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Magnesium in PDB 4y75: Yeast 20S Proteasome in Complex with Ac-Paf-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Paf-Ep, PDB code: 4y75 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.730, 300.060, 145.480, 90.00, 112.85, 90.00
R / Rfree (%) 18.9 / 21.5

Other elements in 4y75:

The structure of Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep (pdb code 4y75). 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-Paf-Ep, PDB code: 4y75:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y75

Go back to Magnesium Binding Sites List in 4y75
Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:61.0
occ:1.00
 O G:MET125 2.3 55.8 1.0
OG1 G:THR8 2.7 50.2 1.0
O G:ARG122 2.8 52.0 1.0
O G:TYR119 2.9 49.8 1.0
O G:ALA123 3.2 57.6 1.0
CG2 G:THR8 3.3 53.1 1.0
C G:MET125 3.4 53.1 1.0
CB G:THR8 3.6 52.4 1.0
C G:ALA123 3.7 55.1 1.0
CA G:ALA123 3.8 52.4 1.0
C G:ARG122 3.9 52.7 1.0
N G:THR8 4.1 53.4 1.0
CA G:ARG126 4.1 47.8 1.0
N G:ARG126 4.1 48.9 1.0
C G:TYR119 4.1 48.8 1.0
N G:MET125 4.2 55.0 1.0
N G:ALA123 4.3 52.8 1.0
CA G:MET125 4.4 55.3 1.0
CD G:PRO127 4.5 46.2 1.0
CA G:THR8 4.5 53.4 1.0
N G:TYR124 4.7 57.5 1.0
C G:ARG126 4.8 47.9 1.0
CA G:TYR119 4.9 46.5 1.0
N G:PRO127 5.0 46.0 1.0
C G:TYR124 5.0 56.2 1.0

Magnesium binding site 2 out of 7 in 4y75

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:61.0
occ:1.00
 O I:ASP177 2.5 51.6 1.0
O I:ALA174 2.6 52.4 1.0
O I:SER180 2.7 44.1 1.0
C I:ALA174 3.6 54.7 1.0
C I:ASP177 3.7 50.1 1.0
C I:SER180 3.8 49.4 1.0
CA I:ASP175 3.9 53.3 1.0
OXT I:ASP204 3.9 52.8 1.0
N I:ASP175 4.1 53.8 1.0
C I:ASP175 4.3 52.2 1.0
N I:ASP177 4.4 49.5 1.0
O I:ASP175 4.5 51.6 1.0
OD1 I:ASP175 4.5 56.0 1.0
CA I:ALA178 4.5 48.0 1.0
N I:ALA178 4.6 47.9 1.0
O I:ALA178 4.6 56.1 1.0
CA I:ASP177 4.6 49.9 1.0
C I:ALA178 4.6 50.0 1.0
CA I:GLY181 4.7 48.9 1.0
N I:SER180 4.7 48.6 1.0
N I:GLY181 4.7 49.0 1.0
CA I:ALA174 4.8 54.6 1.0
NH1 Y:ARG19 4.8 59.9 1.0
CA I:SER180 4.8 49.5 1.0
C I:ASP204 4.8 57.5 1.0
NH2 Y:ARG19 4.9 61.2 1.0
O I:ASP204 4.9 57.3 1.0
N I:ARG176 5.0 50.5 1.0
CB I:ALA174 5.0 54.4 1.0

