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Magnesium in PDB 4ya5: Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Pae-Ep

Enzymatic activity of Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Pae-Ep

All present enzymatic activity of Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Pae-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Pae-Ep, PDB code: 4ya5 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.710, 301.320, 145.930, 90.00, 113.18, 90.00
R / Rfree (%) 22.6 / 24.2

Other elements in 4ya5:

The structure of Yeast 20S Proteasome BETA2-H114D Mutant in Complex with Ac-Pae-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-H114D Mutant in Complex with Ac-Pae-Ep (pdb code 4ya5). 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-H114D Mutant in Complex with Ac-Pae-Ep, PDB code: 4ya5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4ya5

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:43.5
occ:1.00
 O G:MET125 2.2 37.6 1.0
O G:ARG122 2.4 34.4 1.0
OG1 G:THR8 2.6 36.8 1.0
O G:TYR119 2.7 33.1 1.0
CG2 G:THR8 3.3 37.5 1.0
C G:MET125 3.4 40.5 1.0
O G:ALA123 3.4 39.0 1.0
C G:ARG122 3.5 36.3 1.0
CB G:THR8 3.5 37.3 1.0
C G:ALA123 3.6 39.0 1.0
CA G:ALA123 3.6 37.6 1.0
C G:TYR119 3.9 32.1 1.0
N G:ALA123 4.0 36.0 1.0
N G:MET125 4.1 43.0 1.0
N G:THR8 4.2 38.3 1.0
N G:ARG126 4.3 37.7 1.0
CA G:MET125 4.3 44.5 1.0
CA G:ARG126 4.3 36.3 1.0
O G:HOH441 4.4 49.8 1.0
CA G:THR8 4.5 38.1 1.0
N G:TYR124 4.5 40.2 1.0
CD G:PRO127 4.7 32.6 1.0
CA G:TYR119 4.7 31.9 1.0
CA G:ARG122 4.7 38.5 1.0
N G:ARG122 4.8 36.3 1.0
CB G:MET125 4.8 49.7 1.0
N G:THR120 4.9 31.5 1.0
C G:TYR124 4.9 41.5 1.0
C G:ARG126 4.9 34.9 1.0
CB G:ALA123 5.0 37.8 1.0
CA G:THR120 5.0 31.6 1.0

Magnesium binding site 2 out of 7 in 4ya5

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:63.8
occ:1.00
 O I:ASP177 2.3 37.6 1.0
O I:SER180 2.7 40.2 1.0
O I:ALA174 3.1 37.0 1.0
C I:ASP177 3.4 37.5 1.0
O I:ALA178 3.9 42.0 1.0
CA I:ALA178 3.9 37.1 1.0
C I:SER180 4.0 39.8 1.0
OXT I:ASP204 4.0 48.5 1.0
C I:ALA178 4.0 38.6 1.0
N I:ALA178 4.1 35.9 1.0
NH1 Y:ARG19 4.2 45.8 1.0
C I:ALA174 4.2 37.6 1.0
N I:ASP177 4.4 37.8 1.0
N I:SER180 4.5 37.9 1.0
O I:ASP204 4.5 44.3 1.0
CA I:ASP175 4.5 41.1 1.0
CA I:ASP177 4.5 37.5 1.0
NH2 Y:ARG19 4.6 46.6 1.0
C I:ASP175 4.7 41.0 1.0
C I:ASP204 4.7 46.6 1.0
O I:ASP175 4.7 44.0 1.0
CZ Y:ARG19 4.8 45.0 1.0
CA I:SER180 4.8 39.2 1.0
N I:LEU179 4.8 38.0 1.0
N I:ASP175 4.8 39.5 1.0
N I:GLY181 4.9 39.1 1.0
CA I:GLY181 5.0 39.0 1.0

