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Magnesium in PDB 5cza: Yeast 20S Proteasome BETA5-D166N Mutant

Enzymatic activity of Yeast 20S Proteasome BETA5-D166N Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA5-D166N Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-D166N Mutant, PDB code: 5cza 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.770, 301.430, 144.140, 90.00, 112.84, 90.00
R / Rfree (%) 20.6 / 22.4

Other elements in 5cza:

The structure of Yeast 20S Proteasome BETA5-D166N 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 BETA5-D166N Mutant (pdb code 5cza). 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-D166N Mutant, PDB code: 5cza:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5cza

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:34.9
occ:1.00
 O G:MET125 2.2 42.2 1.0
O G:ARG122 2.2 39.0 1.0
O G:TYR119 2.3 34.0 1.0
OG1 G:THR8 2.5 39.3 1.0
O G:HOH416 2.6 34.8 1.0
CG2 G:THR8 3.3 37.7 1.0
C G:ARG122 3.4 39.2 1.0
C G:MET125 3.4 40.2 1.0
CB G:THR8 3.5 38.3 1.0
C G:TYR119 3.5 33.4 1.0
O G:ALA123 3.7 40.9 1.0
CA G:ALA123 3.7 39.0 1.0
C G:ALA123 3.8 40.2 1.0
N G:ALA123 4.0 38.4 1.0
N G:MET125 4.2 43.3 1.0
CA G:TYR119 4.3 32.9 1.0
N G:ARG126 4.3 36.2 1.0
CA G:MET125 4.3 43.8 1.0
CA G:ARG126 4.3 34.6 1.0
N G:THR8 4.4 39.3 1.0
N G:THR120 4.5 33.7 1.0
N G:ARG122 4.5 38.5 1.0
CA G:ARG122 4.5 40.5 1.0
CA G:THR8 4.6 38.8 1.0
CD G:PRO127 4.6 32.4 1.0
N G:TYR124 4.7 41.2 1.0
CA G:THR120 4.7 33.6 1.0
C G:THR120 4.7 34.6 1.0
CB G:MET125 4.8 48.0 1.0
C G:ARG126 4.9 33.0 1.0
CB G:TYR119 4.9 32.8 1.0
N G:GLN121 4.9 34.8 1.0

Magnesium binding site 2 out of 8 in 5cza

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:46.3
occ:1.00
 O I:ASP177 2.3 37.3 1.0
O I:ALA174 2.5 37.9 1.0
O I:SER180 2.5 39.3 1.0
C I:ASP177 3.5 36.6 1.0
C I:ALA174 3.5 37.3 1.0
C I:SER180 3.6 39.2 1.0
O Y:HOH428 3.8 36.7 1.0
CA I:ASP175 3.9 39.6 1.0
N I:ASP175 4.1 38.5 1.0
N I:ASP177 4.2 36.5 1.0
OXT I:ASP204 4.2 47.4 1.0
O I:ALA178 4.3 39.7 1.0
C I:ASP175 4.3 39.9 1.0
N I:ALA178 4.3 36.2 1.0
CA I:ASP177 4.4 37.0 1.0
N I:SER180 4.4 38.2 1.0
CA I:ALA178 4.4 37.3 1.0
C I:ALA178 4.4 39.0 1.0
CA I:SER180 4.5 39.3 1.0
N I:GLY181 4.5 38.5 1.0
O I:ASP175 4.6 41.2 1.0
CA I:GLY181 4.6 38.0 1.0
CA I:ALA174 4.6 35.3 1.0
OD1 I:ASP175 4.7 42.0 1.0
N I:ARG176 4.8 39.5 1.0
CB I:ASP177 4.9 37.4 1.0
CB I:ALA174 4.9 34.4 1.0
NH1 Y:ARG19 4.9 45.8 1.0
CB I:SER180 5.0 40.7 1.0
O I:ASP204 5.0 44.4 1.0

