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Magnesium in PDB 5d0w: Yeast 20S Proteasome BETA5-T1S Mutant

Enzymatic activity of Yeast 20S Proteasome BETA5-T1S Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA5-T1S Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-T1S Mutant, PDB code: 5d0w 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 (°) 133.970, 300.920, 143.870, 90.00, 112.77, 90.00
R / Rfree (%) 17.9 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA5-T1S Mutant (pdb code 5d0w). 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 BETA5-T1S Mutant, PDB code: 5d0w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5d0w

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-T1S 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 BETA5-T1S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:54.2
occ:1.00
O G:MET125 2.1 56.0 1.0
O G:ARG122 2.4 49.1 1.0
O G:TYR119 2.5 45.8 1.0
OG1 G:THR8 2.6 52.2 1.0
CG2 G:THR8 3.2 51.7 1.0
C G:MET125 3.3 55.4 1.0
CB G:THR8 3.4 51.2 1.0
C G:ARG122 3.5 51.3 1.0
O G:ALA123 3.7 57.2 1.0
C G:TYR119 3.7 46.1 1.0
CA G:ALA123 3.8 53.3 1.0
C G:ALA123 3.8 54.4 1.0
N G:ALA123 4.1 52.2 1.0
N G:ARG126 4.2 51.3 1.0
N G:MET125 4.2 58.3 1.0
CA G:ARG126 4.2 49.2 1.0
N G:THR8 4.3 53.3 1.0
CA G:MET125 4.3 59.8 1.0
CD G:PRO127 4.5 45.5 1.0
CA G:TYR119 4.5 45.9 1.0
CA G:THR8 4.5 52.2 1.0
N G:THR120 4.7 46.0 1.0
N G:TYR124 4.7 56.5 1.0
CA G:ARG122 4.7 53.1 1.0
N G:ARG122 4.7 51.4 1.0
C G:ARG126 4.8 47.1 1.0
CA G:THR120 4.8 46.1 1.0
CB G:MET125 4.8 65.0 1.0
C G:THR120 4.9 47.5 1.0
N G:PRO127 4.9 45.2 1.0
CB G:TYR119 5.0 46.0 1.0

Magnesium binding site 2 out of 8 in 5d0w

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-T1S 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 BETA5-T1S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:65.1
occ:1.00
O I:ASP177 2.4 51.5 1.0
O I:SER180 2.6 52.2 1.0
O I:ALA174 2.6 53.1 1.0
O Y:HOH405 3.3 54.6 1.0
C I:ASP177 3.5 50.5 1.0
C I:ALA174 3.7 51.3 1.0
C I:SER180 3.8 52.4 1.0
CA I:ASP175 4.0 54.3 1.0
OXT I:ASP204 4.0 63.7 1.0
N I:ASP177 4.3 51.0 1.0
N I:ASP175 4.3 51.9 1.0
C I:ASP175 4.3 55.6 1.0
CA I:ALA178 4.3 50.1 1.0
O I:ALA178 4.3 53.4 1.0
N I:ALA178 4.3 48.5 1.0
C I:ALA178 4.4 51.3 1.0
O I:ASP175 4.5 59.7 1.0
CA I:ASP177 4.5 50.3 1.0
NH1 Y:ARG19 4.5 54.8 1.0
N I:SER180 4.5 51.7 1.0
O I:ASP204 4.6 63.9 1.0
NH2 Y:ARG19 4.7 56.2 1.0
CA I:SER180 4.7 51.9 1.0
N I:GLY181 4.7 52.5 1.0
CA I:GLY181 4.7 52.4 1.0
C I:ASP204 4.8 60.6 1.0
OD1 I:ASP175 4.8 58.7 1.0
CA I:ALA174 4.9 48.6 1.0
CZ Y:ARG19 5.0 54.9 1.0
N I:ARG176 5.0 54.1 1.0

