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Magnesium in PDB 4y8r: Yeast 20S Proteasome BETA2-H116D Mutant

Enzymatic activity of Yeast 20S Proteasome BETA2-H116D Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA2-H116D Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H116D Mutant, PDB code: 4y8r 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 (°) 134.360, 300.590, 143.850, 90.00, 112.75, 90.00
R / Rfree (%) 20.3 / 22.2

Other elements in 4y8r:

The structure of Yeast 20S Proteasome BETA2-H116D Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-H116D Mutant (pdb code 4y8r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA2-H116D Mutant, PDB code: 4y8r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4y8r

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome BETA2-H116D Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:49.0
occ:1.00
 O G:MET125 2.0 49.1 1.0
O G:TYR119 2.2 43.9 1.0
O G:ARG122 2.3 45.2 1.0
O G:HOH407 2.4 36.0 1.0
OG1 G:THR8 2.7 44.8 1.0
C G:MET125 3.2 47.7 1.0
CG2 G:THR8 3.3 45.2 1.0
C G:TYR119 3.4 41.9 1.0
C G:ARG122 3.5 45.3 1.0
CB G:THR8 3.6 45.1 1.0
O G:ALA123 3.7 49.3 1.0
CA G:ALA123 3.9 45.4 1.0
C G:ALA123 3.9 46.6 1.0
N G:ARG126 4.1 44.1 1.0
CA G:ARG126 4.1 42.5 1.0
N G:MET125 4.1 50.2 1.0
N G:ALA123 4.1 44.9 1.0
CA G:TYR119 4.2 40.8 1.0
CA G:MET125 4.2 51.2 1.0
CD G:PRO127 4.4 40.1 1.0
N G:THR120 4.5 41.5 1.0
N G:THR8 4.5 46.2 1.0
N G:ARG122 4.6 43.9 1.0
CB G:MET125 4.6 55.9 1.0
CA G:ARG122 4.6 46.4 1.0
C G:ARG126 4.6 41.0 1.0
CA G:THR8 4.6 45.6 1.0
CA G:THR120 4.7 40.9 1.0
CB G:TYR119 4.7 41.1 1.0
N G:TYR124 4.7 47.9 1.0
C G:THR120 4.8 41.5 1.0
N G:PRO127 4.8 40.2 1.0

Magnesium binding site 2 out of 9 in 4y8r

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome BETA2-H116D Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:52.8
occ:1.00
 O I:ASP177 2.2 44.2 1.0
O I:SER180 2.5 46.4 1.0
O I:ALA174 2.6 46.1 1.0
C I:ASP177 3.4 44.3 1.0
C I:SER180 3.7 46.9 1.0
C I:ALA174 3.7 45.1 1.0
O I:HOH409 4.0 39.6 1.0
OXT I:ASP204 4.1 52.4 1.0
CA I:ASP175 4.1 47.4 1.0
O I:ALA178 4.2 42.5 1.0
N I:ALA178 4.2 43.6 1.0
CA I:ALA178 4.2 44.6 1.0
C I:ALA178 4.2 44.9 1.0
N I:ASP177 4.3 44.8 1.0
N I:SER180 4.3 46.3 1.0
CA I:ASP177 4.4 44.2 1.0
N I:ASP175 4.4 46.5 1.0
C I:ASP175 4.4 47.0 1.0
CA I:SER180 4.6 47.2 1.0
N I:GLY181 4.6 46.3 1.0
O I:ASP175 4.7 46.4 1.0
NH1 Y:ARG19 4.7 49.5 1.0
CA I:GLY181 4.7 46.5 1.0
O I:ASP204 4.8 49.7 1.0
CA I:ALA174 4.8 43.5 1.0
OD1 I:ASP175 4.9 48.1 1.0
NH2 Y:ARG19 4.9 49.8 1.0
C I:ASP204 4.9 49.7 1.0
CB I:ASP177 4.9 44.5 1.0
N I:LEU179 4.9 44.6 1.0