Magnesium binding site 3 out of 7 in 4y75

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:49.7
occ:1.00
 O Y:ASP168 2.2 46.0 1.0
O Y:ALA165 2.3 51.0 1.0
O I:ASP204 2.3 57.3 1.0
O Y:SER171 2.8 52.1 1.0
C I:ASP204 3.1 57.5 1.0
C Y:ASP168 3.1 46.8 1.0
C Y:ALA165 3.5 50.0 1.0
CA Y:ALA169 3.6 48.3 1.0
CA I:ASP204 3.6 57.2 1.0
N Y:ALA169 3.7 47.2 1.0
O Y:HIS166 3.8 50.5 1.0
C Y:ALA169 3.8 49.9 1.0
O Y:ALA169 3.8 52.2 1.0
C Y:SER171 3.9 51.5 1.0
OXT I:ASP204 4.0 52.8 1.0
C Y:HIS166 4.1 50.2 1.0
CB I:ASP204 4.1 58.7 1.0
N Y:ASP168 4.2 48.4 1.0
NH1 Y:ARG19 4.2 59.9 1.0
CA Y:ASP168 4.3 46.7 1.0
N Y:SER171 4.3 46.4 1.0
CA Y:ALA165 4.4 50.4 1.0
N Y:HIS166 4.4 50.5 1.0
CA Y:HIS166 4.5 49.3 1.0
O Y:ALA164 4.5 52.4 1.0
C Y:ARG167 4.6 48.3 1.0
N Y:TYR170 4.6 48.9 1.0
CA Y:SER171 4.6 48.9 1.0
N Y:ARG167 4.7 49.8 1.0
CZ Y:ARG19 4.8 58.2 1.0
N Y:GLY172 4.9 53.3 1.0
CB Y:ALA169 4.9 47.8 1.0
NH2 Y:ARG19 5.0 61.2 1.0
O Y:ARG167 5.0 46.9 1.0
N I:ASP204 5.0 56.4 1.0
CB Y:SER171 5.0 49.4 1.0

Magnesium binding site 4 out of 7 in 4y75

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:59.4
occ:1.00
 O K:ASP168 2.2 49.2 1.0
O K:ALA165 2.3 47.1 1.0
O W:ASP204 2.3 51.6 1.0
O K:SER171 2.9 52.4 1.0
C W:ASP204 3.1 50.4 1.0
C K:ASP168 3.1 46.2 1.0
C K:ALA165 3.4 47.6 1.0
CA K:ALA169 3.6 46.7 1.0
CA W:ASP204 3.7 49.4 1.0
N K:ALA169 3.7 46.4 1.0
O K:HIS166 3.7 51.6 1.0
C K:ALA169 3.8 48.6 1.0
O K:ALA169 3.9 52.5 1.0
OXT W:ASP204 3.9 54.8 1.0
C K:SER171 3.9 48.1 1.0
C K:HIS166 4.0 49.1 1.0
CB W:ASP204 4.2 48.8 1.0
N K:ASP168 4.2 44.4 1.0
CA K:ASP168 4.3 45.0 1.0
NH1 K:ARG19 4.3 52.1 1.0
N K:HIS166 4.3 46.9 1.0
CA K:ALA165 4.3 48.8 1.0
N K:SER171 4.4 45.7 1.0
CA K:HIS166 4.4 48.0 1.0
O K:ALA164 4.5 50.2 1.0
C K:ARG167 4.6 47.2 1.0
N K:TYR170 4.6 46.4 1.0
CA K:SER171 4.7 46.0 1.0
N K:ARG167 4.7 47.1 1.0
CZ K:ARG19 4.8 52.0 1.0
N K:GLY172 4.9 48.3 1.0
O K:ARG167 4.9 47.8 1.0
CB K:ALA169 4.9 45.3 1.0
CB K:SER171 5.0 44.3 1.0

