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Magnesium in PDB 4ya4: Yeast 20S Proteasome BETA2-H114D Mutant

Enzymatic activity of Yeast 20S Proteasome BETA2-H114D Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA2-H114D Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H114D Mutant, PDB code: 4ya4 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 (°) 134.180, 300.900, 144.310, 90.00, 112.80, 90.00
R / Rfree (%) 21.4 / 23.2

Other elements in 4ya4:

The structure of Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant (pdb code 4ya4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA2-H114D Mutant, PDB code: 4ya4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4ya4

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:42.5
occ:1.00
 O G:MET125 2.2 60.1 1.0
O G:ARG122 2.4 54.3 1.0
OG1 G:THR8 2.5 55.7 1.0
O G:TYR119 2.5 48.8 1.0
CG2 G:THR8 3.2 54.2 1.0
C G:MET125 3.4 57.4 1.0
CB G:THR8 3.4 54.5 1.0
C G:ARG122 3.5 54.5 1.0
O G:ALA123 3.5 56.8 1.0
CA G:ALA123 3.7 55.5 1.0
C G:TYR119 3.7 48.8 1.0
C G:ALA123 3.7 55.5 1.0
N G:ALA123 4.1 55.0 1.0
N G:MET125 4.2 59.6 1.0
N G:THR8 4.2 56.7 1.0
N G:ARG126 4.2 53.3 1.0
CA G:ARG126 4.2 51.9 1.0
CA G:MET125 4.3 61.0 1.0
CA G:THR8 4.4 55.4 1.0
CD G:PRO127 4.5 48.7 1.0
CA G:TYR119 4.5 48.4 1.0
N G:TYR124 4.6 56.6 1.0
N G:THR120 4.7 48.8 1.0
CA G:ARG122 4.7 55.8 1.0
N G:ARG122 4.8 53.5 1.0
CA G:THR120 4.8 48.6 1.0
C G:ARG126 4.8 51.0 1.0
CB G:MET125 4.9 65.0 1.0
C G:THR120 4.9 50.0 1.0
N G:PRO127 5.0 49.2 1.0

Magnesium binding site 2 out of 8 in 4ya4

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:67.4
occ:1.00
 O I:ASP177 2.3 50.2 1.0
O I:SER180 2.6 53.3 1.0
O I:ALA174 3.0 58.0 1.0
C I:ASP177 3.5 50.2 1.0
C I:SER180 3.8 52.3 1.0
OXT I:ASP204 3.8 60.8 1.0
O I:ALA178 3.9 54.5 1.0
C I:ALA178 4.0 51.9 1.0
CA I:ALA178 4.0 50.6 1.0
C I:ALA174 4.1 51.8 1.0
N I:ALA178 4.2 49.8 1.0
N I:SER180 4.4 50.2 1.0
NH1 Y:ARG19 4.4 55.3 1.0
CA I:ASP175 4.4 54.1 1.0
O I:ASP204 4.5 62.8 1.0
N I:ASP177 4.5 49.8 1.0
CA I:ASP177 4.6 49.8 1.0
C I:ASP204 4.6 60.2 1.0
CA I:SER180 4.6 51.2 1.0
C I:ASP175 4.7 52.5 1.0
N I:GLY181 4.7 52.2 1.0
N I:ASP175 4.7 52.9 1.0
NH2 Y:ARG19 4.7 57.0 1.0
CA I:GLY181 4.7 51.9 1.0
O I:ASP175 4.8 54.9 1.0
N I:LEU179 4.8 51.3 1.0
CZ Y:ARG19 5.0 55.9 1.0

Magnesium binding site 3 out of 8 in 4ya4

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:38.1
occ:1.00
 O Y:ASP168 2.1 46.5 1.0
O I:ASP204 2.5 62.8 1.0
O Y:ALA165 2.6 47.7 1.0
O Y:SER171 2.6 45.4 1.0
C Y:ASP168 3.2 46.8 1.0
C I:ASP204 3.3 60.2 1.0
CA Y:ALA169 3.5 46.4 1.0
O Y:ALA169 3.5 48.0 1.0
C Y:ALA169 3.6 47.2 1.0
NH1 Y:ARG19 3.6 55.3 1.0
C Y:ALA165 3.7 47.0 1.0
N Y:ALA169 3.7 47.1 1.0
C Y:SER171 3.8 47.2 1.0
CA I:ASP204 3.8 59.2 1.0
CB I:ASP204 4.1 60.8 1.0
O Y:HIS166 4.1 46.0 1.0
N Y:SER171 4.1 46.5 1.0
OXT I:ASP204 4.2 60.8 1.0
CZ Y:ARG19 4.4 55.9 1.0
N Y:TYR170 4.4 47.8 1.0
CA Y:ASP168 4.4 46.7 1.0
CA Y:ALA165 4.4 46.8 1.0
N Y:ASP168 4.5 45.9 1.0
CA Y:SER171 4.5 47.0 1.0
C Y:HIS166 4.5 46.2 1.0
N Y:HIS166 4.7 47.7 1.0
NH2 Y:ARG19 4.8 57.0 1.0
N Y:GLY172 4.8 47.9 1.0
O Y:ALA164 4.8 47.6 1.0
CB Y:ALA169 4.8 45.8 1.0
C Y:ARG167 4.9 45.0 1.0
CA Y:HIS166 4.9 46.8 1.0
CA Y:GLY172 4.9 48.9 1.0