Magnesium binding site 3 out of 9 in 4y8r

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome BETA2-H116D Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:40.1
occ:1.00
 O K:ASP168 2.2 43.1 1.0
O K:SER171 2.3 46.8 1.0
O K:ALA165 2.3 43.9 1.0
O K:HOH406 2.4 30.4 1.0
O W:ASP204 2.5 47.2 1.0
C W:ASP204 3.2 49.0 1.0
C K:ASP168 3.3 42.1 1.0
C K:ALA165 3.4 43.3 1.0
C K:SER171 3.5 45.8 1.0
NH1 K:ARG19 3.6 51.2 1.0
CA W:ASP204 3.7 48.6 1.0
O K:ALA169 3.8 44.1 1.0
CA K:ALA169 3.8 42.3 1.0
C K:ALA169 3.8 43.3 1.0
CB W:ASP204 3.8 47.6 1.0
N K:ALA169 4.0 42.2 1.0
N K:SER171 4.0 43.9 1.0
CA K:ALA165 4.1 43.4 1.0
OXT W:ASP204 4.1 51.7 1.0
CA K:SER171 4.3 44.0 1.0
O K:HIS166 4.3 44.8 1.0
CZ K:ARG19 4.3 49.5 1.0
N K:GLY172 4.5 46.4 1.0
CA K:ASP168 4.5 41.3 1.0
N K:HIS166 4.5 42.6 1.0
N K:ASP168 4.5 41.2 1.0
C K:HIS166 4.5 42.8 1.0
N K:TYR170 4.5 44.1 1.0
O K:ALA164 4.6 40.7 1.0
CA K:GLY172 4.6 46.9 1.0
NH2 K:ARG19 4.7 50.2 1.0
CB K:SER171 4.7 43.5 1.0
CA K:HIS166 4.8 42.6 1.0
CG W:ASP204 4.8 47.2 1.0
CB K:ALA165 4.9 43.3 1.0
C K:ARG167 5.0 41.3 1.0

Magnesium binding site 4 out of 9 in 4y8r

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome BETA2-H116D Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:48.4
occ:1.00
 O N:HOH317 2.3 30.6 1.0
O N:ILE163 2.4 40.1 1.0
O N:SER169 2.5 41.8 1.0
O N:ASP166 2.7 42.0 1.0
C N:ILE163 3.5 40.3 1.0
CD1 a:LEU34 3.6 45.8 1.0
C N:SER169 3.6 41.1 1.0
C N:ASP166 3.7 39.3 1.0
NH1 N:ARG19 3.8 42.5 1.0
CG2 N:ILE163 3.8 38.9 1.0
CA N:ILE163 4.1 39.4 1.0
CA N:GLY167 4.1 38.3 1.0
N N:GLY167 4.3 38.5 1.0
CZ N:ARG19 4.4 42.0 1.0
CA N:GLY170 4.4 43.1 1.0
O N:GLY167 4.4 39.4 1.0
N N:GLY170 4.4 41.9 1.0
C N:GLY167 4.4 38.3 1.0
CB N:ILE163 4.5 38.7 1.0
N N:SER169 4.6 39.7 1.0
CA N:SER169 4.6 39.5 1.0
N N:LYS164 4.6 41.8 1.0
NH2 N:ARG19 4.7 42.6 1.0
N N:ASP166 4.8 38.6 1.0
CG a:LEU34 4.8 44.9 1.0
CA N:ASP166 4.8 38.9 1.0
C N:LYS164 4.8 43.5 1.0
O N:LYS164 4.9 45.4 1.0
CA N:LYS164 4.9 43.8 1.0
CB N:SER169 4.9 38.7 1.0

