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Magnesium in PDB 4y8s: Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Lae-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Lae-Ep, PDB code: 4y8s 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 (°) 136.350, 300.080, 144.780, 90.00, 112.99, 90.00
R / Rfree (%) 18.8 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Lae-Ep (pdb code 4y8s). 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-Lae-Ep, PDB code: 4y8s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y8s

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

b:57.5
occ:1.00
 O G:MET125 2.2 52.6 1.0
O G:ARG122 2.4 52.6 1.0
O G:TYR119 2.6 53.1 1.0
OG1 G:THR8 2.6 49.4 1.0
C G:MET125 3.4 54.5 1.0
O G:ALA123 3.4 56.0 1.0
CG2 G:THR8 3.5 52.8 1.0
C G:ARG122 3.5 51.1 1.0
CB G:THR8 3.6 50.8 1.0
CA G:ALA123 3.6 50.8 1.0
C G:ALA123 3.7 54.1 1.0
C G:TYR119 3.8 49.6 1.0
N G:ALA123 4.0 48.4 1.0
N G:MET125 4.1 53.7 1.0
N G:ARG126 4.3 52.4 1.0
CA G:MET125 4.3 57.3 1.0
CA G:ARG126 4.3 50.1 1.0
N G:THR8 4.3 52.9 1.0
CA G:TYR119 4.5 48.3 1.0
CD G:PRO127 4.6 46.9 1.0
N G:TYR124 4.6 56.3 1.0
CA G:THR8 4.6 52.1 1.0
CA G:ARG122 4.8 54.1 1.0
CB G:MET125 4.8 62.6 1.0
N G:THR120 4.8 48.5 1.0
N G:ARG122 4.8 51.3 1.0
C G:ARG126 4.9 50.0 1.0
C G:TYR124 5.0 53.8 1.0
CB G:ALA123 5.0 50.9 1.0
CB G:TYR119 5.0 50.3 1.0

Magnesium binding site 2 out of 7 in 4y8s

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

b:57.4
occ:1.00
 OE1 H:GLN91 2.5 54.4 1.0
OD1 N:ASP51 3.0 53.3 1.0
CD H:GLN91 3.3 54.2 1.0
NE2 H:GLN91 3.5 57.5 1.0
OD2 N:ASP51 3.6 56.2 1.0
O N:ASN92 3.6 49.7 1.0
CG N:ASP51 3.7 50.9 1.0
O N:HOH303 4.4 47.9 1.0
C N:ASN92 4.7 49.8 1.0
CG H:GLN91 4.8 49.8 1.0

Magnesium binding site 3 out of 7 in 4y8s

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

b:69.7
occ:1.00
 O I:SER180 2.5 65.2 1.0
O I:ALA174 2.6 57.3 1.0
O I:ASP177 2.7 47.1 1.0
C I:ALA174 3.6 60.0 1.0
C I:SER180 3.8 60.8 1.0
OXT I:ASP204 3.8 61.9 1.0
C I:ASP177 3.8 49.6 1.0
CA I:ASP175 3.8 61.8 1.0
N I:ASP175 4.1 62.0 1.0
C I:ASP175 4.3 59.7 1.0
OD1 I:ASP175 4.4 63.4 1.0
CA I:GLY181 4.4 57.8 1.0
O I:ASP175 4.4 62.9 1.0
N I:ASP177 4.5 51.4 1.0
N I:GLY181 4.5 59.0 1.0
O I:ASP204 4.6 65.8 1.0
C I:ASP204 4.6 59.9 1.0
CA I:ALA178 4.7 51.0 1.0
N I:ALA178 4.7 49.1 1.0
O I:ALA178 4.7 56.4 1.0
C I:ALA178 4.7 54.9 1.0
N I:SER180 4.7 58.1 1.0
CA I:ASP177 4.7 51.2 1.0
CA I:ALA174 4.8 57.9 1.0
CA I:SER180 4.8 58.4 1.0
NH1 Y:ARG19 4.9 75.3 1.0
CB I:ALA174 5.0 57.9 1.0

Magnesium binding site 4 out of 7 in 4y8s

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Lae-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-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:61.9
occ:1.00
 O K:ALA165 2.3 56.7 1.0
O K:ASP168 2.3 57.8 1.0
O W:ASP204 2.6 66.1 1.0
O K:SER171 2.8 61.4 1.0
C W:ASP204 3.1 64.7 1.0
C K:ASP168 3.3 58.1 1.0
C K:ALA165 3.5 54.2 1.0
CA W:ASP204 3.5 60.7 1.0
CA K:ALA169 3.6 60.5 1.0
N K:ALA169 3.8 59.5 1.0
O K:ALA169 3.8 63.8 1.0
O K:HIS166 3.8 51.2 1.0
C K:ALA169 3.8 63.2 1.0
CB W:ASP204 3.9 57.3 1.0
OXT W:ASP204 3.9 71.5 1.0
C K:SER171 4.0 62.2 1.0
NH1 K:ARG19 4.0 76.3 1.0
C K:HIS166 4.2 51.9 1.0
CA K:ALA165 4.3 54.3 1.0
N K:SER171 4.4 62.7 1.0
N K:HIS166 4.4 52.7 1.0
N K:ASP168 4.4 56.4 1.0
CA K:ASP168 4.5 56.0 1.0
CA K:HIS166 4.5 52.4 1.0
CZ K:ARG19 4.6 75.2 1.0
O K:ALA164 4.6 57.6 1.0
N K:TYR170 4.7 64.0 1.0
CA K:SER171 4.7 59.3 1.0
C K:ARG167 4.7 54.2 1.0
NH2 K:ARG19 4.8 79.0 1.0
N W:ASP204 4.8 60.5 1.0
N K:ARG167 4.9 50.4 1.0
CB K:ALA169 5.0 61.4 1.0
N K:GLY172 5.0 65.0 1.0

