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Magnesium in PDB 4y8u: Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pad-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pad-Ep, PDB code: 4y8u 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 (°) 137.120, 302.000, 145.440, 90.00, 113.16, 90.00
R / Rfree (%) 18.6 / 21.4

Other elements in 4y8u:

The structure of Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pad-Ep also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pad-Ep (pdb code 4y8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA2-H116D Mutant in Complex with Ac-Pad-Ep, PDB code: 4y8u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4y8u

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Magnesium binding site 1 out of 6 in the Yeast 20S Proteasome BETA2-H116D Mutant 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 BETA2-H116D Mutant in Complex with Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:61.4
occ:1.00
 O G:MET125 2.1 65.5 1.0
OG1 G:THR8 2.7 53.1 1.0
O G:ARG122 2.7 50.1 1.0
O G:TYR119 2.8 50.1 1.0
CG2 G:THR8 3.3 55.6 1.0
O G:ALA123 3.3 59.6 1.0
C G:MET125 3.3 62.1 1.0
CB G:THR8 3.5 54.6 1.0
C G:ALA123 3.7 57.7 1.0
CA G:ALA123 3.8 56.0 1.0
C G:ARG122 3.8 53.2 1.0
C G:TYR119 4.0 49.0 1.0
CA G:ARG126 4.1 54.8 1.0
N G:ARG126 4.1 56.5 1.0
N G:THR8 4.2 56.8 1.0
N G:MET125 4.2 63.5 1.0
N G:ALA123 4.2 53.5 1.0
CA G:MET125 4.4 65.3 1.0
CA G:THR8 4.5 55.5 1.0
CD G:PRO127 4.5 52.0 1.0
N G:TYR124 4.6 59.3 1.0
C G:ARG126 4.7 54.2 1.0
CA G:TYR119 4.8 48.2 1.0
N G:PRO127 4.9 53.0 1.0
O G:HOH403 4.9 41.2 1.0
C G:TYR124 4.9 61.3 1.0
CB G:MET125 5.0 70.8 1.0

Magnesium binding site 2 out of 6 in 4y8u

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Magnesium binding site 2 out of 6 in the Yeast 20S Proteasome BETA2-H116D Mutant 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 BETA2-H116D Mutant in Complex with Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:51.2
occ:1.00
 O K:ASP168 2.1 55.5 1.0
O K:ALA165 2.2 54.2 1.0
O W:ASP204 2.7 60.3 1.0
O K:SER171 2.9 59.5 1.0
C K:ASP168 3.1 56.0 1.0
C W:ASP204 3.3 63.6 1.0
C K:ALA165 3.3 54.5 1.0
CA K:ALA169 3.7 56.9 1.0
O K:HIS166 3.7 61.0 1.0
CA W:ASP204 3.7 66.0 1.0
N K:ALA169 3.7 56.8 1.0
C K:ALA169 4.0 57.1 1.0
C K:HIS166 4.0 58.1 1.0
O K:ALA169 4.0 57.1 1.0
CB W:ASP204 4.1 64.5 1.0
N K:ASP168 4.1 57.0 1.0
C K:SER171 4.1 58.2 1.0
OXT W:ASP204 4.2 66.3 1.0
CA K:ALA165 4.2 55.2 1.0
CA K:ASP168 4.2 56.0 1.0
NH1 K:ARG19 4.2 69.1 1.0
N K:HIS166 4.3 55.4 1.0
C K:ARG167 4.4 58.2 1.0
CA K:HIS166 4.4 57.2 1.0
O K:ALA164 4.5 53.6 1.0
N K:SER171 4.5 55.7 1.0
N K:ARG167 4.5 57.6 1.0
O K:ARG167 4.6 61.7 1.0
N K:TYR170 4.8 58.3 1.0
CA K:SER171 4.8 55.4 1.0
CZ K:ARG19 5.0 66.7 1.0
CB K:ASP168 5.0 57.2 1.0

Magnesium binding site 3 out of 6 in 4y8u

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Magnesium binding site 3 out of 6 in the Yeast 20S Proteasome BETA2-H116D Mutant 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 BETA2-H116D Mutant in Complex with Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:47.8
occ:1.00
 O N:SER169 2.7 51.0 1.0
O N:ILE163 3.0 52.9 1.0
O N:ASP166 3.1 57.6 1.0
CD1 a:LEU34 3.6 58.8 1.0
NH1 N:ARG19 3.7 55.1 1.0
C N:SER169 3.9 51.8 1.0
CA N:GLY167 4.1 51.6 1.0
O N:GLY167 4.1 54.6 1.0
C N:ASP166 4.1 52.0 1.0
CZ N:ARG19 4.1 54.3 1.0
C N:ILE163 4.1 54.0 1.0
NH2 N:ARG19 4.2 57.0 1.0
CG2 N:ILE163 4.2 51.9 1.0
C N:GLY167 4.3 52.1 1.0
CA N:GLY170 4.4 52.3 1.0
N N:GLY167 4.5 51.0 1.0
N N:GLY170 4.6 51.8 1.0
CA N:ILE163 4.8 51.8 1.0
N N:SER169 4.9 52.0 1.0
CG a:LEU34 4.9 58.7 1.0
CA N:SER169 4.9 49.9 1.0