Magnesium binding site 3 out of 8 in 5cza

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:40.9
occ:1.00
 O Y:ASN168 2.3 35.4 1.0
O I:ASP204 2.4 44.4 1.0
O Y:SER171 2.4 36.7 1.0
O Y:ALA165 2.5 35.4 1.0
C I:ASP204 3.2 44.0 1.0
C Y:ASN168 3.3 34.9 1.0
NH1 Y:ARG19 3.5 45.8 1.0
CA Y:ALA169 3.5 34.5 1.0
C Y:ALA165 3.6 35.4 1.0
C Y:SER171 3.6 36.8 1.0
O Y:ALA169 3.7 35.9 1.0
C Y:ALA169 3.7 35.3 1.0
CA I:ASP204 3.7 43.1 1.0
N Y:ALA169 3.8 34.6 1.0
CB I:ASP204 3.9 43.8 1.0
OXT I:ASP204 4.1 47.4 1.0
N Y:SER171 4.1 35.3 1.0
CA Y:ALA165 4.3 35.5 1.0
CZ Y:ARG19 4.3 44.1 1.0
O Y:HIS166 4.3 34.1 1.0
CA Y:SER171 4.4 35.7 1.0
N Y:TYR170 4.5 35.7 1.0
CA Y:ASN168 4.5 35.4 1.0
N Y:ASN168 4.5 35.6 1.0
C Y:HIS166 4.6 34.5 1.0
N Y:GLY172 4.6 37.6 1.0
N Y:HIS166 4.6 35.5 1.0
NH2 Y:ARG19 4.7 43.8 1.0
O Y:ALA164 4.7 36.0 1.0
CA Y:GLY172 4.8 37.6 1.0
CB Y:SER171 4.9 35.4 1.0
CA Y:HIS166 4.9 34.9 1.0
CG I:ASP204 4.9 43.6 1.0
CB Y:ALA169 4.9 34.1 1.0

Magnesium binding site 4 out of 8 in 5cza

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:41.3
occ:1.00
 O K:SER171 2.3 39.1 1.0
O K:ALA165 2.3 40.3 1.0
O K:ASN168 2.3 37.2 1.0
O W:ASP204 2.5 42.7 1.0
C W:ASP204 3.2 45.2 1.0
C K:ASN168 3.4 35.5 1.0
C K:ALA165 3.4 39.0 1.0
C K:SER171 3.5 39.4 1.0
NH1 K:ARG19 3.6 45.3 1.0
CA W:ASP204 3.6 45.1 1.0
CA K:ALA169 3.7 36.0 1.0
O K:ALA169 3.8 38.1 1.0
C K:ALA169 3.8 37.3 1.0
CB W:ASP204 3.8 45.0 1.0
N K:ALA169 3.9 35.1 1.0
N K:SER171 4.0 38.0 1.0
CA K:ALA165 4.1 38.8 1.0
OXT W:ASP204 4.2 44.5 1.0
CA K:SER171 4.3 37.7 1.0
O K:HIS166 4.3 38.2 1.0
CZ K:ARG19 4.3 44.2 1.0
N K:GLY172 4.4 40.4 1.0
N K:HIS166 4.5 38.2 1.0
N K:ASN168 4.5 35.8 1.0
C K:HIS166 4.5 37.4 1.0
CA K:ASN168 4.5 35.4 1.0
N K:TYR170 4.5 37.7 1.0
O K:ALA164 4.6 37.9 1.0
CA K:GLY172 4.6 41.0 1.0
NH2 K:ARG19 4.7 46.1 1.0
CB K:SER171 4.7 37.2 1.0
CG W:ASP204 4.8 44.5 1.0
CA K:HIS166 4.8 38.0 1.0
CB K:ALA165 4.9 39.2 1.0

Magnesium binding site 5 out of 8 in 5cza

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:41.2
occ:1.00
 O V:ASP166 2.1 42.0 1.0
O V:SER169 2.1 41.1 1.0
O V:ILE163 2.2 40.5 1.0
OXT L:ASP222 2.3 52.3 1.0
C L:ASP222 3.2 54.5 1.0
C V:ASP166 3.2 41.7 1.0
C V:ILE163 3.3 42.9 1.0
C V:SER169 3.3 43.9 1.0
O V:GLY162 3.8 42.4 1.0
NH1 V:ARG19 3.8 45.5 1.0
CA L:ASP222 3.8 55.8 1.0
CA V:LEU167 3.9 42.1 1.0
N V:LEU167 3.9 42.1 1.0
CA V:ILE163 4.0 43.2 1.0
O L:ASP222 4.0 55.2 1.0
N V:SER169 4.1 43.1 1.0
N V:ASP166 4.1 41.9 1.0
C V:LEU167 4.2 41.6 1.0
CA V:SER169 4.2 43.4 1.0
N V:GLY170 4.2 45.5 1.0
CA V:ASP166 4.3 41.3 1.0
CA V:GLY170 4.3 47.6 1.0
N V:TRP164 4.3 44.1 1.0
O V:LEU167 4.3 40.0 1.0
CB L:ASP222 4.3 56.0 1.0
C V:TRP164 4.4 44.9 1.0
CZ V:ARG19 4.4 45.6 1.0
O V:TRP164 4.5 44.9 1.0
CA V:TRP164 4.6 45.3 1.0
CB V:SER169 4.6 43.3 1.0
N V:ASN165 4.7 44.0 1.0
NH2 V:ARG19 4.7 45.3 1.0
C V:GLY162 4.7 42.9 1.0
N V:ILE163 4.9 42.8 1.0
N V:GLY168 4.9 42.4 1.0
C V:ASN165 4.9 42.8 1.0
CB V:ASP166 5.0 41.3 1.0