Magnesium binding site 5 out of 7 in 4y8s

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Lae-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-Lae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:54.9
occ:1.00
 O N:ILE163 2.6 49.2 1.0
O N:SER169 2.6 59.4 1.0
O N:ASP166 3.0 60.0 1.0
C N:ILE163 3.7 48.6 1.0
CD1 a:LEU34 3.7 59.5 1.0
NH1 N:ARG19 3.7 58.2 1.0
CG2 N:ILE163 3.7 44.9 1.0
C N:SER169 3.7 53.0 1.0
C N:ASP166 4.0 52.6 1.0
CA N:GLY167 4.1 52.1 1.0
CA N:GLY170 4.2 55.7 1.0
CA N:ILE163 4.3 46.8 1.0
CZ N:ARG19 4.4 55.2 1.0
N N:GLY170 4.4 54.2 1.0
O N:GLY167 4.4 47.9 1.0
N N:GLY167 4.5 52.4 1.0
C N:GLY167 4.5 49.2 1.0
CB N:ILE163 4.6 47.1 1.0
NH2 N:ARG19 4.7 48.4 1.0
N N:LYS164 4.7 52.7 1.0
CA N:SER169 4.8 46.0 1.0
N N:SER169 4.8 46.6 1.0
CG a:LEU34 5.0 58.3 1.0

Magnesium binding site 6 out of 7 in 4y8s

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

b:54.5
occ:1.00
 O V:ASP166 2.1 52.7 1.0
OXT L:ASP222 2.2 67.8 1.0
O V:ILE163 2.3 59.6 1.0
O V:SER169 2.4 56.6 1.0
C L:ASP222 3.0 67.5 1.0
C V:ASP166 3.0 52.7 1.0
C V:ILE163 3.3 58.6 1.0
C V:SER169 3.6 53.0 1.0
CA L:ASP222 3.7 65.1 1.0
N V:LEU167 3.8 53.7 1.0
O L:ASP222 3.8 72.1 1.0
O V:GLY162 3.8 57.6 1.0
CA V:LEU167 3.8 53.4 1.0
N V:ASP166 3.8 53.3 1.0
NH1 V:ARG19 3.9 66.7 1.0
O V:TRP164 3.9 57.9 1.0
CA V:ASP166 4.0 52.4 1.0
C V:TRP164 4.0 59.1 1.0
CA V:ILE163 4.2 59.9 1.0
N V:TRP164 4.2 56.7 1.0
CB L:ASP222 4.3 65.0 1.0
N V:SER169 4.3 48.5 1.0
C V:LEU167 4.3 51.5 1.0
CA V:TRP164 4.4 57.4 1.0
CA V:SER169 4.5 49.2 1.0
N V:ASN165 4.5 57.3 1.0
C V:ASN165 4.6 54.6 1.0
CZ V:ARG19 4.6 64.6 1.0
N V:GLY170 4.6 54.9 1.0
CA V:GLY170 4.6 56.7 1.0
O V:LEU167 4.7 53.1 1.0
NH2 V:ARG19 4.7 66.1 1.0
C V:GLY162 4.8 55.2 1.0
CD2 V:LEU167 4.8 53.5 1.0
CB V:ASP166 4.9 51.3 1.0
CB V:SER169 4.9 49.5 1.0
O L:ARG221 4.9 61.2 1.0
N V:GLY168 5.0 47.5 1.0
N L:ASP222 5.0 62.8 1.0
N V:ILE163 5.0 56.9 1.0

Magnesium binding site 7 out of 7 in 4y8s

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

b:55.3
occ:1.00
 O Y:ASP168 2.3 55.6 1.0
O Y:ALA165 2.4 51.8 1.0
O I:ASP204 2.6 65.8 1.0
O Y:SER171 2.7 60.3 1.0
C I:ASP204 3.2 59.9 1.0
C Y:ASP168 3.3 53.4 1.0
C Y:ALA165 3.5 51.3 1.0
CA Y:ALA169 3.5 53.8 1.0
CA I:ASP204 3.6 59.4 1.0
O Y:ALA169 3.7 56.8 1.0
C Y:ALA169 3.8 53.0 1.0
N Y:ALA169 3.8 54.2 1.0
C Y:SER171 3.9 58.1 1.0
NH1 Y:ARG19 3.9 75.3 1.0
CB I:ASP204 4.0 58.4 1.0
O Y:HIS166 4.0 55.1 1.0
OXT I:ASP204 4.0 61.9 1.0
N Y:SER171 4.3 58.8 1.0
C Y:HIS166 4.3 53.2 1.0
CA Y:ALA165 4.4 50.3 1.0
CA Y:ASP168 4.5 51.5 1.0
CZ Y:ARG19 4.5 70.4 1.0
N Y:ASP168 4.5 52.3 1.0
N Y:HIS166 4.5 51.4 1.0
N Y:TYR170 4.6 53.8 1.0
CA Y:SER171 4.6 54.6 1.0
CA Y:HIS166 4.7 51.3 1.0
O Y:ALA164 4.7 56.1 1.0
NH2 Y:ARG19 4.7 71.9 1.0
C Y:ARG167 4.8 53.6 1.0
N Y:GLY172 4.9 59.5 1.0
CB Y:ALA169 4.9 56.1 1.0
CA Y:GLY172 5.0 61.6 1.0
N Y:ARG167 5.0 51.7 1.0
N I:ASP204 5.0 56.3 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 23:01:29 2024

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