Magnesium binding site 5 out of 9 in 4y8r

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome BETA2-H116D Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:43.9
occ:1.00
 O N:HOH316 2.3 36.1 1.0
O N:HOH309 2.6 38.5 1.0
OE1 H:GLN91 2.8 54.1 1.0
OD1 N:ASP51 3.4 41.3 1.0
O N:ASN92 3.4 45.3 1.0
OD2 N:ASP51 3.7 43.5 1.0
CD H:GLN91 3.9 59.7 1.0
CG N:ASP51 4.0 40.4 1.0
O N:HOH302 4.3 29.0 1.0
NE2 H:GLN91 4.5 65.4 1.0
C N:ASN92 4.5 46.5 1.0

Magnesium binding site 6 out of 9 in 4y8r

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome BETA2-H116D Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:52.8
occ:1.00
 O V:ILE163 2.1 47.9 1.0
O V:ASP166 2.2 45.3 1.0
OXT L:ASP222 2.2 58.2 1.0
O V:SER169 2.3 49.8 1.0
C L:ASP222 3.1 59.0 1.0
C V:ASP166 3.2 43.5 1.0
C V:ILE163 3.2 46.2 1.0
C V:SER169 3.5 47.8 1.0
CA L:ASP222 3.7 59.0 1.0
O V:GLY162 3.8 44.9 1.0
CA V:LEU167 3.9 44.0 1.0
O L:ASP222 3.9 61.4 1.0
N V:LEU167 3.9 43.3 1.0
NH1 V:ARG19 3.9 50.6 1.0
CA V:ILE163 4.0 45.2 1.0
N V:ASP166 4.1 43.8 1.0
N V:TRP164 4.2 46.8 1.0
C V:TRP164 4.2 46.8 1.0
CA V:ASP166 4.2 42.9 1.0
CB L:ASP222 4.2 59.9 1.0
N V:SER169 4.3 44.4 1.0
C V:LEU167 4.3 43.8 1.0
O V:TRP164 4.3 49.6 1.0
CA V:SER169 4.4 45.6 1.0
N V:GLY170 4.4 49.7 1.0
CA V:GLY170 4.4 51.4 1.0
CA V:TRP164 4.4 46.9 1.0
O V:LEU167 4.5 42.1 1.0
N V:ASN165 4.5 45.5 1.0
CZ V:ARG19 4.6 50.5 1.0
CB V:SER169 4.7 45.8 1.0
C V:ASN165 4.7 44.4 1.0
C V:GLY162 4.7 44.9 1.0
NH2 V:ARG19 4.8 53.3 1.0
N V:ILE163 4.9 45.3 1.0
O L:ARG221 4.9 55.0 1.0
CB V:ASP166 5.0 42.6 1.0
N V:GLY168 5.0 43.2 1.0

Magnesium binding site 7 out of 9 in 4y8r

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome BETA2-H116D Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:59.2
occ:1.00
 O W:ASP177 2.1 45.9 1.0
O W:SER180 2.4 46.3 1.0
O W:ALA174 2.7 43.1 1.0
C W:ASP177 3.2 43.9 1.0
C W:SER180 3.5 45.5 1.0
C W:ALA174 3.8 42.8 1.0
O W:ALA178 4.0 44.0 1.0
C W:ALA178 4.1 43.5 1.0
CA W:ALA178 4.1 42.9 1.0
N W:ALA178 4.1 42.7 1.0
N W:SER180 4.1 46.3 1.0
OXT W:ASP204 4.2 51.7 1.0
N W:ASP177 4.2 44.8 1.0
CA W:ASP177 4.3 44.3 1.0
CA W:ASP175 4.3 46.4 1.0
CA W:SER180 4.4 46.1 1.0
N W:ASP175 4.5 44.8 1.0
N W:GLY181 4.5 44.8 1.0
C W:ASP175 4.6 45.4 1.0
O W:HOH423 4.6 37.2 1.0
CA W:GLY181 4.7 45.4 1.0
NH1 K:ARG19 4.7 51.2 1.0
N W:LEU179 4.7 43.2 1.0
CB W:ASP177 4.8 45.2 1.0
O W:ASP175 4.8 45.4 1.0
CA W:ALA174 4.8 41.2 1.0
CB W:SER180 4.9 47.2 1.0
O W:ASP204 4.9 47.2 1.0
C W:ASP204 5.0 49.0 1.0

