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Magnesium in PDB 4ya1: Yeast 20S Proteasome BETA2-H116N Mutant

Enzymatic activity of Yeast 20S Proteasome BETA2-H116N Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA2-H116N Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H116N Mutant, PDB code: 4ya1 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 (°) 134.860, 302.060, 144.230, 90.00, 112.80, 90.00
R / Rfree (%) 19.8 / 21.8

Other elements in 4ya1:

The structure of Yeast 20S Proteasome BETA2-H116N Mutant also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-H116N Mutant (pdb code 4ya1). 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-H116N Mutant, PDB code: 4ya1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4ya1

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome BETA2-H116N 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-H116N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:36.1
occ:1.00
 O G:MET125 2.1 45.7 1.0
O G:ARG122 2.5 40.6 1.0
OG1 G:THR8 2.5 42.4 1.0
O G:TYR119 2.6 37.0 1.0
CG2 G:THR8 3.2 42.4 1.0
C G:MET125 3.3 45.1 1.0
CB G:THR8 3.4 42.6 1.0
C G:ARG122 3.6 42.4 1.0
O G:ALA123 3.6 45.3 1.0
C G:TYR119 3.8 37.1 1.0
CA G:ALA123 3.8 43.6 1.0
C G:ALA123 3.8 44.5 1.0
CA G:ARG126 4.2 39.8 1.0
N G:ALA123 4.2 42.5 1.0
N G:ARG126 4.2 41.2 1.0
N G:THR8 4.2 44.7 1.0
N G:MET125 4.2 49.1 1.0
CA G:MET125 4.3 49.4 1.0
CA G:THR8 4.4 43.7 1.0
CD G:PRO127 4.4 37.2 1.0
CA G:TYR119 4.6 37.2 1.0
N G:THR120 4.7 36.6 1.0
N G:TYR124 4.7 46.3 1.0
C G:ARG126 4.8 38.2 1.0
CA G:ARG122 4.8 44.0 1.0
N G:ARG122 4.8 41.8 1.0
CA G:THR120 4.8 37.4 1.0
CB G:MET125 4.9 53.9 1.0
N G:PRO127 4.9 37.4 1.0
C G:THR120 4.9 38.1 1.0

Magnesium binding site 2 out of 9 in 4ya1

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome BETA2-H116N 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-H116N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:48.3
occ:1.00
 OE1 H:GLN91 2.6 52.9 1.0
OD1 N:ASP51 3.2 40.0 1.0
CD H:GLN91 3.7 54.4 1.0
OD2 N:ASP51 3.8 41.7 1.0
O N:ASN92 3.8 43.5 1.0
CG N:ASP51 3.9 36.4 1.0
NE2 H:GLN91 4.2 60.9 1.0
O N:HOH305 4.4 27.6 1.0
C N:ASN92 4.9 42.6 1.0
CG H:GLN91 5.0 50.3 1.0

Magnesium binding site 3 out of 9 in 4ya1

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome BETA2-H116N 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-H116N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.3
occ:1.00
 O I:ASP177 2.4 40.1 1.0
O I:SER180 2.4 44.1 1.0
O I:ALA174 2.4 42.2 1.0
C I:ALA174 3.5 39.8 1.0
C I:ASP177 3.6 39.6 1.0
C I:SER180 3.6 42.0 1.0
CA I:ASP175 3.9 42.6 1.0
N I:ASP175 4.1 41.0 1.0
OXT I:ASP204 4.2 49.3 1.0
N I:ASP177 4.3 39.8 1.0
C I:ASP175 4.3 41.5 1.0
O I:ALA178 4.4 41.6 1.0
N I:SER180 4.4 40.5 1.0
N I:ALA178 4.5 38.6 1.0
CA I:ASP177 4.5 39.2 1.0
C I:ALA178 4.5 40.3 1.0
CA I:ALA178 4.5 39.8 1.0
O I:ASP175 4.5 41.9 1.0
N I:GLY181 4.5 40.9 1.0
CA I:SER180 4.5 41.6 1.0
CA I:GLY181 4.6 40.9 1.0
CA I:ALA174 4.6 37.8 1.0
OD1 I:ASP175 4.6 45.7 1.0
CB I:ALA174 4.9 36.5 1.0
NH1 Y:ARG19 4.9 44.6 1.0
N I:ARG176 4.9 40.5 1.0
CB I:ASP177 5.0 39.6 1.0
O I:ASP204 5.0 48.9 1.0
CB I:SER180 5.0 42.9 1.0

