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Magnesium in PDB 4y8o: Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep

Enzymatic activity of Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep

All present enzymatic activity of Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep, PDB code: 4y8o 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.390, 298.810, 146.440, 90.00, 113.09, 90.00
R / Rfree (%) 20.9 / 23.1

Other elements in 4y8o:

The structure of Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant 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 BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep (pdb code 4y8o). 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 BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep, PDB code: 4y8o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y8o

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant 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 BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:50.5
occ:1.00
 O G:MET125 2.4 51.2 1.0
OG1 G:THR8 2.6 49.2 1.0
O G:ARG122 2.6 49.2 1.0
O G:TYR119 2.8 46.0 1.0
CG2 G:THR8 3.2 50.0 1.0
O G:ALA123 3.3 54.1 1.0
CB G:THR8 3.5 49.8 1.0
C G:MET125 3.5 50.0 1.0
C G:ARG122 3.7 49.8 1.0
C G:ALA123 3.7 52.5 1.0
CA G:ALA123 3.8 50.4 1.0
C G:TYR119 4.0 44.4 1.0
N G:THR8 4.1 52.0 1.0
N G:ALA123 4.2 49.3 1.0
CA G:ARG126 4.3 45.3 1.0
N G:ARG126 4.3 46.6 1.0
N G:MET125 4.3 51.1 1.0
CA G:THR8 4.4 50.7 1.0
CA G:MET125 4.5 53.0 1.0
CD G:PRO127 4.5 42.6 1.0
CA G:TYR119 4.7 43.3 1.0
N G:TYR124 4.7 54.9 1.0
C G:ARG126 4.9 44.5 1.0
N G:THR120 5.0 43.0 1.0
CA G:ARG122 5.0 52.1 1.0

Magnesium binding site 2 out of 7 in 4y8o

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant 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 BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:61.2
occ:1.00
 O I:ASP177 2.5 47.6 1.0
O I:ALA174 2.6 50.8 1.0
O I:SER180 2.6 48.2 1.0
C I:ALA174 3.6 51.3 1.0
C I:ASP177 3.7 47.1 1.0
O I:HOH404 3.7 39.9 1.0
C I:SER180 3.8 46.8 1.0
CA I:ASP175 3.9 51.2 1.0
OXT I:ASP204 3.9 57.5 1.0
N I:ASP175 4.1 51.4 1.0
C I:ASP175 4.3 50.2 1.0
N I:ASP177 4.4 46.5 1.0
O I:ASP175 4.5 49.5 1.0
OD1 I:ASP175 4.5 52.7 1.0
N I:ALA178 4.6 45.1 1.0
O I:ALA178 4.6 46.6 1.0
CA I:ALA178 4.6 45.9 1.0
CA I:ASP177 4.6 47.7 1.0
CA I:GLY181 4.6 46.8 1.0
C I:ALA178 4.6 47.5 1.0
N I:GLY181 4.6 46.3 1.0
N I:SER180 4.6 47.1 1.0
CA I:ALA174 4.7 51.1 1.0
CA I:SER180 4.7 47.1 1.0
C I:ASP204 4.9 56.3 1.0
NH1 Y:ARG19 4.9 56.4 1.0
N I:ARG176 4.9 47.9 1.0
CB I:ALA174 4.9 51.7 1.0
O I:ASP204 4.9 59.3 1.0