Magnesium binding site 3 out of 8 in 5d0w

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-T1S 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 BETA5-T1S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:53.4
occ:1.00
O Y:ASP168 2.3 47.6 1.0
O Y:ALA165 2.3 49.5 1.0
O I:ASP204 2.5 63.9 1.0
O Y:SER171 2.6 47.6 1.0
C I:ASP204 3.2 60.6 1.0
C Y:ASP168 3.3 48.2 1.0
C Y:ALA165 3.5 48.7 1.0
CA I:ASP204 3.6 59.7 1.0
CA Y:ALA169 3.7 48.7 1.0
C Y:SER171 3.8 49.2 1.0
NH1 Y:ARG19 3.8 54.8 1.0
CB I:ASP204 3.8 61.0 1.0
O Y:ALA169 3.9 49.1 1.0
C Y:ALA169 3.9 48.9 1.0
N Y:ALA169 3.9 49.1 1.0
OXT I:ASP204 4.0 63.7 1.0
O Y:HIS166 4.0 46.8 1.0
CA Y:ALA165 4.2 48.0 1.0
N Y:SER171 4.2 47.8 1.0
C Y:HIS166 4.3 47.4 1.0
N Y:ASP168 4.4 47.9 1.0
CA Y:ASP168 4.4 47.9 1.0
N Y:HIS166 4.5 49.8 1.0
CA Y:SER171 4.5 47.8 1.0
CZ Y:ARG19 4.5 54.9 1.0
O Y:ALA164 4.6 49.0 1.0
N Y:TYR170 4.6 48.4 1.0
CA Y:HIS166 4.7 48.1 1.0
N Y:GLY172 4.8 50.0 1.0
C Y:ARG167 4.8 47.7 1.0
NH2 Y:ARG19 4.9 56.2 1.0
CG I:ASP204 4.9 62.4 1.0
CA Y:GLY172 4.9 49.4 1.0
N Y:ARG167 4.9 46.6 1.0
CB Y:SER171 4.9 47.5 1.0
N I:ASP204 5.0 58.6 1.0

Magnesium binding site 4 out of 8 in 5d0w

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-T1S 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 BETA5-T1S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:50.7
occ:1.00
O K:ASP168 2.2 47.2 1.0
O K:ALA165 2.3 50.4 1.0
O K:SER171 2.4 53.6 1.0
O W:ASP204 2.6 63.0 1.0
C W:ASP204 3.2 61.3 1.0
C K:ASP168 3.3 47.0 1.0
C K:ALA165 3.4 48.6 1.0
C K:SER171 3.6 50.4 1.0
CA W:ASP204 3.6 57.6 1.0
NH1 K:ARG19 3.7 56.8 1.0
CA K:ALA169 3.8 47.7 1.0
CB W:ASP204 3.8 56.3 1.0
C K:ALA169 3.9 48.3 1.0
O K:ALA169 3.9 48.8 1.0
N K:ALA169 3.9 47.4 1.0
N K:SER171 4.1 49.1 1.0
CA K:ALA165 4.1 49.1 1.0
OXT W:ASP204 4.1 68.4 1.0
O K:HIS166 4.2 50.9 1.0
CA K:SER171 4.3 48.1 1.0
CA K:ASP168 4.4 45.8 1.0
N K:ASP168 4.4 46.1 1.0
C K:HIS166 4.4 48.4 1.0
CZ K:ARG19 4.4 56.5 1.0
N K:HIS166 4.5 47.0 1.0
O K:ALA164 4.5 49.3 1.0
N K:TYR170 4.6 48.8 1.0
N K:GLY172 4.6 50.3 1.0
CB K:SER171 4.7 46.6 1.0
CA K:GLY172 4.7 51.2 1.0
CA K:HIS166 4.8 47.7 1.0
NH2 K:ARG19 4.8 60.1 1.0
CG W:ASP204 4.9 56.9 1.0
C K:ARG167 4.9 47.6 1.0
CB K:ALA165 5.0 48.7 1.0
N K:ARG167 5.0 48.4 1.0

Magnesium binding site 5 out of 8 in 5d0w

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-T1S 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 BETA5-T1S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:63.4
occ:1.00
O V:ILE163 2.1 48.7 1.0
O V:ASP166 2.2 50.8 1.0
OXT L:ASP222 2.2 74.4 1.0
O V:SER169 2.3 50.5 1.0
C L:ASP222 3.1 69.1 1.0
C V:ASP166 3.2 50.1 1.0
C V:ILE163 3.3 51.6 1.0
C V:SER169 3.5 51.1 1.0
CA L:ASP222 3.7 66.6 1.0
O V:GLY162 3.8 48.5 1.0
CA V:LEU167 3.9 49.4 1.0
N V:LEU167 3.9 49.4 1.0
NH1 V:ARG19 3.9 58.5 1.0
O L:ASP222 4.0 70.5 1.0
CA V:ILE163 4.0 51.3 1.0
N V:ASP166 4.1 49.1 1.0
N V:TRP164 4.2 52.2 1.0
C V:TRP164 4.2 54.7 1.0
CA V:ASP166 4.2 48.8 1.0
C V:LEU167 4.3 48.2 1.0
CB L:ASP222 4.3 65.9 1.0
N V:SER169 4.3 50.1 1.0
O V:TRP164 4.3 58.1 1.0
N V:GLY170 4.4 52.8 1.0
CA V:SER169 4.4 50.8 1.0
CA V:GLY170 4.4 55.9 1.0
O V:LEU167 4.4 47.0 1.0
CA V:TRP164 4.4 53.2 1.0
CZ V:ARG19 4.6 57.6 1.0
N V:ASN165 4.6 52.9 1.0
CB V:SER169 4.8 50.3 1.0
C V:GLY162 4.8 50.4 1.0
C V:ASN165 4.8 49.7 1.0
NH2 V:ARG19 4.8 59.0 1.0
N V:ILE163 4.9 50.6 1.0
O L:ARG221 5.0 61.4 1.0
N V:GLY168 5.0 49.6 1.0

