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Magnesium in PDB 5fga: Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans)

Enzymatic activity of Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans)

All present enzymatic activity of Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans):
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans), PDB code: 5fga 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.350, 300.500, 144.440, 90.00, 113.10, 90.00
R / Rfree (%) 18.8 / 21.4

Other elements in 5fga:

The structure of Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) (pdb code 5fga). 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-K33A Mutant (Propeptide Expressed in Trans), PDB code: 5fga:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5fga

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans)


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-K33A Mutant (Propeptide Expressed in Trans) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:63.5
occ:1.00
 O G:MET125 2.2 51.0 1.0
O G:ARG122 2.5 41.2 1.0
OG1 G:THR8 2.6 40.4 1.0
O G:TYR119 2.7 41.5 1.0
CG2 G:THR8 3.3 45.5 1.0
C G:MET125 3.3 49.8 1.0
O G:ALA123 3.4 54.3 1.0
CB G:THR8 3.5 45.0 1.0
C G:ARG122 3.6 45.4 1.0
C G:ALA123 3.7 50.6 1.0
CA G:ALA123 3.7 47.8 1.0
C G:TYR119 3.9 40.9 1.0
N G:ALA123 4.1 46.1 1.0
N G:ARG126 4.1 46.7 1.0
CA G:ARG126 4.1 45.3 1.0
N G:MET125 4.1 52.0 1.0
N G:THR8 4.2 46.9 1.0
CA G:MET125 4.3 53.7 1.0
CD G:PRO127 4.5 42.5 1.0
O G:HOH420 4.5 58.3 1.0
CA G:THR8 4.5 46.1 1.0
N G:TYR124 4.6 52.0 1.0
CA G:TYR119 4.6 41.1 1.0
C G:ARG126 4.8 44.0 1.0
CA G:ARG122 4.8 48.3 1.0
N G:THR120 4.9 40.3 1.0
CB G:MET125 4.9 58.6 1.0
N G:ARG122 4.9 44.3 1.0
C G:TYR124 4.9 51.5 1.0
N G:PRO127 5.0 42.4 1.0

Magnesium binding site 2 out of 8 in 5fga

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans)


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-K33A Mutant (Propeptide Expressed in Trans) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:72.4
occ:1.00
 O I:ASP177 2.5 51.4 1.0
O I:SER180 2.8 47.1 1.0
O I:ALA174 3.1 50.1 1.0
OXT I:ASP204 3.5 62.8 1.0
C I:ASP177 3.6 51.1 1.0
C I:SER180 4.0 51.1 1.0
O I:ALA178 4.0 56.0 1.0
NH1 Y:ARG19 4.0 58.2 1.0
CA I:ALA178 4.2 51.4 1.0
C I:ALA174 4.2 50.3 1.0
C I:ALA178 4.2 54.2 1.0
O I:ASP204 4.2 57.3 1.0
C I:ASP204 4.3 58.7 1.0
N I:ALA178 4.3 49.9 1.0
CA I:ASP175 4.4 52.3 1.0
NH2 Y:ARG19 4.5 57.1 1.0
N I:ASP177 4.6 50.4 1.0
CZ Y:ARG19 4.7 57.1 1.0
N I:SER180 4.7 49.3 1.0
C I:ASP175 4.7 53.8 1.0
CA I:ASP177 4.7 50.3 1.0
N I:ASP175 4.8 50.5 1.0
O I:ASP175 4.8 57.7 1.0
CA I:GLY181 4.9 50.2 1.0
N I:GLY181 4.9 49.9 1.0
CA I:SER180 4.9 51.1 1.0
OD1 I:ASP175 5.0 55.3 1.0

Magnesium binding site 3 out of 8 in 5fga

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans)


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-K33A Mutant (Propeptide Expressed in Trans) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:57.8
occ:1.00
 O Y:ASP168 2.2 49.1 1.0
O I:ASP204 2.4 57.3 1.0
O Y:ALA165 2.5 48.8 1.0
O Y:SER171 2.9 51.4 1.0
C I:ASP204 3.1 58.7 1.0
C Y:ASP168 3.2 47.6 1.0
CA Y:ALA169 3.5 47.4 1.0
CA I:ASP204 3.6 57.1 1.0
O Y:ALA169 3.6 49.2 1.0
C Y:ALA165 3.6 47.2 1.0
N Y:ALA169 3.7 47.6 1.0
C Y:ALA169 3.7 49.2 1.0
O Y:HIS166 3.8 50.3 1.0
OXT I:ASP204 3.9 62.8 1.0
NH1 Y:ARG19 3.9 58.2 1.0
CB I:ASP204 4.1 57.9 1.0
C Y:SER171 4.1 49.3 1.0
C Y:HIS166 4.2 46.6 1.0
N Y:ASP168 4.3 47.9 1.0
CA Y:ASP168 4.4 47.7 1.0
N Y:SER171 4.4 48.5 1.0
CA Y:ALA165 4.5 47.2 1.0
N Y:HIS166 4.6 47.0 1.0
N Y:TYR170 4.6 49.4 1.0
CA Y:HIS166 4.7 46.5 1.0
C Y:ARG167 4.7 48.8 1.0
CZ Y:ARG19 4.7 57.1 1.0
O Y:ALA164 4.8 44.7 1.0
CA Y:SER171 4.8 47.9 1.0
CB Y:ALA169 4.8 46.5 1.0
N Y:ARG167 4.9 46.3 1.0
N I:ASP204 5.0 56.4 1.0

