:HIS166 4.3 37.3 1.0
CZ Y:ARG19 4.3 51.1 1.0
N Y:TYR170 4.5 39.8 1.0
CA Y:ALA165 4.5 38.0 1.0
CA Y:ASP168 4.6 39.1 1.0
CA Y:SER171 4.6 38.6 1.0
N Y:ASP168 4.6 39.3 1.0
C Y:HIS166 4.6 37.2 1.0
NH2 Y:ARG19 4.7 52.6 1.0
N Y:HIS166 4.8 37.2 1.0
CB Y:ALA169 4.9 39.4 1.0
N Y:GLY172 4.9 38.8 1.0
C Y:ARG167 5.0 38.9 1.0
O Y:ALA164 5.0 37.5 1.0

Magnesium binding site 4 out of 7 in 4y69

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pad-Ep


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 Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:43.4
occ:1.00
 O K:ASP168 2.3 37.9 1.0
O W:ASP204 2.3 53.3 1.0
O K:ALA165 2.4 40.7 1.0
O K:SER171 2.8 42.3 1.0
C W:ASP204 3.1 50.8 1.0
C K:ASP168 3.3 38.3 1.0
C K:ALA165 3.6 40.1 1.0
CA K:ALA169 3.6 39.5 1.0
CA W:ASP204 3.7 48.8 1.0
O K:ALA169 3.8 40.4 1.0
C K:ALA169 3.8 40.5 1.0
NH1 K:ARG19 3.8 48.9 1.0
N K:ALA169 3.8 38.6 1.0
OXT W:ASP204 3.9 53.5 1.0
C K:SER171 4.0 41.7 1.0
O K:HIS166 4.0 41.9 1.0
CB W:ASP204 4.0 48.3 1.0
C K:HIS166 4.3 40.2 1.0
CA K:ALA165 4.4 40.3 1.0
N K:SER171 4.4 40.2 1.0
N K:ASP168 4.4 38.7 1.0
CA K:ASP168 4.4 38.2 1.0
N K:HIS166 4.6 39.4 1.0
CZ K:ARG19 4.6 47.8 1.0
N K:TYR170 4.6 41.7 1.0
CA K:HIS166 4.7 39.6 1.0
CA K:SER171 4.7 40.7 1.0
C K:ARG167 4.7 39.4 1.0
O K:ALA164 4.8 41.4 1.0
N K:ARG167 4.9 39.0 1.0
NH2 K:ARG19 4.9 48.9 1.0
CB K:ALA169 5.0 39.7 1.0
N K:GLY172 5.0 41.9 1.0
CG W:ASP204 5.0 48.3 1.0

Magnesium binding site 5 out of 7 in 4y69

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pad-Ep


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 Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:64.5
occ:1.00
 OXT L:ASP222 2.0 62.4 1.0
O V:ASP166 2.1 39.5 1.0
O V:ILE163 2.3 38.8 1.0
O V:SER169 2.4 41.2 1.0
C L:ASP222 3.0 61.0 1.0
C V:ASP166 3.1 39.9 1.0
C V:ILE163 3.4 41.2 1.0
C V:SER169 3.5 41.1 1.0
CA L:ASP222 3.7 59.4 1.0
CA V:LEU167 3.8 40.5 1.0
N V:LEU167 3.8 40.5 1.0
NH1 V:ARG19 3.9 53.8 1.0
O L:ASP222 3.9 68.0 1.0
O V:GLY162 4.0 37.1 1.0
N V:ASP166 4.1 40.4 1.0
C V:LEU167 4.2 40.7 1.0
CA V:ILE163 4.2 41.7 1.0
CA V:ASP166 4.2 39.6 1.0
CB L:ASP222 4.2 58.7 1.0
N V:SER169 4.3 39.4 1.0
C V:TRP164 4.3 44.7 1.0
O V:TRP164 4.3 46.3 1.0
O V:LEU167 4.4 40.0 1.0
N V:TRP164 4.4 42.6 1.0
CA V:SER169 4.4 40.0 1.0
N V:GLY170 4.4 43.1 1.0
CA V:GLY170 4.5 46.4 1.0
CZ V:ARG19 4.5 52.5 1.0
CA V:TRP164 4.6 44.1 1.0
N V:ASN165 4.7 43.4 1.0
NH2 V:ARG19 4.7 56.3 1.0
CB V:SER169 4.8 39.8 1.0
C V:ASN165 4.8 41.8 1.0
N V:GLY168 4.9 40.4 1.0
C V:GLY162 4.9 39.9 1.0
CD2 V:LEU167 5.0 41.0 1.0

