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Magnesium in PDB 4y8t: Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-Ep

Enzymatic activity of Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-Ep

All present enzymatic activity of Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-Ep, PDB code: 4y8t 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 (°) 136.400, 301.590, 145.630, 90.00, 113.03, 90.00
R / Rfree (%) 18.1 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-Ep (pdb code 4y8t). 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 BETA2-H116D Mutant in Complex with Ac-Pae-Ep, PDB code: 4y8t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y8t

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-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 BETA2-H116D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:65.2
occ:1.00
 O G:MET125 2.2 57.5 1.0
O G:ARG122 2.5 53.2 1.0
OG1 G:THR8 2.6 51.0 1.0
O G:TYR119 2.8 54.1 1.0
O G:ALA123 3.3 62.3 1.0
CG2 G:THR8 3.3 56.2 1.0
C G:MET125 3.4 62.0 1.0
CB G:THR8 3.5 52.2 1.0
C G:ARG122 3.6 54.7 1.0
C G:ALA123 3.6 56.9 1.0
CA G:ALA123 3.7 52.6 1.0
C G:TYR119 3.9 51.6 1.0
N G:ALA123 4.1 53.3 1.0
N G:MET125 4.1 64.6 1.0
N G:THR8 4.2 54.7 1.0
N G:ARG126 4.2 58.9 1.0
CA G:ARG126 4.3 55.5 1.0
CA G:MET125 4.3 66.5 1.0
CA G:THR8 4.5 53.4 1.0
N G:TYR124 4.5 57.9 1.0
O G:HOH424 4.6 64.2 1.0
CD G:PRO127 4.6 49.3 1.0
CA G:TYR119 4.6 49.7 1.0
CA G:ARG122 4.8 56.5 1.0
N G:ARG122 4.8 52.8 1.0
CB G:MET125 4.9 70.2 1.0
C G:TYR124 4.9 61.0 1.0
C G:ARG126 4.9 52.0 1.0
N G:THR120 5.0 49.5 1.0

Magnesium binding site 2 out of 7 in 4y8t

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-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 BETA2-H116D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:63.1
occ:1.00
 O I:HOH416 2.5 60.6 1.0
O I:ASP177 2.5 57.8 1.0
O I:SER180 2.9 59.8 1.0
O I:ALA174 3.2 52.1 1.0
O Y:HOH412 3.5 52.0 1.0
C I:ASP177 3.6 56.8 1.0
OXT I:ASP204 3.6 72.0 1.0
O I:ALA178 4.0 64.4 1.0
CA I:ALA178 4.1 52.6 1.0
C I:SER180 4.1 60.0 1.0
O I:HOH408 4.1 55.7 1.0
C I:ALA178 4.1 60.2 1.0
O I:ASP204 4.1 69.1 1.0
NH1 Y:ARG19 4.2 68.5 1.0
N I:ALA178 4.2 54.5 1.0
C I:ALA174 4.3 54.0 1.0
C I:ASP204 4.3 68.1 1.0
CA I:ASP175 4.5 57.0 1.0
NH2 Y:ARG19 4.5 68.5 1.0
N I:ASP177 4.6 58.6 1.0
CA I:ASP177 4.6 57.5 1.0
N I:SER180 4.7 56.2 1.0
CZ Y:ARG19 4.7 68.5 1.0
C I:ASP175 4.7 58.2 1.0
O I:ASP175 4.7 67.2 1.0
N I:ASP175 4.8 54.8 1.0
N I:LEU179 4.9 61.4 1.0
CA I:SER180 5.0 56.8 1.0
CA I:GLY181 5.0 58.0 1.0
N I:GLY181 5.0 58.7 1.0