Magnesium binding site 4 out of 6 in 4y8u

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Magnesium binding site 4 out of 6 in the Yeast 20S Proteasome BETA2-H116D Mutant 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 BETA2-H116D Mutant in Complex with Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:69.9
occ:1.00
 OXT L:ASP222 2.0 90.0 1.0
O V:ILE163 2.2 62.0 1.0
O V:ASP166 2.2 58.1 1.0
O V:SER169 2.7 59.1 1.0
C L:ASP222 3.1 86.2 1.0
C V:ASP166 3.1 58.5 1.0
C V:ILE163 3.3 61.8 1.0
CA L:ASP222 3.7 84.1 1.0
CA V:LEU167 3.8 58.0 1.0
N V:LEU167 3.8 58.5 1.0
C V:SER169 3.8 58.8 1.0
O V:TRP164 3.9 66.6 1.0
N V:ASP166 4.0 57.7 1.0
O V:GLY162 4.0 59.0 1.0
O L:ASP222 4.0 86.8 1.0
C V:TRP164 4.0 62.9 1.0
NH1 V:ARG19 4.1 75.2 1.0
CA V:ASP166 4.1 57.6 1.0
N V:TRP164 4.2 62.6 1.0
CA V:ILE163 4.3 60.8 1.0
C V:LEU167 4.3 58.1 1.0
CB L:ASP222 4.3 83.4 1.0
CA V:TRP164 4.3 63.1 1.0
N V:ASN165 4.5 61.4 1.0
O V:LEU167 4.5 56.9 1.0
N V:SER169 4.5 57.7 1.0
C V:ASN165 4.6 59.6 1.0
CA V:SER169 4.7 57.5 1.0
CZ V:ARG19 4.7 72.4 1.0
N V:GLY170 4.7 60.1 1.0
CA V:GLY170 4.7 63.4 1.0
CD2 V:LEU167 4.8 59.1 1.0
O L:ARG221 4.8 79.1 1.0
NH2 V:ARG19 4.9 77.6 1.0
C V:GLY162 4.9 59.3 1.0
N L:ASP222 5.0 80.8 1.0

Magnesium binding site 5 out of 6 in 4y8u

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Magnesium binding site 5 out of 6 in the Yeast 20S Proteasome BETA2-H116D Mutant 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 BETA2-H116D Mutant in Complex with Ac-Pad-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:56.0
occ:1.00
 O I:ASP204 2.3 74.9 1.0
O Y:ASP168 2.4 55.6 1.0
O Y:ALA165 2.5 56.0 1.0
O Y:SER171 2.9 53.1 1.0
C I:ASP204 3.1 72.3 1.0
C Y:ASP168 3.3 55.2 1.0
CA Y:ALA169 3.6 56.6 1.0
C Y:ALA165 3.6 53.8 1.0
CA I:ASP204 3.7 70.0 1.0
O Y:ALA169 3.7 53.6 1.0
C Y:ALA169 3.8 55.5 1.0
NH1 Y:ARG19 3.8 71.8 1.0
N Y:ALA169 3.9 56.4 1.0
OXT I:ASP204 4.0 75.7 1.0
O Y:HIS166 4.0 59.8 1.0
CB I:ASP204 4.0 71.0 1.0
C Y:SER171 4.1 55.0 1.0
C Y:HIS166 4.4 55.0 1.0
CA Y:ALA165 4.5 53.2 1.0
N Y:SER171 4.5 55.5 1.0
N Y:ASP168 4.5 56.0 1.0
CA Y:ASP168 4.5 56.0 1.0
CZ Y:ARG19 4.6 71.0 1.0
N Y:HIS166 4.6 53.7 1.0
N Y:TYR170 4.7 57.2 1.0
CA Y:HIS166 4.7 54.4 1.0
C Y:ARG167 4.7 56.2 1.0
CA Y:SER171 4.9 54.6 1.0
O Y:ALA164 4.9 56.2 1.0
NH2 Y:ARG19 4.9 70.6 1.0
CB Y:ALA169 4.9 57.9 1.0
O Y:ARG167 4.9 59.2 1.0
N Y:ARG167 5.0 53.6 1.0
CG I:ASP204 5.0 73.5 1.0

Magnesium binding site 6 out of 6 in 4y8u

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

b:70.7
occ:1.00
 O Z:VAL198 2.4 62.7 1.0
O Z:THR192 2.9 70.6 1.0
O Z:HIS195 3.2 55.8 1.0
O Z:ASP222 3.4 81.9 1.0
C Z:VAL198 3.6 63.7 1.0
NH2 Z:ARG28 3.7 73.5 1.0
CG2 Z:THR192 3.7 69.4 1.0
O Z:ILE196 3.8 67.8 1.0
C Z:THR192 3.9 70.5 1.0
CA Z:THR192 4.2 70.1 1.0
C Z:ILE196 4.2 62.6 1.0
OD1 Z:ASP222 4.2 85.5 1.0
CA Z:ILE196 4.2 61.2 1.0
C Z:HIS195 4.2 59.1 1.0
NH2 H:ARG19 4.3 77.8 1.0
N Z:VAL198 4.4 58.7 1.0
CA Z:GLY199 4.5 67.9 1.0
N Z:GLY199 4.5 65.2 1.0
C Z:ASP222 4.5 84.7 1.0
CB Z:THR192 4.5 68.7 1.0
CZ Z:ARG28 4.5 71.4 1.0
CA Z:VAL198 4.6 61.6 1.0
NH1 Z:ARG28 4.7 74.1 1.0
N Z:ILE196 4.7 59.0 1.0
O Z:LYS220 4.7 70.1 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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