Magnesium binding site 5 out of 7 in 4y75

Go back to Magnesium Binding Sites List in 4y75
Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:69.8
occ:1.00
 O V:ILE163 2.1 65.8 1.0
O V:ASP166 2.2 59.7 1.0
OXT L:ASP222 2.3 62.7 1.0
O V:SER169 2.9 62.0 1.0
C L:ASP222 3.0 61.5 1.0
C V:ASP166 3.1 62.3 1.0
C V:ILE163 3.1 69.1 1.0
O V:TRP164 3.6 61.1 1.0
CA L:ASP222 3.6 59.6 1.0
C V:TRP164 3.6 63.1 1.0
O V:GLY162 3.7 64.5 1.0
N V:ASP166 3.7 59.8 1.0
O L:ASP222 3.8 65.8 1.0
N V:LEU167 3.9 63.7 1.0
N V:TRP164 3.9 68.7 1.0
CA V:TRP164 4.0 66.6 1.0
CA V:ASP166 4.0 61.0 1.0
CA V:LEU167 4.0 62.6 1.0
N V:ASN165 4.1 62.3 1.0
C V:SER169 4.1 61.3 1.0
CA V:ILE163 4.1 66.9 1.0
CB L:ASP222 4.3 60.5 1.0
C V:ASN165 4.3 60.8 1.0
NH1 V:ARG19 4.4 64.6 1.0
NH2 V:ARG19 4.5 61.2 1.0
C V:LEU167 4.6 61.1 1.0
O L:ARG221 4.7 54.9 1.0
C V:GLY162 4.7 64.4 1.0
CA V:ASN165 4.7 63.2 1.0
CZ V:ARG19 4.7 62.0 1.0
N V:SER169 4.8 58.9 1.0
N L:ASP222 4.9 61.0 1.0
CD2 V:LEU167 4.9 60.5 1.0
N V:ILE163 4.9 63.5 1.0
CA V:SER169 4.9 60.9 1.0
CB V:ASP166 4.9 59.5 1.0
O V:LEU167 4.9 62.8 1.0
N V:GLY170 5.0 62.8 1.0
CA V:GLY170 5.0 64.0 1.0

Magnesium binding site 6 out of 7 in 4y75

Go back to Magnesium Binding Sites List in 4y75
Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:61.8
occ:1.00
 O N:SER169 2.4 50.9 1.0
O N:ILE163 2.5 51.5 1.0
O N:ASP166 2.8 50.8 1.0
CD1 a:LEU34 3.6 49.4 1.0
C N:SER169 3.6 47.7 1.0
C N:ILE163 3.7 50.6 1.0
C N:ASP166 3.9 47.5 1.0
NH1 N:ARG19 3.9 48.4 1.0
CG2 N:ILE163 4.0 49.3 1.0
CA N:GLY167 4.2 46.0 1.0
CA N:GLY170 4.3 49.6 1.0
CA N:ILE163 4.4 49.5 1.0
N N:GLY170 4.4 48.8 1.0
O N:GLY167 4.4 43.4 1.0
CZ N:ARG19 4.4 47.2 1.0
N N:GLY167 4.5 46.7 1.0
C N:GLY167 4.5 45.8 1.0
N N:SER169 4.6 44.7 1.0
NH2 N:ARG19 4.6 46.7 1.0
CA N:SER169 4.6 44.4 1.0
N N:LYS164 4.7 50.7 1.0
CB N:ILE163 4.8 48.6 1.0
O N:LYS164 4.9 55.9 1.0
C N:LYS164 4.9 52.0 1.0
CG a:LEU34 4.9 49.5 1.0
CA N:LYS164 5.0 51.1 1.0

Magnesium binding site 7 out of 7 in 4y75

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Paf-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-Paf-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:71.0
occ:1.00
 O Z:VAL198 2.5 57.7 1.0
O Z:THR192 2.7 65.9 1.0
O Z:HIS195 3.0 48.5 1.0
NH2 Z:ARG28 3.5 63.4 1.0
CG2 Z:THR192 3.7 62.9 1.0
O Z:ASP222 3.7 62.3 1.0
C Z:VAL198 3.7 58.4 1.0
C Z:THR192 3.7 63.3 1.0
O Z:ILE196 3.9 55.1 1.0
C Z:HIS195 4.0 53.6 1.0
CA Z:THR192 4.1 62.1 1.0
CA Z:ILE196 4.1 52.8 1.0
C Z:ILE196 4.2 54.1 1.0
OD1 Z:ASP222 4.4 61.8 1.0
NH2 H:ARG19 4.5 66.9 1.0
CB Z:THR192 4.5 61.1 1.0
N Z:VAL198 4.5 54.6 1.0
CZ Z:ARG28 4.5 60.6 1.0
N Z:ILE196 4.6 54.3 1.0
N Z:GLY199 4.6 58.1 1.0
CA Z:GLY199 4.6 59.7 1.0
C Z:ASP222 4.6 65.5 1.0
CA Z:VAL198 4.7 56.2 1.0
NH1 Z:ARG28 4.8 61.1 1.0
O Z:LYS220 4.9 63.1 1.0
N Z:GLU193 4.9 60.4 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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