Magnesium binding site 6 out of 7 in 4y69

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pad-Ep


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 Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:36.1
occ:1.00
 O N:SER169 2.7 35.0 1.0
O N:ILE163 2.9 34.4 1.0
O N:ASP166 3.2 35.9 1.0
NH1 N:ARG19 3.4 36.1 1.0
CD1 a:LEU34 3.6 41.0 1.0
C N:SER169 3.9 34.4 1.0
CZ N:ARG19 4.0 35.3 1.0
C N:ILE163 4.1 34.8 1.0
CG2 N:ILE163 4.1 32.6 1.0
C N:ASP166 4.2 33.7 1.0
CA N:GLY167 4.2 33.1 1.0
O N:GLY167 4.2 34.8 1.0
NH2 N:ARG19 4.3 36.5 1.0
CA N:GLY170 4.4 34.9 1.0
C N:GLY167 4.5 33.4 1.0
N N:GLY167 4.6 32.7 1.0
N N:GLY170 4.6 34.4 1.0
CA N:ILE163 4.7 33.3 1.0
O N:HOH303 4.9 28.4 1.0
CG a:LEU34 4.9 41.0 1.0
N N:SER169 4.9 33.9 1.0
NE N:ARG19 5.0 34.6 1.0
CA N:SER169 5.0 32.8 1.0

Magnesium binding site 7 out of 7 in 4y69

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Pad-Ep


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 Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:45.4
occ:1.00
 O Z:VAL198 2.7 43.8 1.0
O Z:HIS195 2.7 39.7 1.0
O Z:THR192 2.7 50.7 1.0
C Z:HIS195 3.7 42.7 1.0
O Z:ILE196 3.7 45.3 1.0
CA Z:ILE196 3.7 43.8 1.0
C Z:THR192 3.8 51.3 1.0
C Z:VAL198 3.8 45.0 1.0
O Z:ASP222 3.9 66.6 1.0
C Z:ILE196 3.9 43.3 1.0
NH2 Z:ARG28 4.0 51.8 1.0
CG2 Z:THR192 4.1 52.5 1.0
N Z:ILE196 4.1 43.2 1.0
NH2 H:ARG19 4.2 57.4 1.0
CA Z:THR192 4.2 51.0 1.0
N Z:VAL198 4.3 43.0 1.0
CA Z:VAL198 4.6 44.4 1.0
OD1 Z:ASP222 4.7 63.2 1.0
CB Z:THR192 4.8 50.8 1.0
NH1 H:ARG19 4.8 53.3 1.0
N Z:GLN197 4.8 42.5 1.0
C Z:ASP222 4.8 65.9 1.0
CZ H:ARG19 4.8 53.5 1.0
N Z:GLY199 4.8 46.0 1.0
N Z:HIS195 4.9 44.0 1.0
CA Z:HIS195 4.9 42.7 1.0
CA Z:GLY199 4.9 47.7 1.0
N Z:GLU193 5.0 52.2 1.0
CZ Z:ARG28 5.0 51.6 1.0

Reference:

E.M.Huber, G.De Bruin, W.Heinemeyer, G.Paniagua Soriano, H.S.Overkleeft, M.Groll. Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors. J.Am.Chem.Soc. V. 137 7835 2015.
ISSN: ESSN 1520-5126
PubMed: 26020686
DOI: 10.1021/JACS.5B03688
Page generated: Sat Sep 28 22:47:48 2024

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