Magnesium binding site 3 out of 7 in 4y8o

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant 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 BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:53.1
occ:1.00
 O Y:ASP168 2.3 48.7 1.0
O I:ASP204 2.3 59.3 1.0
O Y:ALA165 2.4 47.2 1.0
O Y:SER171 2.6 49.8 1.0
C I:ASP204 3.1 56.3 1.0
C Y:ASP168 3.3 45.9 1.0
C Y:ALA165 3.5 48.0 1.0
CA I:ASP204 3.6 56.3 1.0
CA Y:ALA169 3.6 45.7 1.0
C Y:SER171 3.8 48.3 1.0
O Y:ALA169 3.8 51.0 1.0
C Y:ALA169 3.8 47.3 1.0
N Y:ALA169 3.9 45.1 1.0
O Y:HIS166 4.0 49.4 1.0
CB I:ASP204 4.0 56.4 1.0
OXT I:ASP204 4.0 57.5 1.0
NH1 Y:ARG19 4.0 56.4 1.0
N Y:SER171 4.3 45.4 1.0
C Y:HIS166 4.3 48.1 1.0
CA Y:ALA165 4.4 47.5 1.0
N Y:ASP168 4.4 45.5 1.0
CA Y:ASP168 4.5 44.4 1.0
N Y:HIS166 4.5 48.3 1.0
CZ Y:ARG19 4.5 55.0 1.0
CA Y:SER171 4.6 46.2 1.0
CA Y:HIS166 4.6 47.5 1.0
O Y:ALA164 4.6 47.6 1.0
N Y:TYR170 4.7 46.7 1.0
N Y:GLY172 4.7 49.6 1.0
NH2 Y:ARG19 4.8 58.3 1.0
C Y:ARG167 4.8 46.7 1.0
CA Y:GLY172 4.8 51.6 1.0
N Y:ARG167 4.9 48.1 1.0
N I:ASP204 5.0 55.9 1.0
CB Y:SER171 5.0 46.0 1.0

Magnesium binding site 4 out of 7 in 4y8o

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant 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 BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:61.3
occ:1.00
 O K:ASP168 2.2 48.0 1.0
O K:ALA165 2.3 45.9 1.0
O W:ASP204 2.3 53.0 1.0
O K:SER171 2.8 46.2 1.0
C K:ASP168 3.1 45.3 1.0
C W:ASP204 3.2 51.2 1.0
C K:ALA165 3.4 46.3 1.0
CA K:ALA169 3.6 44.8 1.0
O K:HIS166 3.7 49.6 1.0
CA W:ASP204 3.7 50.8 1.0
N K:ALA169 3.7 44.7 1.0
C K:ALA169 3.9 47.0 1.0
O K:ALA169 3.9 50.4 1.0
C K:SER171 4.0 46.1 1.0
C K:HIS166 4.0 46.9 1.0
OXT W:ASP204 4.0 53.1 1.0
CB W:ASP204 4.1 50.3 1.0
N K:ASP168 4.2 45.3 1.0
CA K:ASP168 4.3 43.9 1.0
NH1 K:ARG19 4.3 53.1 1.0
N K:HIS166 4.3 45.9 1.0
CA K:ALA165 4.3 46.9 1.0
CA K:HIS166 4.4 46.5 1.0
N K:SER171 4.4 44.2 1.0
O K:ALA164 4.5 47.7 1.0
C K:ARG167 4.6 46.2 1.0
N K:ARG167 4.6 45.5 1.0
CA K:SER171 4.7 44.5 1.0
N K:TYR170 4.7 45.9 1.0
CZ K:ARG19 4.8 52.1 1.0
N K:GLY172 4.9 47.2 1.0
O K:ARG167 4.9 47.8 1.0
CB K:ALA169 5.0 43.8 1.0