Magnesium binding site 6 out of 8 in 5cza

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:41.8
occ:1.00
 O N:SER169 2.5 33.1 1.0
O N:ILE163 2.6 35.2 1.0
O N:ASP166 2.8 34.7 1.0
NH1 N:ARG19 3.5 37.0 1.0
CD1 a:LEU34 3.6 40.9 1.0
C N:SER169 3.6 33.9 1.0
C N:ILE163 3.7 35.6 1.0
C N:ASP166 3.8 34.0 1.0
CG2 N:ILE163 4.0 34.1 1.0
CA N:GLY167 4.0 33.6 1.0
CZ N:ARG19 4.1 37.1 1.0
O N:GLY167 4.2 34.7 1.0
C N:GLY167 4.3 33.8 1.0
N N:GLY167 4.3 33.8 1.0
CA N:ILE163 4.3 34.6 1.0
CA N:GLY170 4.4 36.1 1.0
NH2 N:ARG19 4.4 38.0 1.0
N N:GLY170 4.5 35.3 1.0
N N:SER169 4.6 33.3 1.0
CA N:SER169 4.7 33.2 1.0
CB N:ILE163 4.8 34.0 1.0
CG a:LEU34 4.8 40.1 1.0
N N:LYS164 4.8 37.5 1.0
NE N:ARG19 4.9 36.8 1.0
N N:ASP166 4.9 34.1 1.0
CA N:ASP166 5.0 34.0 1.0

Magnesium binding site 7 out of 8 in 5cza

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:49.0
occ:1.00
 O W:ASP177 2.2 39.5 1.0
O W:SER180 2.3 42.3 1.0
O W:HOH434 2.6 40.3 1.0
O W:ALA174 2.7 39.8 1.0
C W:ASP177 3.4 38.6 1.0
C W:SER180 3.5 40.8 1.0
C W:ALA174 3.8 38.5 1.0
O W:ALA178 3.9 40.5 1.0
C W:ALA178 4.1 39.3 1.0
OXT W:ASP204 4.1 44.5 1.0
N W:SER180 4.1 39.8 1.0
CA W:ALA178 4.2 38.5 1.0
N W:ALA178 4.2 38.1 1.0
CA W:ASP175 4.3 40.9 1.0
N W:ASP177 4.3 38.7 1.0
CA W:SER180 4.4 40.3 1.0
CA W:ASP177 4.4 39.0 1.0
N W:GLY181 4.5 40.3 1.0
N W:ASP175 4.5 39.8 1.0
CA W:GLY181 4.6 39.9 1.0
C W:ASP175 4.6 40.4 1.0
NH1 K:ARG19 4.7 45.3 1.0
N W:LEU179 4.8 39.1 1.0
CA W:ALA174 4.8 36.1 1.0
O W:ASP175 4.9 42.0 1.0
O W:ASP204 4.9 42.7 1.0
CB W:ASP177 4.9 39.5 1.0
CB W:SER180 4.9 40.7 1.0
C W:ASP204 4.9 45.2 1.0
OD1 W:ASP175 5.0 43.1 1.0

Magnesium binding site 8 out of 8 in 5cza

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:64.1
occ:1.00
 O Z:VAL198 2.5 43.5 1.0
O Z:HIS195 2.7 37.1 1.0
O Z:THR192 2.8 47.8 1.0
C Z:HIS195 3.7 38.2 1.0
O Z:ILE196 3.7 41.7 1.0
CA Z:ILE196 3.7 38.5 1.0
C Z:VAL198 3.7 42.8 1.0
C Z:THR192 3.8 48.3 1.0
NH2 Z:ARG28 3.8 46.1 1.0
C Z:ILE196 3.8 39.1 1.0
O Z:ASP222 3.9 58.1 1.0
CG2 Z:THR192 4.1 49.5 1.0
CA Z:THR192 4.1 48.2 1.0
N Z:ILE196 4.1 37.9 1.0
NH2 H:ARG19 4.2 53.1 1.0
N Z:VAL198 4.3 40.2 1.0
CA Z:VAL198 4.5 41.2 1.0
OD1 Z:ASP222 4.7 54.8 1.0
N Z:GLN197 4.7 38.9 1.0
N Z:GLY199 4.7 43.7 1.0
CB Z:THR192 4.7 48.8 1.0
C Z:ASP222 4.8 57.4 1.0
CZ Z:ARG28 4.8 46.2 1.0
CA Z:GLY199 4.8 44.2 1.0
NH1 H:ARG19 4.9 52.5 1.0
CA Z:HIS195 4.9 39.2 1.0
N Z:HIS195 4.9 40.4 1.0
CZ H:ARG19 4.9 51.8 1.0
CB Z:VAL198 4.9 40.9 1.0
N Z:GLU193 5.0 49.6 1.0
NH1 Z:ARG28 5.0 47.6 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 02:21:30 2024

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