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Magnesium in PDB 5fg9: Yeast 20S Proteasome BETA2-T(-2)V Mutant

Enzymatic activity of Yeast 20S Proteasome BETA2-T(-2)V Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA2-T(-2)V Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-T(-2)V Mutant, PDB code: 5fg9 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.570, 301.550, 145.130, 90.00, 113.36, 90.00
R / Rfree (%) 20.9 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-T(-2)V Mutant (pdb code 5fg9). 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-T(-2)V Mutant, PDB code: 5fg9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5fg9

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:47.4
occ:1.00
 O G:MET125 2.1 43.9 1.0
O G:ARG122 2.5 40.7 1.0
OG1 G:THR8 2.6 39.2 1.0
O G:TYR119 2.7 36.0 1.0
C G:MET125 3.3 43.8 1.0
CG2 G:THR8 3.3 39.8 1.0
O G:ALA123 3.4 43.5 1.0
CB G:THR8 3.5 39.7 1.0
C G:ARG122 3.6 40.9 1.0
C G:ALA123 3.7 43.3 1.0
CA G:ALA123 3.7 41.2 1.0
C G:TYR119 3.9 35.2 1.0
N G:MET125 4.1 44.9 1.0
N G:ALA123 4.1 40.4 1.0
N G:ARG126 4.1 40.1 1.0
CA G:ARG126 4.1 38.2 1.0
CA G:MET125 4.2 47.2 1.0
N G:THR8 4.3 40.6 1.0
CD G:PRO127 4.5 34.9 1.0
CA G:THR8 4.5 40.0 1.0
N G:TYR124 4.6 44.1 1.0
CA G:TYR119 4.6 35.2 1.0
C G:ARG126 4.8 36.4 1.0
CB G:MET125 4.8 52.0 1.0
CA G:ARG122 4.8 42.0 1.0
N G:ARG122 4.9 38.8 1.0
N G:THR120 4.9 34.5 1.0
C G:TYR124 4.9 44.5 1.0
N G:PRO127 5.0 35.2 1.0

Magnesium binding site 2 out of 9 in 5fg9

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

b:56.2
occ:1.00
 O I:ASP177 2.5 41.7 1.0
O I:SER180 2.6 44.8 1.0
O I:ALA174 2.8 43.6 1.0
C I:ASP177 3.6 41.1 1.0
C I:SER180 3.8 43.9 1.0
C I:ALA174 3.8 42.9 1.0
OXT I:ASP204 3.9 47.8 1.0
CA I:ASP175 4.1 44.7 1.0
O I:ALA178 4.3 43.2 1.0
CA I:ALA178 4.4 41.1 1.0
N I:ASP175 4.4 44.3 1.0
C I:ALA178 4.4 42.6 1.0
N I:ALA178 4.4 40.3 1.0
N I:ASP177 4.5 41.9 1.0
C I:ASP175 4.5 44.3 1.0
N I:SER180 4.6 42.4 1.0
O I:ASP204 4.6 46.1 1.0
NH1 Y:ARG19 4.6 49.3 1.0
CA I:ASP177 4.6 41.0 1.0
CA I:GLY181 4.6 43.1 1.0
C I:ASP204 4.7 46.4 1.0
N I:GLY181 4.7 43.2 1.0
O I:ASP175 4.7 46.6 1.0
NH2 Y:ARG19 4.7 47.8 1.0
OD1 I:ASP175 4.7 45.9 1.0
CA I:SER180 4.7 43.8 1.0
CA I:ALA174 5.0 40.8 1.0

Magnesium binding site 3 out of 9 in 5fg9

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:54.4
occ:1.00
 O J:THR124 3.1 36.3 1.0
N J:ASP120 3.3 33.9 1.0
OE1 J:GLN118 3.3 37.3 1.0
CB J:ASP120 3.5 34.7 1.0
CG J:GLN118 3.7 35.3 1.0
CG J:ASP120 3.7 35.5 1.0
CE1 J:HIS133 3.8 34.1 1.0
OD2 J:ASP120 3.8 36.8 1.0
C J:ILE119 3.9 33.5 1.0
O J:GLN118 3.9 34.0 1.0
CD J:GLN118 4.0 35.8 1.0
CA J:ASP120 4.0 34.4 1.0
CA J:ILE119 4.1 33.0 1.0
CB J:THR124 4.2 37.3 1.0
C J:GLN118 4.2 33.8 1.0
C J:THR124 4.2 36.9 1.0
N J:ILE119 4.3 33.1 1.0
OD1 J:ASP120 4.4 36.5 1.0
CG2 J:THR124 4.6 36.6 1.0
ND1 J:HIS133 4.6 34.7 1.0
CB J:GLN118 4.6 34.4 1.0
NE2 J:HIS133 4.7 33.3 1.0
O J:ILE119 4.8 34.5 1.0
CA J:THR124 4.8 37.1 1.0

