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Magnesium in PDB 4y9y: Yeast 20S Proteasome BETA2-H116E Mutant

Enzymatic activity of Yeast 20S Proteasome BETA2-H116E Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA2-H116E Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H116E Mutant, PDB code: 4y9y 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.010, 300.430, 144.370, 90.00, 112.72, 90.00
R / Rfree (%) 17.6 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-H116E Mutant (pdb code 4y9y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA2-H116E Mutant, PDB code: 4y9y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4y9y

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Magnesium binding site 1 out of 10 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:52.3
occ:1.00
 O G:MET125 2.1 57.9 1.0
O G:TYR119 2.4 49.9 1.0
O G:ARG122 2.4 52.2 1.0
OG1 G:THR8 2.6 49.2 1.0
CG2 G:THR8 3.2 52.2 1.0
C G:MET125 3.3 56.0 1.0
CB G:THR8 3.4 51.3 1.0
C G:ARG122 3.6 52.6 1.0
C G:TYR119 3.6 47.9 1.0
O G:ALA123 3.8 56.8 1.0
CA G:ALA123 3.9 54.0 1.0
C G:ALA123 3.9 55.1 1.0
N G:ALA123 4.2 53.3 1.0
CA G:ARG126 4.2 50.5 1.0
N G:ARG126 4.2 51.2 1.0
N G:MET125 4.3 58.8 1.0
N G:THR8 4.3 54.9 1.0
CA G:MET125 4.3 60.1 1.0
CA G:TYR119 4.4 47.5 1.0
CD G:PRO127 4.4 48.2 1.0
CA G:THR8 4.5 52.5 1.0
N G:THR120 4.6 45.9 1.0
CA G:THR120 4.7 47.1 1.0
N G:ARG122 4.7 53.0 1.0
C G:ARG126 4.7 49.3 1.0
CA G:ARG122 4.7 55.5 1.0
N G:TYR124 4.8 58.6 1.0
C G:THR120 4.8 48.4 1.0
CB G:MET125 4.8 66.3 1.0
N G:PRO127 4.9 47.7 1.0
CB G:TYR119 4.9 47.7 1.0

Magnesium binding site 2 out of 10 in 4y9y

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Magnesium binding site 2 out of 10 in the Yeast 20S Proteasome BETA2-H116E Mutant


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast 20S Proteasome BETA2-H116E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:53.1
occ:1.00
 O H:HOH407 2.3 57.7 1.0
OE1 H:GLN91 2.3 65.6 1.0
OD1 N:ASP51 3.2 51.1 1.0
CD H:GLN91 3.2 64.5 1.0
NE2 H:GLN91 3.4 66.1 1.0
O N:ASN92 3.6 54.3 1.0
OD2 N:ASP51 3.7 53.3 1.0
CG N:ASP51 3.8 47.7 1.0
O N:HOH307 4.5 52.5 1.0
CG H:GLN91 4.6 61.2 1.0
C N:ASN92 4.7 53.6 1.0
OE1 H:GLU116 5.0 62.7 1.0

Magnesium binding site 3 out of 10 in 4y9y

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Magnesium binding site 3 out of 10 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:77.2
occ:1.00
 O I:ASP177 2.6 56.8 1.0
O I:SER180 2.7 56.9 1.0
O I:ALA174 2.8 54.9 1.0
C I:ASP177 3.7 53.7 1.0
OXT I:ASP204 3.8 70.1 1.0
C I:ALA174 3.8 54.7 1.0
C I:SER180 3.9 55.8 1.0
CA I:ASP175 4.1 56.6 1.0
O I:ALA178 4.4 57.5 1.0
N I:ASP175 4.4 57.4 1.0
C I:ASP175 4.4 55.8 1.0
CA I:ALA178 4.5 53.2 1.0
N I:ASP177 4.5 54.3 1.0
N I:ALA178 4.5 51.2 1.0
C I:ALA178 4.5 55.5 1.0
NH1 Y:ARG19 4.5 62.1 1.0
O I:ASP204 4.5 63.8 1.0
O I:ASP175 4.6 56.8 1.0
C I:ASP204 4.6 62.4 1.0
NH2 Y:ARG19 4.7 64.0 1.0
N I:SER180 4.7 53.6 1.0
CA I:ASP177 4.7 53.0 1.0
CA I:GLY181 4.7 54.8 1.0
OD1 I:ASP175 4.7 60.7 1.0
N I:GLY181 4.8 54.9 1.0
CA I:SER180 4.9 55.0 1.0
CZ Y:ARG19 5.0 61.5 1.0
CA I:ALA174 5.0 51.8 1.0