Magnesium binding site 4 out of 8 in 4ya4

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:41.4
occ:1.00
 O K:ASP168 2.0 51.0 1.0
O K:ALA165 2.2 51.4 1.0
O W:ASP204 2.7 59.5 1.0
O K:SER171 2.7 56.1 1.0
C K:ASP168 3.0 48.9 1.0
C K:ALA165 3.4 49.8 1.0
C W:ASP204 3.4 60.8 1.0
CA K:ALA169 3.6 49.4 1.0
N K:ALA169 3.6 49.3 1.0
O W:HOH413 3.7 42.2 1.0
O K:HIS166 3.7 49.9 1.0
C K:ALA169 3.8 50.2 1.0
CA W:ASP204 3.8 59.8 1.0
O K:ALA169 3.9 50.4 1.0
C K:SER171 3.9 52.3 1.0
N K:ASP168 4.0 46.8 1.0
C K:HIS166 4.0 49.5 1.0
CA K:ASP168 4.1 47.7 1.0
NH1 K:ARG19 4.1 57.5 1.0
CA K:ALA165 4.1 50.2 1.0
CB W:ASP204 4.1 58.7 1.0
N K:SER171 4.3 50.2 1.0
OXT W:ASP204 4.3 66.1 1.0
N K:HIS166 4.3 48.7 1.0
O K:ALA164 4.4 50.2 1.0
C K:ARG167 4.4 47.8 1.0
CA K:HIS166 4.5 49.2 1.0
N K:TYR170 4.5 50.9 1.0
CA K:SER171 4.6 50.3 1.0
N K:ARG167 4.6 49.3 1.0
O K:ARG167 4.8 46.8 1.0
CB K:ASP168 4.8 48.0 1.0
CZ K:ARG19 4.8 57.2 1.0
CB K:SER171 4.9 49.4 1.0
CB K:ALA169 5.0 48.8 1.0
N K:GLY172 5.0 51.8 1.0
O W:HOH411 5.0 42.3 1.0

Magnesium binding site 5 out of 8 in 4ya4

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:66.6
occ:1.00
 O V:ASP166 2.0 54.5 1.0
OXT L:ASP222 2.2 66.5 1.0
O V:ILE163 2.2 47.8 1.0
O V:SER169 2.5 54.9 1.0
C V:ASP166 3.0 54.3 1.0
C L:ASP222 3.1 67.3 1.0
C V:ILE163 3.3 53.6 1.0
C V:SER169 3.6 56.0 1.0
N V:LEU167 3.7 54.2 1.0
CA V:LEU167 3.7 53.8 1.0
CA L:ASP222 3.8 67.8 1.0
O V:GLY162 3.8 55.7 1.0
O L:ASP222 3.9 67.3 1.0
N V:ASP166 4.0 52.7 1.0
NH1 V:ARG19 4.0 59.4 1.0
CA V:ASP166 4.1 52.5 1.0
O V:TRP164 4.1 55.5 1.0
C V:TRP164 4.1 56.0 1.0
CA V:ILE163 4.2 54.5 1.0
C V:LEU167 4.2 53.5 1.0
N V:TRP164 4.3 55.9 1.0
N V:SER169 4.3 53.5 1.0
CB L:ASP222 4.4 68.2 1.0
CA V:TRP164 4.4 56.1 1.0
O V:LEU167 4.5 53.8 1.0
CA V:SER169 4.5 54.8 1.0
N V:ASN165 4.5 54.1 1.0
N V:GLY170 4.5 58.8 1.0
CA V:GLY170 4.6 60.7 1.0
C V:ASN165 4.6 53.2 1.0
CZ V:ARG19 4.6 59.3 1.0
C V:GLY162 4.8 54.9 1.0
CB V:SER169 4.8 54.8 1.0
NH2 V:ARG19 4.9 60.6 1.0
CB V:ASP166 4.9 51.5 1.0
N V:GLY168 4.9 53.1 1.0
CD2 V:LEU167 4.9 53.9 1.0
O L:ARG221 5.0 66.4 1.0