Magnesium binding site 6 out of 8 in 5d0w

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-T1S 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 BETA5-T1S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:54.5
occ:1.00
O N:SER169 2.4 42.6 1.0
O N:ILE163 2.6 45.7 1.0
O N:ASP166 2.8 47.1 1.0
NH1 N:ARG19 3.5 46.2 1.0
CD1 a:LEU34 3.6 48.8 1.0
C N:SER169 3.6 44.4 1.0
C N:ILE163 3.8 45.3 1.0
C N:ASP166 3.8 43.5 1.0
CG2 N:ILE163 4.0 43.8 1.0
CA N:GLY167 4.0 42.9 1.0
CZ N:ARG19 4.1 45.6 1.0
O N:GLY167 4.2 42.2 1.0
C N:GLY167 4.3 42.4 1.0
N N:GLY167 4.3 43.0 1.0
CA N:ILE163 4.4 44.2 1.0
CA N:GLY170 4.4 46.9 1.0
NH2 N:ARG19 4.4 47.3 1.0
N N:GLY170 4.4 45.5 1.0
N N:SER169 4.6 43.9 1.0
CA N:SER169 4.6 43.3 1.0
CB N:ILE163 4.8 43.5 1.0
CG a:LEU34 4.8 48.0 1.0
N N:LYS164 4.9 46.6 1.0
NE N:ARG19 4.9 45.2 1.0
N N:ASP166 5.0 42.6 1.0
CA N:ASP166 5.0 43.0 1.0

Magnesium binding site 7 out of 8 in 5d0w

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-T1S 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 BETA5-T1S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:66.8
occ:1.00
O N:HOH310 2.2 45.9 1.0
OD1 N:ASP51 3.2 48.2 1.0
O N:ASN92 3.3 52.4 1.0
NE2 H:GLN91 3.4 75.7 1.0
OD2 N:ASP51 3.7 44.4 1.0
CG N:ASP51 3.9 43.2 1.0
O N:HOH308 4.0 47.6 1.0
C N:ASN92 4.5 49.7 1.0
CD H:GLN91 4.6 72.2 1.0

Magnesium binding site 8 out of 8 in 5d0w

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-T1S 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 BETA5-T1S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:75.9
occ:1.00
O Z:VAL198 2.5 53.1 1.0
O Z:HIS195 2.6 45.6 1.0
O Z:THR192 2.8 58.2 1.0
O Z:ILE196 3.6 53.1 1.0
C Z:HIS195 3.6 50.2 1.0
C Z:VAL198 3.7 53.8 1.0
CA Z:ILE196 3.7 50.7 1.0
NH2 Z:ARG28 3.7 59.9 1.0
C Z:ILE196 3.8 50.9 1.0
C Z:THR192 3.8 59.9 1.0
O Z:ASP222 3.9 71.9 1.0
CG2 Z:THR192 4.0 61.4 1.0
CA Z:THR192 4.1 59.7 1.0
N Z:ILE196 4.1 50.1 1.0
N Z:VAL198 4.2 53.4 1.0
NH2 H:ARG19 4.3 59.2 1.0
CA Z:VAL198 4.5 53.4 1.0
N Z:GLN197 4.6 49.7 1.0
N Z:GLY199 4.7 54.3 1.0
CB Z:THR192 4.7 60.8 1.0
CZ Z:ARG28 4.7 58.5 1.0
OD1 Z:ASP222 4.8 68.6 1.0
CA Z:GLY199 4.8 56.0 1.0
C Z:ASP222 4.8 73.3 1.0
CA Z:HIS195 4.9 51.2 1.0
CB Z:VAL198 4.9 52.8 1.0
N Z:HIS195 4.9 53.1 1.0
NH1 H:ARG19 5.0 61.3 1.0
NH1 Z:ARG28 5.0 60.0 1.0

Reference:

E.M.Huber, W.Heinemeyer, X.Li, C.S.Arendt, M.Hochstrasser, M.Groll. A Unified Mechanism For Proteolysis and Autocatalytic Activation in the 20S Proteasome. Nat Commun V. 7 10900 2016.
ISSN: ESSN 2041-1723
PubMed: 26964885
DOI: 10.1038/NCOMMS10900
Page generated: Sun Sep 29 02:25:54 2024

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