Magnesium binding site 4 out of 9 in 4ya1

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome BETA2-H116N 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-H116N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:40.6
occ:1.00
 O Y:ASP168 2.2 36.3 1.0
O Y:ALA165 2.4 37.5 1.0
O I:ASP204 2.4 48.9 1.0
O Y:SER171 2.7 37.8 1.0
C I:ASP204 3.2 46.7 1.0
C Y:ASP168 3.2 36.7 1.0
CA Y:ALA169 3.6 36.4 1.0
C Y:ALA165 3.6 36.3 1.0
CA I:ASP204 3.7 46.0 1.0
O Y:ALA169 3.7 36.4 1.0
C Y:ALA169 3.7 36.6 1.0
NH1 Y:ARG19 3.7 44.6 1.0
N Y:ALA169 3.8 36.6 1.0
C Y:SER171 3.9 38.4 1.0
CB I:ASP204 4.0 46.9 1.0
OXT I:ASP204 4.0 49.3 1.0
O Y:HIS166 4.1 34.5 1.0
N Y:SER171 4.2 36.3 1.0
CA Y:ALA165 4.3 36.5 1.0
C Y:HIS166 4.4 34.8 1.0
CA Y:ASP168 4.4 36.7 1.0
N Y:ASP168 4.4 35.8 1.0
N Y:TYR170 4.5 36.9 1.0
CZ Y:ARG19 4.5 43.9 1.0
N Y:HIS166 4.6 35.6 1.0
CA Y:SER171 4.6 37.2 1.0
O Y:ALA164 4.7 36.5 1.0
CA Y:HIS166 4.8 34.9 1.0
C Y:ARG167 4.8 34.9 1.0
N Y:GLY172 4.9 38.6 1.0
NH2 Y:ARG19 4.9 44.8 1.0
CB Y:ALA169 5.0 35.7 1.0
CG I:ASP204 5.0 46.6 1.0
N Y:ARG167 5.0 34.9 1.0

Magnesium binding site 5 out of 9 in 4ya1

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome BETA2-H116N 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-H116N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:41.6
occ:1.00
 O K:ALA165 2.3 38.0 1.0
O K:ASP168 2.4 35.9 1.0
O W:ASP204 2.4 47.8 1.0
O K:SER171 2.8 39.9 1.0
C W:ASP204 3.0 46.6 1.0
C K:ASP168 3.3 35.8 1.0
C K:ALA165 3.4 36.6 1.0
CA W:ASP204 3.5 44.4 1.0
CA K:ALA169 3.7 36.8 1.0
NH1 K:ARG19 3.8 46.1 1.0
CB W:ASP204 3.8 43.9 1.0
O K:ALA169 3.9 38.2 1.0
OXT W:ASP204 3.9 51.3 1.0
N K:ALA169 3.9 36.3 1.0
C K:ALA169 3.9 37.4 1.0
O K:HIS166 3.9 38.9 1.0
C K:SER171 4.0 38.7 1.0
O W:HOH406 4.1 27.3 1.0
C K:HIS166 4.2 36.5 1.0
CA K:ALA165 4.3 37.0 1.0
N K:SER171 4.4 38.5 1.0
N K:ASP168 4.4 34.7 1.0
N K:HIS166 4.4 35.5 1.0
CA K:ASP168 4.5 35.3 1.0
CA K:HIS166 4.6 35.8 1.0
CZ K:ARG19 4.6 44.8 1.0
O K:ALA164 4.7 36.3 1.0
N K:TYR170 4.7 38.1 1.0
CA K:SER171 4.7 37.8 1.0
C K:ARG167 4.8 35.4 1.0
N K:ARG167 4.9 35.9 1.0
CG W:ASP204 4.9 44.5 1.0
N W:ASP204 4.9 43.9 1.0
NH2 K:ARG19 5.0 47.3 1.0
N K:GLY172 5.0 39.2 1.0

Magnesium binding site 6 out of 9 in 4ya1

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome BETA2-H116N 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-H116N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:49.0
occ:1.00
 O V:ILE163 2.1 39.5 1.0
O V:ASP166 2.2 39.5 1.0
OXT L:ASP222 2.2 54.9 1.0
O V:SER169 2.4 40.9 1.0
C L:ASP222 3.1 53.2 1.0
C V:ILE163 3.2 38.9 1.0
C V:ASP166 3.2 37.5 1.0
C V:SER169 3.5 40.4 1.0
O V:GLY162 3.7 35.7 1.0
CA L:ASP222 3.7 53.5 1.0
CA V:LEU167 3.9 37.5 1.0
CA V:ILE163 3.9 38.1 1.0
N V:LEU167 3.9 37.2 1.0
O L:ASP222 4.0 55.6 1.0
NH1 V:ARG19 4.0 44.9 1.0
N V:ASP166 4.0 37.2 1.0
N V:TRP164 4.1 39.7 1.0
C V:TRP164 4.2 40.0 1.0
CA V:ASP166 4.2 36.6 1.0
CB L:ASP222 4.2 54.7 1.0
O V:TRP164 4.3 41.9 1.0
N V:SER169 4.3 37.6 1.0
C V:LEU167 4.3 37.5 1.0
CA V:SER169 4.3 38.7 1.0
CA V:TRP164 4.4 40.0 1.0
N V:GLY170 4.4 41.2 1.0
CA V:GLY170 4.4 43.8 1.0
N V:ASN165 4.5 38.7 1.0
O V:LEU167 4.5 37.3 1.0
CZ V:ARG19 4.6 43.7 1.0
C V:GLY162 4.7 37.4 1.0
CB V:SER169 4.7 38.0 1.0
C V:ASN165 4.7 37.4 1.0
N V:ILE163 4.8 38.1 1.0
NH2 V:ARG19 4.8 45.6 1.0
CB V:ASP166 5.0 36.0 1.0
CG2 V:ILE163 5.0 38.3 1.0