Magnesium binding site 6 out of 8 in 4ya4

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:42.9
occ:1.00
 O N:SER169 2.5 42.1 1.0
O N:ILE163 2.8 42.7 1.0
O N:ASP166 2.8 45.5 1.0
NH1 N:ARG19 3.3 45.9 1.0
CD1 a:LEU34 3.5 52.9 1.0
C N:SER169 3.7 44.6 1.0
C N:ASP166 3.8 44.4 1.0
C N:ILE163 3.9 44.8 1.0
CA N:GLY167 4.0 43.5 1.0
CZ N:ARG19 4.0 46.2 1.0
CG2 N:ILE163 4.1 44.6 1.0
O N:GLY167 4.2 43.0 1.0
C N:GLY167 4.3 42.5 1.0
N N:GLY167 4.3 44.1 1.0
NH2 N:ARG19 4.3 48.5 1.0
CA N:GLY170 4.4 48.0 1.0
CA N:ILE163 4.5 44.6 1.0
N N:GLY170 4.5 46.5 1.0
N N:SER169 4.6 43.7 1.0
CA N:SER169 4.7 43.5 1.0
CG a:LEU34 4.7 51.7 1.0
NE N:ARG19 4.9 46.5 1.0
CB N:ILE163 4.9 44.3 1.0
N N:LYS164 5.0 47.2 1.0

Magnesium binding site 7 out of 8 in 4ya4

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:45.0
occ:1.00
 O W:ASP177 2.1 52.7 1.0
O W:SER180 2.4 52.2 1.0
O W:ALA174 2.8 50.2 1.0
C W:ASP177 3.3 53.0 1.0
O W:HOH411 3.5 42.3 1.0
C W:SER180 3.6 52.7 1.0
C W:ALA174 3.9 52.0 1.0
O W:ALA178 3.9 52.8 1.0
C W:ALA178 4.0 52.4 1.0
OXT W:ASP204 4.0 66.1 1.0
CA W:ALA178 4.1 52.4 1.0
N W:ALA178 4.1 51.8 1.0
N W:SER180 4.2 54.0 1.0
N W:ASP177 4.3 53.3 1.0
CA W:ASP175 4.3 56.9 1.0
CA W:ASP177 4.4 52.8 1.0
CA W:SER180 4.4 53.7 1.0
N W:GLY181 4.5 52.2 1.0
N W:ASP175 4.6 55.2 1.0
NH1 K:ARG19 4.6 57.5 1.0
C W:ASP175 4.6 56.1 1.0
CA W:GLY181 4.6 53.4 1.0
N W:LEU179 4.7 52.0 1.0
O W:ASP175 4.8 57.5 1.0
O W:ASP204 4.8 59.5 1.0
CB W:ASP177 4.9 53.9 1.0
C W:ASP204 4.9 60.8 1.0
CA W:ALA174 4.9 49.9 1.0
CB W:SER180 4.9 53.8 1.0
NH2 K:ARG19 5.0 58.9 1.0

Magnesium binding site 8 out of 8 in 4ya4

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:53.8
occ:1.00
 O Z:VAL198 2.4 58.6 1.0
O Z:HIS195 2.6 52.7 1.0
O Z:THR192 3.0 61.1 1.0
O Z:ILE196 3.4 55.3 1.0
NH2 Z:ARG28 3.5 63.2 1.0
CA Z:ILE196 3.5 53.6 1.0
C Z:ILE196 3.6 53.9 1.0
C Z:VAL198 3.6 57.8 1.0
C Z:HIS195 3.6 53.8 1.0
O Z:ASP222 3.8 74.6 1.0
N Z:ILE196 4.0 53.1 1.0
N Z:VAL198 4.0 54.2 1.0
C Z:THR192 4.0 62.0 1.0
CG2 Z:THR192 4.2 65.7 1.0
CA Z:THR192 4.3 62.8 1.0
CA Z:VAL198 4.3 56.0 1.0
NH2 H:ARG19 4.4 65.0 1.0
N Z:GLN197 4.4 53.0 1.0
CZ Z:ARG28 4.5 61.6 1.0
N Z:GLY199 4.6 58.3 1.0
CA Z:GLY199 4.7 59.1 1.0
C Z:ASP222 4.8 74.3 1.0
NH1 Z:ARG28 4.8 62.9 1.0
OD1 Z:ASP222 4.8 70.4 1.0
CB Z:ILE196 4.9 53.6 1.0
CB Z:VAL198 4.9 55.5 1.0
CB Z:THR192 4.9 64.4 1.0
NH1 H:ARG19 4.9 62.1 1.0
CA Z:HIS195 4.9 53.9 1.0
C Z:GLN197 4.9 53.1 1.0
CZ H:ARG19 5.0 62.9 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 23:06:52 2024

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