Magnesium binding site 4 out of 10 in 4y9y

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Magnesium binding site 4 out of 10 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:60.9
occ:1.00
 O K:ASP168 2.3 49.9 1.0
O W:ASP204 2.4 57.5 1.0
O K:ALA165 2.5 53.8 1.0
O K:SER171 2.6 55.9 1.0
C W:ASP204 3.1 60.5 1.0
C K:ASP168 3.3 48.6 1.0
CA K:ALA169 3.6 49.9 1.0
C K:ALA165 3.6 52.6 1.0
CA W:ASP204 3.7 59.1 1.0
NH1 K:ARG19 3.7 62.3 1.0
O K:ALA169 3.7 52.4 1.0
C K:ALA169 3.7 51.8 1.0
C K:SER171 3.8 53.9 1.0
N K:ALA169 3.8 47.9 1.0
CB W:ASP204 3.9 57.7 1.0
OXT W:ASP204 4.0 64.5 1.0
O K:HIS166 4.1 55.9 1.0
N K:SER171 4.2 49.2 1.0
CA K:ALA165 4.4 52.4 1.0
CZ K:ARG19 4.4 60.6 1.0
C K:HIS166 4.5 51.6 1.0
CA K:ASP168 4.5 48.1 1.0
N K:ASP168 4.5 49.5 1.0
N K:TYR170 4.5 52.3 1.0
CA K:SER171 4.5 51.1 1.0
N K:HIS166 4.6 50.8 1.0
O K:ALA164 4.7 51.0 1.0
CA K:HIS166 4.8 50.6 1.0
NH2 K:ARG19 4.8 63.0 1.0
N K:GLY172 4.8 54.4 1.0
C K:ARG167 4.9 51.2 1.0
CG W:ASP204 4.9 56.4 1.0
CB K:ALA169 5.0 48.3 1.0
CA K:GLY172 5.0 55.5 1.0
CB K:SER171 5.0 51.1 1.0

Magnesium binding site 5 out of 10 in 4y9y

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Magnesium binding site 5 out of 10 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:65.1
occ:1.00
 O N:SER169 2.8 45.4 1.0
O N:ILE163 2.8 49.6 1.0
O N:ASP166 3.1 50.6 1.0
CD1 a:LEU34 3.5 51.3 1.0
NH1 N:ARG19 3.5 50.4 1.0
C N:ILE163 3.9 49.1 1.0
C N:SER169 4.0 47.8 1.0
CG2 N:ILE163 4.0 47.6 1.0
CZ N:ARG19 4.1 49.7 1.0
C N:ASP166 4.1 48.7 1.0
CA N:GLY167 4.3 47.1 1.0
NH2 N:ARG19 4.3 50.8 1.0
O N:GLY167 4.5 48.5 1.0
CA N:GLY170 4.5 50.3 1.0
CA N:ILE163 4.6 48.7 1.0
N N:GLY167 4.6 48.0 1.0
C N:GLY167 4.6 46.7 1.0
N N:GLY170 4.7 49.5 1.0
CG a:LEU34 4.8 50.7 1.0
O N:LYS164 4.9 54.3 1.0
N N:LYS164 4.9 49.6 1.0
CB N:ILE163 4.9 48.0 1.0
N N:SER169 5.0 46.2 1.0