Magnesium binding site 7 out of 9 in 4ya1

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome BETA2-H116N 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-H116N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:42.4
occ:1.00
 O N:ILE163 2.5 34.1 1.0
O N:SER169 2.5 34.4 1.0
O N:ASP166 2.8 35.6 1.0
CD1 a:LEU34 3.5 38.4 1.0
NH1 N:ARG19 3.6 35.9 1.0
C N:ILE163 3.6 34.9 1.0
C N:SER169 3.7 35.2 1.0
C N:ASP166 3.8 33.9 1.0
CG2 N:ILE163 3.9 33.2 1.0
CA N:GLY167 4.1 32.6 1.0
CZ N:ARG19 4.3 35.8 1.0
CA N:ILE163 4.3 33.9 1.0
O N:GLY167 4.4 31.6 1.0
N N:GLY167 4.4 33.0 1.0
C N:GLY167 4.4 32.5 1.0
CA N:GLY170 4.5 37.1 1.0
NH2 N:ARG19 4.5 36.2 1.0
N N:GLY170 4.5 36.0 1.0
N N:SER169 4.7 33.7 1.0
N N:LYS164 4.7 36.5 1.0
CA N:SER169 4.7 33.6 1.0
CB N:ILE163 4.7 33.0 1.0
CG a:LEU34 4.8 38.0 1.0
O N:LYS164 4.9 39.6 1.0
C N:LYS164 4.9 38.0 1.0
N N:ASP166 4.9 34.4 1.0
CA N:ASP166 5.0 34.0 1.0
CA N:LYS164 5.0 38.5 1.0

Magnesium binding site 8 out of 9 in 4ya1

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome BETA2-H116N 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-H116N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:42.1
occ:1.00
 O W:ASP177 2.5 41.2 1.0
O W:SER180 2.5 43.6 1.0
O W:ALA174 2.8 38.2 1.0
C W:ASP177 3.6 39.4 1.0
C W:SER180 3.7 40.8 1.0
C W:ALA174 3.8 37.9 1.0
O W:HOH405 3.8 42.1 1.0
OXT W:ASP204 4.0 51.3 1.0
CA W:ASP175 4.2 41.9 1.0
O W:ALA178 4.2 40.3 1.0
C W:ALA178 4.3 38.6 1.0
CA W:ALA178 4.4 38.7 1.0
N W:ASP175 4.4 40.2 1.0
N W:ALA178 4.4 38.6 1.0
N W:SER180 4.4 41.2 1.0
N W:ASP177 4.4 39.9 1.0
C W:ASP175 4.5 42.0 1.0
CA W:ASP177 4.6 39.5 1.0
N W:GLY181 4.6 39.6 1.0
CA W:SER180 4.6 40.8 1.0
NH1 K:ARG19 4.6 46.1 1.0
CA W:GLY181 4.6 39.5 1.0
O W:ASP175 4.7 44.5 1.0
O W:ASP204 4.7 47.8 1.0
C W:ASP204 4.8 46.6 1.0
OD1 W:ASP175 4.8 45.7 1.0
NH2 K:ARG19 4.8 47.3 1.0
CA W:ALA174 4.9 35.6 1.0

Magnesium binding site 9 out of 9 in 4ya1

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome BETA2-H116N 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-H116N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:59.1
occ:1.00
 O Z:VAL198 2.6 40.4 1.0
O Z:HIS195 2.7 36.4 1.0
O Z:THR192 3.0 45.3 1.0
O Z:ILE196 3.6 38.6 1.0
CA Z:ILE196 3.6 38.4 1.0
NH2 Z:ARG28 3.7 44.6 1.0
C Z:HIS195 3.7 38.9 1.0
C Z:ILE196 3.7 38.0 1.0
C Z:VAL198 3.8 41.5 1.0
O Z:ASP222 3.8 55.5 1.0
C Z:THR192 4.0 46.4 1.0
N Z:ILE196 4.1 38.9 1.0
NH2 H:ARG19 4.2 50.2 1.0
CG2 Z:THR192 4.2 48.9 1.0
N Z:VAL198 4.3 40.7 1.0
CA Z:THR192 4.3 46.8 1.0
CA Z:VAL198 4.6 41.1 1.0
N Z:GLN197 4.6 38.0 1.0
CZ Z:ARG28 4.7 44.5 1.0
C Z:ASP222 4.7 56.4 1.0
OD1 Z:ASP222 4.7 51.7 1.0
N Z:GLY199 4.7 42.4 1.0
NH1 H:ARG19 4.8 50.4 1.0
CZ H:ARG19 4.8 49.4 1.0
CA Z:GLY199 4.9 43.9 1.0
CB Z:THR192 4.9 48.2 1.0
CB Z:ILE196 4.9 37.9 1.0
NH1 Z:ARG28 4.9 46.7 1.0
CA Z:HIS195 4.9 39.0 1.0
OXT Z:ASP222 5.0 55.4 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: Mon Dec 14 19:52:42 2020

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