Magnesium binding site 4 out of 9 in 5fg9

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:41.3
occ:1.00
 O K:ALA165 2.3 41.7 1.0
O K:ASP168 2.4 37.7 1.0
O K:SER171 2.4 40.3 1.0
O W:ASP204 2.4 47.5 1.0
C W:ASP204 3.1 46.9 1.0
C K:ASP168 3.4 37.7 1.0
C K:ALA165 3.4 40.1 1.0
CA W:ASP204 3.5 46.7 1.0
C K:SER171 3.6 41.6 1.0
NH1 K:ARG19 3.7 45.5 1.0
CB W:ASP204 3.8 46.9 1.0
CA K:ALA169 3.8 38.0 1.0
O K:ALA169 3.9 41.7 1.0
C K:ALA169 3.9 39.8 1.0
OXT W:ASP204 4.0 46.5 1.0
N K:ALA169 4.0 37.6 1.0
CA K:ALA165 4.2 40.5 1.0
O K:HIS166 4.2 40.6 1.0
N K:SER171 4.2 41.0 1.0
CZ K:ARG19 4.4 45.1 1.0
C K:HIS166 4.4 38.4 1.0
CA K:SER171 4.4 40.6 1.0
N K:HIS166 4.5 39.3 1.0
N K:ASP168 4.6 38.0 1.0
CA K:ASP168 4.6 37.2 1.0
N K:GLY172 4.6 42.9 1.0
O K:ALA164 4.6 39.2 1.0
N K:TYR170 4.7 39.7 1.0
NH2 K:ARG19 4.7 47.0 1.0
CA K:GLY172 4.7 44.2 1.0
CA K:HIS166 4.7 39.0 1.0
CG W:ASP204 4.8 47.5 1.0
CB K:SER171 4.9 40.3 1.0
N W:ASP204 4.9 46.5 1.0
CB K:ALA165 5.0 40.3 1.0

Magnesium binding site 5 out of 9 in 5fg9

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:46.9
occ:1.00
 O K:ILE82 2.7 37.5 1.0
O K:HOH405 2.9 36.8 1.0
C K:ILE82 3.5 36.8 1.0
CA K:ILE82 3.6 36.4 1.0
N K:LEU86 3.8 33.0 1.0
CB K:ASN85 3.8 35.0 1.0
CG2 K:ILE82 3.8 36.3 1.0
CB K:LEU86 4.1 33.6 1.0
CB K:ILE82 4.2 36.3 1.0
CA K:LEU86 4.2 33.1 1.0
C K:ASN85 4.3 33.7 1.0
CH2 K:TRP58 4.3 32.2 1.0
CA K:ASN85 4.6 34.5 1.0
O K:LYS81 4.6 35.0 1.0
CG1 K:ILE82 4.7 36.5 1.0
N K:LEU83 4.8 36.5 1.0
N K:ILE82 4.8 36.0 1.0
O K:HOH434 4.9 52.9 1.0
CG K:ASN85 4.9 35.3 1.0
OD1 K:ASN85 4.9 38.0 1.0
N K:ASN85 5.0 34.4 1.0

Magnesium binding site 6 out of 9 in 5fg9

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:40.9
occ:1.00
 O N:ILE163 2.6 37.9 1.0
O N:SER169 2.6 37.2 1.0
O N:ASP166 3.0 40.2 1.0
CD1 a:LEU34 3.6 43.6 1.0
NH1 N:ARG19 3.6 37.7 1.0
C N:ILE163 3.7 37.4 1.0
C N:SER169 3.8 37.2 1.0
CG2 N:ILE163 3.9 35.2 1.0
C N:ASP166 3.9 37.0 1.0
CA N:GLY167 4.2 35.4 1.0
CZ N:ARG19 4.2 37.6 1.0
CA N:ILE163 4.3 36.2 1.0
O N:GLY167 4.4 35.2 1.0
CA N:GLY170 4.4 37.5 1.0
N N:GLY167 4.4 35.9 1.0
NH2 N:ARG19 4.5 37.5 1.0
C N:GLY167 4.5 35.0 1.0
N N:GLY170 4.6 37.1 1.0
N N:LYS164 4.7 39.1 1.0
CB N:ILE163 4.8 35.5 1.0
N N:SER169 4.8 35.4 1.0
CA N:SER169 4.8 35.5 1.0
CG a:LEU34 4.8 43.5 1.0
O N:LYS164 4.9 42.1 1.0
C N:LYS164 4.9 40.8 1.0
CA N:LYS164 5.0 41.4 1.0
N N:ASP166 5.0 36.6 1.0