Magnesium binding site 3 out of 7 in 4y8t

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-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 BETA2-H116D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:65.9
occ:1.00
 O K:ALA165 2.3 57.3 1.0
O K:ASP168 2.3 54.6 1.0
O W:ASP204 2.4 47.1 1.0
O K:SER171 2.7 58.2 1.0
C W:ASP204 3.1 47.2 1.0
C K:ASP168 3.3 54.0 1.0
C K:ALA165 3.5 57.1 1.0
CA W:ASP204 3.5 55.7 1.0
CA K:ALA169 3.6 54.6 1.0
NH1 K:ARG19 3.7 72.1 1.0
CB W:ASP204 3.8 55.0 1.0
N K:ALA169 3.8 54.1 1.0
C K:ALA169 3.8 56.7 1.0
O K:ALA169 3.9 57.9 1.0
C K:SER171 3.9 56.3 1.0
OXT W:ASP204 4.0 55.6 1.0
O K:HIS166 4.1 59.3 1.0
CA K:ALA165 4.2 56.5 1.0
C K:HIS166 4.4 57.5 1.0
N K:SER171 4.4 52.5 1.0
N K:ASP168 4.5 56.1 1.0
CZ K:ARG19 4.5 70.5 1.0
CA K:ASP168 4.5 53.9 1.0
N K:HIS166 4.5 59.1 1.0
N K:TYR170 4.6 57.9 1.0
CA K:HIS166 4.7 59.7 1.0
CA K:SER171 4.7 52.9 1.0
O K:ALA164 4.8 60.0 1.0
NH2 K:ARG19 4.8 71.4 1.0
CG W:ASP204 4.8 56.5 1.0
C K:ARG167 4.8 54.9 1.0
N K:GLY172 4.8 57.2 1.0
CA K:GLY172 4.9 57.9 1.0
N W:ASP204 4.9 55.7 1.0
O W:HOH306 4.9 60.6 1.0
N K:ARG167 5.0 54.0 1.0
CB K:ALA169 5.0 53.9 1.0

Magnesium binding site 4 out of 7 in 4y8t

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-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 BETA2-H116D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:57.9
occ:1.00
 O N:SER169 2.8 59.1 1.0
O N:ILE163 2.8 50.7 1.0
O N:HOH323 2.8 42.5 1.0
O N:ASP166 3.1 35.2 1.0
CD1 a:LEU34 3.5 57.6 1.0
NH1 N:ARG19 3.6 61.9 1.0
C N:SER169 3.9 52.8 1.0
C N:ILE163 4.0 50.3 1.0
CA N:GLY167 4.0 46.4 1.0
C N:ASP166 4.0 34.1 1.0
CG2 N:ILE163 4.1 45.1 1.0
O N:GLY167 4.3 50.8 1.0
CZ N:ARG19 4.3 61.8 1.0
C N:GLY167 4.4 48.4 1.0
N N:GLY167 4.4 43.5 1.0
CA N:GLY170 4.4 55.6 1.0
NH2 N:ARG19 4.5 62.6 1.0
N N:GLY170 4.6 54.0 1.0
CA N:ILE163 4.6 48.4 1.0
CG a:LEU34 4.7 59.2 1.0
N N:SER169 4.9 50.8 1.0
CA N:SER169 4.9 49.1 1.0
CB N:ILE163 5.0 47.2 1.0
N N:LYS164 5.0 53.5 1.0

Magnesium binding site 5 out of 7 in 4y8t

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-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 BETA2-H116D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:74.7
occ:1.00
 OXT L:ASP222 2.2 75.5 1.0
O V:ASP166 2.2 62.1 1.0
O V:SER169 2.2 59.8 1.0
O V:ILE163 2.2 61.5 1.0
O V:HOH416 2.5 52.4 1.0
C L:ASP222 3.1 75.5 1.0
C V:ASP166 3.2 59.4 1.0
C V:ILE163 3.3 59.9 1.0
C V:SER169 3.4 58.0 1.0
CA L:ASP222 3.7 73.5 1.0
O V:GLY162 3.8 50.6 1.0
NH1 V:ARG19 3.9 76.6 1.0
CA V:LEU167 3.9 63.0 1.0
N V:LEU167 3.9 62.7 1.0
CA V:ILE163 4.1 58.5 1.0
O L:ASP222 4.1 78.3 1.0
N V:ASP166 4.1 58.3 1.0
CB L:ASP222 4.2 71.0 1.0
N V:SER169 4.2 55.6 1.0
CA V:ASP166 4.2 57.0 1.0
N V:GLY170 4.3 57.5 1.0
N V:TRP164 4.3 59.8 1.0
CA V:SER169 4.3 54.4 1.0
CA V:GLY170 4.3 59.5 1.0
C V:LEU167 4.3 60.9 1.0
C V:TRP164 4.4 61.3 1.0
CZ V:ARG19 4.4 70.9 1.0
O V:TRP164 4.5 61.2 1.0
NH2 V:ARG19 4.5 68.8 1.0
CA V:TRP164 4.6 59.9 1.0
O V:LEU167 4.6 61.2 1.0
N V:ASN165 4.7 62.0 1.0
CB V:SER169 4.8 52.6 1.0
C V:GLY162 4.8 52.2 1.0
C V:ASN165 4.9 59.1 1.0
N V:ILE163 4.9 56.2 1.0
N V:GLY168 5.0 56.6 1.0
CB V:ASP166 5.0 55.7 1.0