Magnesium binding site 3 out of 7 in 4ya5

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:37.0
occ:1.00
 O Y:SER171 2.3 36.7 1.0
O Y:ASP168 2.3 35.6 1.0
O Y:HOH417 2.3 22.9 1.0
O Y:ALA165 2.4 35.6 1.0
O I:ASP204 2.5 44.3 1.0
C I:ASP204 3.3 46.6 1.0
C Y:ASP168 3.3 35.6 1.0
C Y:SER171 3.5 37.2 1.0
C Y:ALA165 3.5 35.7 1.0
NH1 Y:ARG19 3.6 45.8 1.0
O Y:ALA169 3.7 36.9 1.0
CA Y:ALA169 3.8 35.9 1.0
C Y:ALA169 3.8 36.5 1.0
CA I:ASP204 3.8 45.6 1.0
N Y:ALA169 4.0 35.8 1.0
CB I:ASP204 4.0 45.7 1.0
N Y:SER171 4.0 36.8 1.0
CA Y:ALA165 4.1 36.0 1.0
OXT I:ASP204 4.2 48.5 1.0
CA Y:SER171 4.3 36.8 1.0
CZ Y:ARG19 4.4 45.0 1.0
N Y:GLY172 4.5 37.4 1.0
O Y:HIS166 4.5 36.0 1.0
CA Y:ASP168 4.5 36.1 1.0
N Y:TYR170 4.5 37.2 1.0
N Y:ASP168 4.5 36.7 1.0
N Y:HIS166 4.6 35.9 1.0
O Y:ALA164 4.6 36.2 1.0
C Y:HIS166 4.6 35.1 1.0
CA Y:GLY172 4.6 37.4 1.0
NH2 Y:ARG19 4.7 46.6 1.0
CB Y:SER171 4.7 36.4 1.0
CA Y:HIS166 4.9 35.5 1.0
CG I:ASP204 4.9 44.9 1.0
CB Y:ALA165 4.9 36.5 1.0

Magnesium binding site 4 out of 7 in 4ya5

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:42.9
occ:1.00
 O K:ALA165 2.3 36.7 1.0
O K:SER171 2.3 38.7 1.0
O K:ASP168 2.3 36.7 1.0
O W:ASP204 2.4 43.5 1.0
O K:HOH414 2.6 29.8 1.0
C W:ASP204 3.2 45.7 1.0
C K:ALA165 3.4 36.8 1.0
C K:ASP168 3.4 36.0 1.0
C K:SER171 3.5 38.2 1.0
CA W:ASP204 3.6 45.6 1.0
NH1 K:ARG19 3.7 46.3 1.0
O K:ALA169 3.8 38.5 1.0
CB W:ASP204 3.8 45.1 1.0
CA K:ALA169 3.9 36.4 1.0
C K:ALA169 3.9 37.8 1.0
N K:ALA169 4.0 36.1 1.0
CA K:ALA165 4.0 37.4 1.0
OXT W:ASP204 4.1 46.6 1.0
N K:SER171 4.1 38.3 1.0
CA K:SER171 4.3 37.6 1.0
O K:HIS166 4.4 39.1 1.0
CZ K:ARG19 4.4 44.6 1.0
N K:HIS166 4.5 36.5 1.0
N K:GLY172 4.5 38.4 1.0
N K:ASP168 4.5 35.3 1.0
CA K:ASP168 4.5 35.2 1.0
C K:HIS166 4.5 36.4 1.0
O K:ALA164 4.6 36.4 1.0
CA K:GLY172 4.6 40.1 1.0
N K:TYR170 4.7 38.3 1.0
NH2 K:ARG19 4.8 46.0 1.0
CA K:HIS166 4.8 36.2 1.0
CG W:ASP204 4.8 44.8 1.0
CB K:SER171 4.8 37.0 1.0
CB K:ALA165 4.9 37.5 1.0