Magnesium binding site 8 out of 9 in 4y8r

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome BETA2-H116D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast 20S Proteasome BETA2-H116D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:45.6
occ:1.00
 O Y:ASP168 2.3 45.0 1.0
O I:ASP204 2.4 49.7 1.0
O Y:ALA165 2.5 42.5 1.0
O Y:SER171 2.7 46.2 1.0
C I:ASP204 3.2 49.7 1.0
C Y:ASP168 3.3 42.8 1.0
CA Y:ALA169 3.6 42.4 1.0
C Y:ALA165 3.6 41.8 1.0
NH1 Y:ARG19 3.7 49.5 1.0
O Y:ALA169 3.7 42.7 1.0
CA I:ASP204 3.7 50.1 1.0
C Y:ALA169 3.7 42.7 1.0
N Y:ALA169 3.8 42.2 1.0
C Y:SER171 3.9 44.7 1.0
OXT I:ASP204 4.0 52.4 1.0
CB I:ASP204 4.0 50.4 1.0
O Y:HIS166 4.1 41.4 1.0
N Y:SER171 4.3 43.2 1.0
CA Y:ALA165 4.4 42.6 1.0
C Y:HIS166 4.4 40.9 1.0
CA Y:ASP168 4.5 42.9 1.0
CZ Y:ARG19 4.5 49.5 1.0
N Y:ASP168 4.5 42.4 1.0
N Y:TYR170 4.5 42.7 1.0
CA Y:SER171 4.6 43.7 1.0
N Y:HIS166 4.6 41.4 1.0
O Y:ALA164 4.8 43.4 1.0
CA Y:HIS166 4.8 40.8 1.0
NH2 Y:ARG19 4.8 49.8 1.0
C Y:ARG167 4.9 41.9 1.0
N Y:GLY172 4.9 44.7 1.0
CB Y:ALA169 5.0 41.6 1.0
CA Y:GLY172 5.0 44.9 1.0

Magnesium binding site 9 out of 9 in 4y8r

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome BETA2-H116D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Yeast 20S Proteasome BETA2-H116D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:55.6
occ:1.00
 O Z:HOH404 2.4 35.6 1.0
O Z:HIS195 2.4 44.9 1.0
O Z:THR192 2.4 54.8 1.0
O Z:VAL198 2.6 48.1 1.0
C Z:HIS195 3.4 44.8 1.0
C Z:THR192 3.5 54.3 1.0
CA Z:ILE196 3.7 44.2 1.0
C Z:VAL198 3.8 48.4 1.0
CA Z:THR192 3.9 52.9 1.0
O Z:ILE196 3.9 50.4 1.0
C Z:ILE196 3.9 45.4 1.0
CG2 Z:THR192 4.0 54.2 1.0
N Z:ILE196 4.0 43.8 1.0
NH2 Z:ARG28 4.1 50.1 1.0
NH2 H:ARG19 4.3 57.5 1.0
N Z:VAL198 4.3 45.6 1.0
O Z:ASP222 4.3 60.0 1.0
CA Z:VAL198 4.5 47.1 1.0
N Z:HIS195 4.5 47.2 1.0
CB Z:THR192 4.5 53.8 1.0
CA Z:HIS195 4.6 45.1 1.0
N Z:GLU193 4.7 54.2 1.0
O Z:ALA191 4.7 50.8 1.0
N Z:GLN197 4.7 44.6 1.0
OD1 Z:ASP222 4.8 59.9 1.0
N Z:GLY199 4.8 49.2 1.0
CB Z:VAL198 4.8 46.6 1.0
CZ H:ARG19 4.9 56.0 1.0
NH1 H:ARG19 5.0 56.1 1.0
CA Z:GLY199 5.0 50.1 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 23:01:29 2024

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