Magnesium binding site 6 out of 7 in 4y8t

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-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 BETA2-H116D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:56.9
occ:1.00
 O Y:ASP168 2.3 56.9 1.0
O I:ASP204 2.4 69.1 1.0
O Y:ALA165 2.5 61.9 1.0
O Y:SER171 2.5 55.4 1.0
O Y:HOH417 2.6 62.5 1.0
C I:ASP204 3.2 68.1 1.0
C Y:ASP168 3.3 53.5 1.0
NH1 Y:ARG19 3.5 68.5 1.0
CA Y:ALA169 3.6 54.2 1.0
C Y:ALA165 3.6 55.4 1.0
O Y:ALA169 3.7 56.5 1.0
CA I:ASP204 3.7 67.4 1.0
C Y:ALA169 3.7 56.7 1.0
C Y:SER171 3.7 56.9 1.0
N Y:ALA169 3.8 55.4 1.0
CB I:ASP204 3.9 64.2 1.0
OXT I:ASP204 4.0 72.0 1.0
N Y:SER171 4.2 54.6 1.0
CZ Y:ARG19 4.2 68.5 1.0
CA Y:ALA165 4.3 51.0 1.0
O Y:HIS166 4.3 52.0 1.0
N Y:TYR170 4.5 57.2 1.0
CA Y:ASP168 4.5 51.9 1.0
CA Y:SER171 4.6 54.4 1.0
N Y:ASP168 4.6 55.7 1.0
C Y:HIS166 4.6 52.0 1.0
NH2 Y:ARG19 4.6 68.5 1.0
N Y:HIS166 4.7 55.4 1.0
N Y:GLY172 4.7 58.7 1.0
CA Y:GLY172 4.8 60.4 1.0
CG I:ASP204 4.8 64.4 1.0
O Y:ALA164 4.8 51.1 1.0
CA Y:HIS166 4.9 52.1 1.0
CB Y:ALA169 4.9 53.5 1.0
C Y:ARG167 5.0 57.7 1.0

Magnesium binding site 7 out of 7 in 4y8t

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pae-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 BETA2-H116D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:60.9
occ:1.00
 O Z:THR192 2.4 57.2 1.0
O Z:VAL198 2.5 56.6 1.0
O Z:HIS195 2.9 55.9 1.0
C Z:THR192 3.4 57.6 1.0
CG2 Z:THR192 3.7 58.2 1.0
C Z:VAL198 3.7 54.7 1.0
CA Z:THR192 3.8 57.8 1.0
C Z:HIS195 3.9 55.8 1.0
O Z:ASP222 3.9 68.5 1.0
NH2 Z:ARG28 3.9 59.6 1.0
O Z:ILE196 4.0 63.9 1.0
CA Z:ILE196 4.1 59.0 1.0
C Z:ILE196 4.2 59.5 1.0
OD1 Z:ASP222 4.2 65.2 1.0
NH2 H:ARG19 4.3 74.9 1.0
CB Z:THR192 4.4 58.2 1.0
N Z:ILE196 4.4 56.5 1.0
N Z:VAL198 4.5 49.9 1.0
CA Z:VAL198 4.6 50.5 1.0
N Z:GLY199 4.6 54.5 1.0
N Z:GLU193 4.6 57.7 1.0
CA Z:GLY199 4.7 57.0 1.0
C Z:ASP222 4.8 70.9 1.0
N Z:HIS195 4.9 53.9 1.0
CB Z:VAL198 4.9 49.5 1.0
CZ Z:ARG28 4.9 61.3 1.0
O Z:ALA191 4.9 63.2 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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