Magnesium binding site 4 out of 8 in 5fga

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans)


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-K33A Mutant (Propeptide Expressed in Trans) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:56.1
occ:1.00
 O K:ASP168 2.2 43.3 1.0
O W:ASP204 2.3 57.9 1.0
O K:ALA165 2.3 49.5 1.0
O K:SER171 2.7 52.2 1.0
C W:ASP204 3.0 57.6 1.0
C K:ASP168 3.2 47.6 1.0
CA W:ASP204 3.5 57.4 1.0
C K:ALA165 3.5 49.5 1.0
CA K:ALA169 3.6 48.5 1.0
O K:ALA169 3.7 50.7 1.0
C K:ALA169 3.7 50.2 1.0
N K:ALA169 3.8 48.0 1.0
NH1 K:ARG19 3.9 58.4 1.0
O K:HIS166 3.9 53.0 1.0
C K:SER171 3.9 51.0 1.0
CB W:ASP204 3.9 56.1 1.0
OXT W:ASP204 3.9 60.6 1.0
C K:HIS166 4.3 49.5 1.0
N K:SER171 4.3 51.2 1.0
CA K:ALA165 4.3 49.6 1.0
N K:ASP168 4.4 48.3 1.0
CA K:ASP168 4.4 47.9 1.0
N K:HIS166 4.5 49.6 1.0
N K:TYR170 4.6 51.5 1.0
CZ K:ARG19 4.6 56.7 1.0
CA K:SER171 4.6 49.5 1.0
CA K:HIS166 4.7 49.4 1.0
O K:ALA164 4.7 49.3 1.0
C K:ARG167 4.8 49.8 1.0
N W:ASP204 4.9 57.7 1.0
N K:GLY172 4.9 51.7 1.0
N K:ARG167 4.9 48.7 1.0
CG W:ASP204 4.9 55.2 1.0
NH2 K:ARG19 5.0 59.9 1.0
CB K:ALA169 5.0 47.6 1.0

Magnesium binding site 5 out of 8 in 5fga

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans)


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-K33A Mutant (Propeptide Expressed in Trans) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:58.2
occ:1.00
 O V:ASP166 2.1 43.5 1.0
O V:ILE163 2.1 48.7 1.0
OXT L:ASP222 2.2 70.6 1.0
O V:SER169 2.3 48.6 1.0
C L:ASP222 3.1 65.8 1.0
C V:ASP166 3.2 46.7 1.0
C V:ILE163 3.2 49.9 1.0
C V:SER169 3.5 49.8 1.0
CA L:ASP222 3.8 64.3 1.0
O V:GLY162 3.8 47.2 1.0
CA V:LEU167 3.9 49.0 1.0
NH1 V:ARG19 3.9 58.4 1.0
N V:LEU167 3.9 47.9 1.0
O L:ASP222 4.0 66.0 1.0
CA V:ILE163 4.0 48.5 1.0
N V:ASP166 4.1 46.2 1.0
N V:TRP164 4.2 50.8 1.0
CA V:ASP166 4.2 46.6 1.0
C V:LEU167 4.3 49.5 1.0
C V:TRP164 4.3 49.6 1.0
N V:SER169 4.3 48.3 1.0
CB L:ASP222 4.3 65.2 1.0
N V:GLY170 4.4 50.7 1.0
CA V:GLY170 4.4 53.5 1.0
O V:TRP164 4.4 51.8 1.0
CA V:SER169 4.4 48.8 1.0
O V:LEU167 4.4 50.3 1.0
CA V:TRP164 4.5 50.5 1.0
CZ V:ARG19 4.5 56.0 1.0
N V:ASN165 4.6 47.7 1.0
NH2 V:ARG19 4.7 56.2 1.0
C V:GLY162 4.7 47.4 1.0
CB V:SER169 4.8 49.7 1.0
C V:ASN165 4.8 46.1 1.0
N V:ILE163 4.9 47.9 1.0
O L:ARG221 5.0 60.1 1.0
N V:GLY168 5.0 49.7 1.0
CB V:ASP166 5.0 46.1 1.0