Magnesium binding site 6 out of 10 in 4y9y

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Magnesium binding site 6 out of 10 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:77.5
occ:1.00
 OXT L:ASP222 2.1 73.5 1.0
O V:ILE163 2.2 52.3 1.0
O V:ASP166 2.3 52.8 1.0
O V:SER169 2.6 54.4 1.0
C L:ASP222 3.1 70.9 1.0
C V:ASP166 3.2 52.7 1.0
C V:ILE163 3.3 54.6 1.0
C V:SER169 3.7 53.8 1.0
CA L:ASP222 3.7 68.8 1.0
CA V:LEU167 3.8 53.0 1.0
N V:LEU167 3.9 51.3 1.0
O V:GLY162 3.9 53.6 1.0
O L:ASP222 3.9 73.8 1.0
N V:ASP166 4.0 52.9 1.0
NH1 V:ARG19 4.1 62.0 1.0
C V:TRP164 4.1 56.5 1.0
O V:TRP164 4.1 62.7 1.0
CA V:ILE163 4.2 54.1 1.0
N V:TRP164 4.2 55.9 1.0
CA V:ASP166 4.2 51.6 1.0
C V:LEU167 4.3 53.6 1.0
CB L:ASP222 4.3 69.8 1.0
CA V:TRP164 4.3 55.7 1.0
N V:ASN165 4.5 55.2 1.0
O V:LEU167 4.5 54.8 1.0
N V:SER169 4.5 51.8 1.0
CA V:SER169 4.6 53.7 1.0
N V:GLY170 4.6 55.5 1.0
CA V:GLY170 4.6 60.9 1.0
C V:ASN165 4.6 53.3 1.0
CZ V:ARG19 4.7 60.6 1.0
C V:GLY162 4.8 54.2 1.0
NH2 V:ARG19 4.9 62.5 1.0
O L:ARG221 4.9 69.5 1.0
CB V:SER169 4.9 53.6 1.0
CD2 V:LEU167 4.9 51.3 1.0

Magnesium binding site 7 out of 10 in 4y9y

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Magnesium binding site 7 out of 10 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:30.0
occ:1.00
 OE1 V:GLN91 2.4 65.1 1.0
CD V:GLN91 3.4 65.5 1.0
O b:ASN92 3.6 58.0 1.0
NE2 V:GLN91 3.8 64.3 1.0
OD1 b:ASP51 3.8 53.3 1.0
O b:HOH305 3.9 43.1 1.0
OD2 b:ASP51 4.0 53.1 1.0
CG b:ASP51 4.4 49.7 1.0
C b:ASN92 4.7 58.2 1.0
CG V:GLN91 4.8 64.2 1.0

Magnesium binding site 8 out of 10 in 4y9y

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Magnesium binding site 8 out of 10 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:67.6
occ:1.00
 O W:ASP177 2.2 55.0 1.0
O W:SER180 2.6 55.8 1.0
O W:ALA174 2.9 55.3 1.0
C W:ASP177 3.4 53.2 1.0
O W:HOH405 3.7 55.8 1.0
C W:SER180 3.8 54.3 1.0
OXT W:ASP204 3.9 64.5 1.0
O W:ALA178 3.9 54.8 1.0
CA W:ALA178 4.0 53.0 1.0
C W:ALA178 4.0 54.0 1.0
C W:ALA174 4.1 54.5 1.0
N W:ALA178 4.1 51.9 1.0
NH1 K:ARG19 4.3 62.3 1.0
N W:SER180 4.4 56.3 1.0
N W:ASP177 4.4 53.9 1.0
CA W:ASP175 4.4 55.4 1.0
CA W:ASP177 4.4 53.6 1.0
O W:ASP204 4.5 57.5 1.0
C W:ASP175 4.6 54.5 1.0
CA W:SER180 4.7 55.1 1.0
C W:ASP204 4.7 60.5 1.0
N W:ASP175 4.7 55.9 1.0
NH2 K:ARG19 4.7 63.0 1.0
O W:ASP175 4.8 53.2 1.0
N W:GLY181 4.8 53.3 1.0
N W:LEU179 4.8 53.0 1.0
CA W:GLY181 4.9 53.7 1.0
CZ K:ARG19 4.9 60.6 1.0