Magnesium binding site 5 out of 7 in 4ya5

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:48.2
occ:1.00
 OXT L:ASP222 2.2 50.5 1.0
O V:ILE163 2.2 35.3 1.0
O V:ASP166 2.2 37.7 1.0
O V:SER169 2.2 41.0 1.0
C L:ASP222 3.1 54.8 1.0
C V:ASP166 3.3 36.9 1.0
C V:ILE163 3.3 37.6 1.0
C V:SER169 3.4 38.5 1.0
CA L:ASP222 3.7 55.8 1.0
NH1 V:ARG19 3.9 46.0 1.0
O V:GLY162 3.9 33.9 1.0
CA V:LEU167 3.9 37.8 1.0
O L:ASP222 3.9 57.1 1.0
N V:LEU167 4.0 37.4 1.0
CA V:ILE163 4.1 37.8 1.0
CB L:ASP222 4.1 56.5 1.0
N V:ASP166 4.2 37.6 1.0
N V:SER169 4.2 36.7 1.0
N V:GLY170 4.3 39.5 1.0
C V:LEU167 4.3 37.9 1.0
CA V:ASP166 4.3 37.0 1.0
N V:TRP164 4.3 38.8 1.0
CA V:SER169 4.3 37.0 1.0
CA V:GLY170 4.3 42.4 1.0
C V:TRP164 4.4 39.9 1.0
O V:LEU167 4.5 37.7 1.0
CZ V:ARG19 4.5 45.4 1.0
O V:TRP164 4.5 41.0 1.0
CA V:TRP164 4.5 40.4 1.0
N V:ASN165 4.7 39.2 1.0
NH2 V:ARG19 4.7 47.7 1.0
CB V:SER169 4.7 36.9 1.0
C V:GLY162 4.8 36.7 1.0
C V:ASN165 4.9 37.7 1.0
N V:ILE163 5.0 37.3 1.0

Magnesium binding site 6 out of 7 in 4ya5

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:47.0
occ:1.00
 O N:SER169 2.5 35.5 1.0
O N:ILE163 2.9 34.4 1.0
O N:ASP166 3.0 37.5 1.0
NH1 N:ARG19 3.4 36.8 1.0
CD1 a:LEU34 3.6 38.3 1.0
C N:SER169 3.7 34.4 1.0
C N:ASP166 4.0 34.7 1.0
CA N:GLY167 4.0 33.1 1.0
C N:ILE163 4.0 35.2 1.0
CZ N:ARG19 4.1 36.8 1.0
O N:GLY167 4.1 33.9 1.0
CG2 N:ILE163 4.1 32.6 1.0
C N:GLY167 4.3 33.2 1.0
NH2 N:ARG19 4.3 38.0 1.0
N N:GLY167 4.4 33.2 1.0
CA N:GLY170 4.4 35.2 1.0
N N:GLY170 4.5 34.1 1.0
CA N:ILE163 4.6 33.4 1.0
N N:SER169 4.7 33.1 1.0
CA N:SER169 4.8 32.8 1.0
CG a:LEU34 4.9 38.4 1.0
NE N:ARG19 4.9 36.4 1.0
CB N:ILE163 5.0 32.6 1.0

Magnesium binding site 7 out of 7 in 4ya5

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant in Complex with Ac-Pae-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:50.7
occ:1.00
 O Z:HOH414 2.5 35.3 1.0
O Z:THR192 2.5 46.4 1.0
O Z:VAL198 2.5 40.0 1.0
O Z:HIS195 2.5 35.2 1.0
C Z:THR192 3.5 47.4 1.0
C Z:HIS195 3.6 39.0 1.0
C Z:VAL198 3.7 41.7 1.0
CA Z:THR192 3.8 47.4 1.0
CG2 Z:THR192 3.9 48.8 1.0
CA Z:ILE196 3.9 39.7 1.0
O Z:ILE196 4.0 44.2 1.0
C Z:ILE196 4.0 40.3 1.0
NH2 Z:ARG28 4.1 46.7 1.0
N Z:ILE196 4.1 38.9 1.0
N Z:VAL198 4.2 39.8 1.0
O Z:ASP222 4.3 55.5 1.0
NH2 H:ARG19 4.4 49.9 1.0
CA Z:VAL198 4.4 41.3 1.0
CB Z:THR192 4.5 48.0 1.0
N Z:HIS195 4.6 41.1 1.0
CA Z:HIS195 4.7 39.6 1.0
N Z:GLU193 4.7 48.4 1.0
N Z:GLY199 4.7 42.0 1.0
O Z:ALA191 4.7 44.0 1.0
CB Z:VAL198 4.7 41.0 1.0
N Z:GLN197 4.8 39.0 1.0
CA Z:GLY199 4.9 43.1 1.0
OD1 Z:ASP222 4.9 57.4 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 23:07:50 2024

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