Magnesium binding site 5 out of 7 in 4y8o

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant 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 BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:63.6
occ:1.00
 O V:ASP166 2.3 55.2 1.0
O V:ILE163 2.4 57.8 1.0
OXT L:ASP222 2.4 61.5 1.0
C L:ASP222 3.1 61.9 1.0
C V:ASP166 3.1 56.1 1.0
O V:TRP164 3.1 62.5 1.0
C V:TRP164 3.3 57.6 1.0
C V:ILE163 3.4 59.1 1.0
N V:ASP166 3.4 53.2 1.0
O V:SER169 3.5 53.8 1.0
N V:ASN165 3.7 54.4 1.0
CA L:ASP222 3.7 60.5 1.0
O L:ASP222 3.7 67.1 1.0
N V:LEU167 3.8 56.2 1.0
CA V:TRP164 3.8 60.1 1.0
O V:GLY162 3.8 54.5 1.0
CA V:ASP166 3.9 54.1 1.0
C V:ASN165 3.9 54.4 1.0
N V:TRP164 4.0 57.5 1.0
CA V:LEU167 4.0 55.9 1.0
CA V:ASN165 4.2 55.5 1.0
CA V:ILE163 4.5 61.1 1.0
O L:ARG221 4.6 57.6 1.0
CB L:ASP222 4.6 60.0 1.0
CD2 V:LEU167 4.6 54.3 1.0
O V:ASN165 4.6 55.3 1.0
C V:SER169 4.7 55.7 1.0
C V:LEU167 4.8 56.0 1.0
CD1 L:ILE35 4.8 55.1 1.0
C V:GLY162 4.9 57.3 1.0
N L:ASP222 4.9 58.6 1.0
CB V:ASP166 4.9 52.8 1.0
NH1 V:ARG19 5.0 59.6 1.0

Magnesium binding site 6 out of 7 in 4y8o

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant 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 BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:62.2
occ:1.00
 O N:SER169 2.5 48.3 1.0
O N:ILE163 2.7 48.4 1.0
O N:ASP166 2.8 47.0 1.0
CD1 a:LEU34 3.5 47.9 1.0
C N:SER169 3.7 45.4 1.0
C N:ILE163 3.8 48.1 1.0
C N:ASP166 3.9 44.6 1.0
NH1 N:ARG19 4.0 46.6 1.0
CG2 N:ILE163 4.1 47.3 1.0
CA N:GLY167 4.1 43.6 1.0
O N:GLY167 4.4 44.6 1.0
CA N:GLY170 4.4 47.5 1.0
N N:GLY167 4.4 44.2 1.0
CZ N:ARG19 4.4 46.0 1.0
C N:GLY167 4.5 43.6 1.0
CA N:ILE163 4.5 47.0 1.0
N N:GLY170 4.5 46.6 1.0
NH2 N:ARG19 4.5 46.4 1.0
N N:SER169 4.6 41.7 1.0
O a:HOH308 4.6 49.6 1.0
CA N:SER169 4.7 41.5 1.0
N N:LYS164 4.8 48.3 1.0
CG a:LEU34 4.9 48.4 1.0
O N:LYS164 4.9 51.9 1.0
CB N:ILE163 4.9 46.5 1.0
C N:LYS164 4.9 49.6 1.0

Magnesium binding site 7 out of 7 in 4y8o

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome BETA7-DELTA7_CTER Mutant 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 BETA7-DELTA7_CTER Mutant in Complex with Ac-Paf- Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:60.5
occ:1.00
 O Z:VAL198 2.5 55.0 1.0
O Z:THR192 2.7 58.7 1.0
CG2 Z:THR192 3.3 61.2 1.0
O Z:HIS195 3.4 48.8 1.0
O Z:ASP222 3.6 65.5 1.0
C Z:THR192 3.6 60.5 1.0
NH2 Z:ARG28 3.6 62.7 1.0
C Z:VAL198 3.7 54.9 1.0
CA Z:THR192 3.9 60.4 1.0
OD1 Z:ASP222 4.1 65.4 1.0
CB Z:THR192 4.2 59.7 1.0
O Z:ILE196 4.3 53.1 1.0
CA Z:GLY199 4.4 55.8 1.0
C Z:HIS195 4.5 50.5 1.0
NH2 H:ARG19 4.5 63.6 1.0
N Z:GLY199 4.5 54.2 1.0
CZ Z:ARG28 4.5 59.6 1.0
C Z:ASP222 4.5 65.8 1.0
O Z:LYS220 4.6 62.9 1.0
CA Z:ILE196 4.6 51.0 1.0
C Z:ILE196 4.6 50.4 1.0
NH1 Z:ARG28 4.7 60.8 1.0
N Z:VAL198 4.7 51.8 1.0
CA Z:VAL198 4.8 53.2 1.0
N Z:GLU193 4.8 60.5 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 23:01:28 2024

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