Magnesium binding site 9 out of 10 in 4y9y

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Magnesium binding site 9 out of 10 in the Yeast 20S Proteasome BETA2-H116E 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-H116E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:63.5
occ:1.00
 O Y:ASP168 2.3 52.3 1.0
O Y:ALA165 2.5 50.8 1.0
O I:ASP204 2.5 63.8 1.0
O Y:SER171 2.7 54.7 1.0
C I:ASP204 3.2 62.4 1.0
C Y:ASP168 3.3 51.7 1.0
CA Y:ALA169 3.6 51.7 1.0
C Y:ALA165 3.6 51.2 1.0
CA I:ASP204 3.7 60.8 1.0
O Y:ALA169 3.7 50.9 1.0
NH1 Y:ARG19 3.7 62.1 1.0
C Y:ALA169 3.8 51.0 1.0
N Y:ALA169 3.8 51.3 1.0
C Y:SER171 3.9 53.4 1.0
O Y:HIS166 4.0 50.4 1.0
CB I:ASP204 4.0 61.7 1.0
OXT I:ASP204 4.1 70.1 1.0
N Y:SER171 4.3 52.5 1.0
C Y:HIS166 4.4 50.4 1.0
CA Y:ALA165 4.4 51.2 1.0
CA Y:ASP168 4.4 51.3 1.0
N Y:ASP168 4.4 51.9 1.0
CZ Y:ARG19 4.5 61.5 1.0
N Y:TYR170 4.6 50.5 1.0
N Y:HIS166 4.6 52.1 1.0
CA Y:SER171 4.6 51.9 1.0
O Y:ALA164 4.8 51.2 1.0
CA Y:HIS166 4.8 50.6 1.0
C Y:ARG167 4.8 51.5 1.0
NH2 Y:ARG19 4.9 64.0 1.0
N Y:GLY172 4.9 53.7 1.0
CB Y:ALA169 4.9 50.6 1.0
N Y:ARG167 5.0 50.3 1.0

Magnesium binding site 10 out of 10 in 4y9y

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Magnesium binding site 10 out of 10 in the Yeast 20S Proteasome BETA2-H116E Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Yeast 20S Proteasome BETA2-H116E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:67.8
occ:1.00
 O Z:VAL198 2.6 52.5 1.0
O Z:HIS195 2.8 52.0 1.0
O Z:THR192 2.8 62.8 1.0
O Z:ILE196 3.6 56.9 1.0
O Z:ASP222 3.7 78.3 1.0
NH2 Z:ARG28 3.7 62.3 1.0
CA Z:ILE196 3.8 54.9 1.0
C Z:HIS195 3.8 55.4 1.0
C Z:VAL198 3.8 57.3 1.0
C Z:ILE196 3.9 55.0 1.0
C Z:THR192 3.9 62.6 1.0
CG2 Z:THR192 4.0 63.1 1.0
NH2 H:ARG19 4.2 66.8 1.0
N Z:ILE196 4.2 54.8 1.0
CA Z:THR192 4.2 61.7 1.0
N Z:VAL198 4.4 54.4 1.0
OD1 Z:ASP222 4.6 73.4 1.0
CA Z:VAL198 4.6 56.1 1.0
C Z:ASP222 4.6 76.3 1.0
CZ Z:ARG28 4.7 62.1 1.0
N Z:GLY199 4.7 58.1 1.0
N Z:GLN197 4.8 54.1 1.0
CB Z:THR192 4.8 62.3 1.0
NH1 H:ARG19 4.8 70.3 1.0
CA Z:GLY199 4.8 59.5 1.0
CZ H:ARG19 4.8 67.2 1.0
NH1 Z:ARG28 4.9 63.2 1.0
OXT Z:ASP222 5.0 79.2 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 23:05:48 2024

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