Magnesium binding site 7 out of 9 in 5fg9

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:52.9
occ:1.00
 O V:ILE163 2.1 42.3 1.0
OXT L:ASP222 2.2 56.2 1.0
O V:ASP166 2.2 41.6 1.0
O V:SER169 2.3 46.0 1.0
C L:ASP222 3.1 57.8 1.0
C V:ILE163 3.2 43.7 1.0
C V:ASP166 3.3 42.0 1.0
C V:SER169 3.4 45.4 1.0
CA L:ASP222 3.7 59.9 1.0
O V:GLY162 3.8 42.0 1.0
O L:ASP222 3.9 55.4 1.0
NH1 V:ARG19 3.9 49.6 1.0
CA V:LEU167 4.0 42.3 1.0
N V:LEU167 4.0 42.3 1.0
CA V:ILE163 4.0 43.0 1.0
N V:ASP166 4.1 41.9 1.0
N V:TRP164 4.2 45.1 1.0
CB L:ASP222 4.2 61.3 1.0
C V:TRP164 4.3 44.9 1.0
N V:SER169 4.3 42.8 1.0
CA V:ASP166 4.3 41.6 1.0
N V:GLY170 4.3 47.6 1.0
CA V:GLY170 4.3 49.3 1.0
C V:LEU167 4.3 42.0 1.0
CA V:SER169 4.4 43.4 1.0
O V:TRP164 4.4 44.6 1.0
CA V:TRP164 4.4 45.6 1.0
O V:LEU167 4.5 40.1 1.0
CZ V:ARG19 4.5 49.7 1.0
N V:ASN165 4.6 44.0 1.0
NH2 V:ARG19 4.7 51.0 1.0
CB V:SER169 4.7 43.2 1.0
C V:GLY162 4.8 42.2 1.0
C V:ASN165 4.9 42.6 1.0
N V:ILE163 4.9 42.4 1.0
O L:ARG221 5.0 55.5 1.0
CG2 V:ILE163 5.0 43.1 1.0

Magnesium binding site 8 out of 9 in 5fg9

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:40.0
occ:1.00
 O Y:ASP168 2.2 41.4 1.0
O Y:SER171 2.5 41.5 1.0
O Y:ALA165 2.5 44.0 1.0
O I:ASP204 2.6 46.1 1.0
C Y:ASP168 3.2 40.7 1.0
C I:ASP204 3.3 46.4 1.0
CA Y:ALA169 3.5 40.3 1.0
C Y:ALA165 3.6 42.0 1.0
O Y:ALA169 3.6 42.8 1.0
NH1 Y:ARG19 3.6 49.3 1.0
C Y:ALA169 3.6 41.2 1.0
C Y:SER171 3.7 42.4 1.0
N Y:ALA169 3.8 40.9 1.0
CA I:ASP204 3.9 46.9 1.0
N Y:SER171 4.1 41.3 1.0
CB I:ASP204 4.1 48.0 1.0
OXT I:ASP204 4.2 47.8 1.0
O Y:HIS166 4.2 40.5 1.0
CA Y:ALA165 4.3 41.0 1.0
CA Y:ASP168 4.4 40.6 1.0
N Y:TYR170 4.4 40.8 1.0
CA Y:SER171 4.4 41.4 1.0
CZ Y:ARG19 4.4 48.4 1.0
N Y:ASP168 4.4 41.7 1.0
C Y:HIS166 4.5 39.8 1.0
N Y:HIS166 4.7 41.6 1.0
O Y:ALA164 4.7 42.9 1.0
N Y:GLY172 4.7 42.9 1.0
NH2 Y:ARG19 4.8 47.8 1.0
CA Y:HIS166 4.9 40.4 1.0
CB Y:SER171 4.9 41.2 1.0
CA Y:GLY172 4.9 42.4 1.0
C Y:ARG167 4.9 41.0 1.0
CB Y:ALA169 4.9 39.9 1.0

Magnesium binding site 9 out of 9 in 5fg9

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

b:59.7
occ:1.00
 O Z:VAL198 2.4 47.1 1.0
O Z:THR192 2.8 52.1 1.0
O Z:HIS195 2.8 40.8 1.0
C Z:VAL198 3.6 46.5 1.0
NH2 Z:ARG28 3.7 47.9 1.0
O Z:ILE196 3.8 45.5 1.0
C Z:THR192 3.8 52.1 1.0
C Z:HIS195 3.8 42.9 1.0
O Z:ASP222 3.9 55.4 1.0
CA Z:ILE196 3.9 43.0 1.0
CG2 Z:THR192 3.9 53.1 1.0
C Z:ILE196 4.0 43.1 1.0
CA Z:THR192 4.1 52.1 1.0
N Z:VAL198 4.2 43.9 1.0
NH2 H:ARG19 4.3 53.9 1.0
N Z:ILE196 4.3 43.3 1.0
CA Z:VAL198 4.4 45.2 1.0
N Z:GLY199 4.5 47.0 1.0
OD1 Z:ASP222 4.6 52.6 1.0
CA Z:GLY199 4.6 47.2 1.0
CB Z:THR192 4.7 53.3 1.0
CZ Z:ARG28 4.7 48.9 1.0
C Z:ASP222 4.8 58.6 1.0
N Z:GLN197 4.8 42.6 1.0
CB Z:VAL198 4.9 45.0 1.0
NH1 Z:ARG28 4.9 49.5 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 04:10:02 2024

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