Magnesium binding site 6 out of 8 in 5fga

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans)


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-K33A Mutant (Propeptide Expressed in Trans) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:49.5
occ:1.00
 O N:SER169 2.8 45.7 1.0
O N:ILE163 2.9 43.2 1.0
O N:ASP166 3.3 45.0 1.0
NH1 N:ARG19 3.4 46.3 1.0
CD1 a:LEU34 3.6 49.1 1.0
CZ N:ARG19 4.0 46.1 1.0
CG2 N:ILE163 4.0 42.6 1.0
C N:SER169 4.0 43.9 1.0
C N:ILE163 4.0 43.7 1.0
NH2 N:ARG19 4.2 47.9 1.0
CA N:GLY167 4.3 42.2 1.0
C N:ASP166 4.3 42.2 1.0
CA N:GLY170 4.4 45.2 1.0
O N:GLY167 4.5 42.8 1.0
C N:GLY167 4.6 42.1 1.0
CA N:ILE163 4.7 42.7 1.0
N N:GLY170 4.7 43.8 1.0
N N:GLY167 4.7 41.9 1.0
NE N:ARG19 4.9 46.8 1.0
CG a:LEU34 4.9 48.6 1.0
CB N:ILE163 5.0 41.9 1.0

Magnesium binding site 7 out of 8 in 5fga

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans)


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-K33A Mutant (Propeptide Expressed in Trans) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:73.9
occ:1.00
 O W:ASP177 2.5 51.2 1.0
O W:ALA174 2.6 46.8 1.0
O W:SER180 2.7 57.8 1.0
C W:ALA174 3.6 50.8 1.0
C W:ASP177 3.7 51.1 1.0
O W:HOH405 3.7 53.4 1.0
OXT W:ASP204 3.8 60.6 1.0
C W:SER180 3.9 54.8 1.0
CA W:ASP175 3.9 53.1 1.0
N W:ASP175 4.2 53.2 1.0
C W:ASP175 4.3 52.4 1.0
N W:ASP177 4.4 52.0 1.0
NH1 K:ARG19 4.5 58.4 1.0
OD1 W:ASP175 4.5 57.6 1.0
O W:ALA178 4.5 49.9 1.0
O W:ASP175 4.5 55.0 1.0
N W:ALA178 4.6 50.4 1.0
CA W:ALA178 4.6 50.6 1.0
CA W:ASP177 4.6 51.6 1.0
C W:ALA178 4.6 50.6 1.0
CA W:GLY181 4.6 53.0 1.0
C W:ASP204 4.7 57.6 1.0
N W:GLY181 4.7 53.7 1.0
N W:SER180 4.7 53.0 1.0
O W:ASP204 4.7 57.9 1.0
NH2 K:ARG19 4.7 59.9 1.0
CA W:ALA174 4.8 48.6 1.0
CA W:SER180 4.8 53.6 1.0
N W:ARG176 4.9 50.0 1.0
CZ K:ARG19 5.0 56.7 1.0

Magnesium binding site 8 out of 8 in 5fga

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans)


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-K33A Mutant (Propeptide Expressed in Trans) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:61.2
occ:1.00
 O Z:VAL198 2.5 48.5 1.0
O Z:THR192 2.8 57.3 1.0
O Z:HIS195 3.2 46.4 1.0
O Z:ASP222 3.4 68.0 1.0
NH2 Z:ARG28 3.6 55.6 1.0
C Z:VAL198 3.7 50.2 1.0
CG2 Z:THR192 3.8 58.5 1.0
C Z:THR192 3.8 57.9 1.0
O Z:ILE196 3.9 53.2 1.0
CA Z:THR192 4.2 58.1 1.0
NH2 H:ARG19 4.2 60.2 1.0
CA Z:ILE196 4.2 48.0 1.0
C Z:HIS195 4.2 48.8 1.0
C Z:ILE196 4.2 48.0 1.0
OD1 Z:ASP222 4.2 68.1 1.0
C Z:ASP222 4.4 67.5 1.0
CZ Z:ARG28 4.5 55.5 1.0
N Z:VAL198 4.5 47.5 1.0
CA Z:GLY199 4.5 52.1 1.0
N Z:GLY199 4.6 50.9 1.0
CB Z:THR192 4.6 58.1 1.0
NH1 Z:ARG28 4.7 56.9 1.0
N Z:ILE196 4.7 47.9 1.0
CA Z:VAL198 4.7 49.7 1.0
O Z:LYS220 4.7 56.4 1.0
OXT Z:ASP222 4.8 67.4 1.0
CZ H:ARG19 5.0 57.8 1.0
N Z:GLU193 5.0 58.0 1.0
NH1 H:ARG19 5.0 57.2 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 04:10:28 2024

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