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Magnesium in PDB 5cz4: Yeast 20S Proteasome at 2.3 A Resolution

Enzymatic activity of Yeast 20S Proteasome at 2.3 A Resolution

All present enzymatic activity of Yeast 20S Proteasome at 2.3 A Resolution:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome at 2.3 A Resolution, PDB code: 5cz4 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 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 137.020, 300.930, 145.760, 90.00, 113.13, 90.00
R / Rfree (%) 21.1 / 22.8

Other elements in 5cz4:

The structure of Yeast 20S Proteasome at 2.3 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome at 2.3 A Resolution (pdb code 5cz4). 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 at 2.3 A Resolution, PDB code: 5cz4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5cz4

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome at 2.3 A Resolution


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 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:42.4
occ:1.00
 O G:MET125 2.1 41.0 1.0
O G:TYR119 2.3 34.0 1.0
O G:ARG122 2.3 37.8 1.0
OG1 G:THR8 2.6 39.5 1.0
CG2 G:THR8 3.3 39.4 1.0
C G:MET125 3.3 42.2 1.0
C G:ARG122 3.4 39.5 1.0
C G:TYR119 3.5 35.2 1.0
CB G:THR8 3.5 39.7 1.0
O G:ALA123 3.8 41.6 1.0
CA G:ALA123 3.9 40.5 1.0
C G:ALA123 4.0 41.5 1.0
N G:ALA123 4.1 39.7 1.0
N G:MET125 4.2 45.2 1.0
CA G:TYR119 4.2 35.3 1.0
N G:ARG126 4.2 38.4 1.0
CA G:MET125 4.3 46.3 1.0
CA G:ARG126 4.3 37.5 1.0
N G:THR120 4.5 35.0 1.0
CD G:PRO127 4.5 35.2 1.0
N G:THR8 4.5 40.9 1.0
N G:ARG122 4.5 38.3 1.0
CA G:ARG122 4.6 41.2 1.0
CA G:THR120 4.6 35.1 1.0
CA G:THR8 4.7 40.7 1.0
CB G:MET125 4.7 51.0 1.0
C G:THR120 4.7 35.7 1.0
CB G:TYR119 4.8 35.7 1.0
C G:ARG126 4.8 35.8 1.0
N G:TYR124 4.8 42.5 1.0
N G:PRO127 4.9 35.2 1.0
O G:HOH441 5.0 52.9 1.0
N G:GLN121 5.0 36.2 1.0

Magnesium binding site 2 out of 8 in 5cz4

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome at 2.3 A Resolution


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 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.8
occ:1.00
 O I:HOH429 2.3 40.6 1.0
O I:SER180 2.3 42.4 1.0
O I:ASP177 2.4 39.9 1.0
O I:ALA174 2.4 39.3 1.0
C I:ALA174 3.5 39.7 1.0
C I:SER180 3.5 41.6 1.0
C I:ASP177 3.6 39.4 1.0
O Y:HOH421 3.8 50.6 1.0
CA I:ASP175 4.0 42.1 1.0
N I:ASP175 4.1 40.9 1.0
N I:ASP177 4.3 39.2 1.0
OXT I:ASP204 4.3 47.7 1.0
O I:HOH413 4.3 43.3 1.0
N I:GLY181 4.4 40.6 1.0
N I:SER180 4.4 40.6 1.0
C I:ASP175 4.4 41.6 1.0
CA I:GLY181 4.4 40.1 1.0
CA I:SER180 4.4 41.5 1.0
CA I:ASP177 4.5 39.3 1.0
O I:ALA178 4.5 41.4 1.0
N I:ALA178 4.5 39.3 1.0
CA I:ALA174 4.5 37.6 1.0
C I:ALA178 4.6 40.2 1.0
CA I:ALA178 4.6 39.5 1.0
O I:ASP175 4.7 43.3 1.0
OD1 I:ASP175 4.7 46.1 1.0
CB I:ALA174 4.8 36.5 1.0
CB I:SER180 4.8 43.1 1.0
CB I:ASP177 4.9 39.7 1.0
N I:ARG176 4.9 40.1 1.0

Magnesium binding site 3 out of 8 in 5cz4

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome at 2.3 A Resolution


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 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:42.9
occ:1.00
 O K:ALA165 2.3 39.4 1.0
O W:ASP204 2.3 44.8 1.0
O K:ASP168 2.3 38.0 1.0
O K:SER171 2.4 38.5 1.0
C W:ASP204 3.1 45.6 1.0
C K:ASP168 3.4 36.2 1.0
C K:ALA165 3.4 38.4 1.0
CA W:ASP204 3.5 44.7 1.0
C K:SER171 3.6 39.8 1.0
NH1 K:ARG19 3.7 45.8 1.0
CB W:ASP204 3.7 44.2 1.0
O K:ALA169 3.8 38.5 1.0
CA K:ALA169 3.9 36.9 1.0
C K:ALA169 3.9 38.3 1.0
OXT W:ASP204 4.0 46.4 1.0
N K:ALA169 4.0 36.1 1.0
CA K:ALA165 4.1 38.2 1.0
N K:SER171 4.1 39.2 1.0
O K:HIS166 4.3 36.3 1.0
CA K:SER171 4.4 39.0 1.0
CZ K:ARG19 4.4 45.0 1.0
N K:HIS166 4.5 37.2 1.0
C K:HIS166 4.5 36.2 1.0
N K:ASP168 4.5 34.7 1.0
CA K:ASP168 4.5 35.8 1.0
N K:GLY172 4.6 40.4 1.0
N K:TYR170 4.7 38.3 1.0
O K:ALA164 4.7 38.4 1.0
CA K:GLY172 4.7 41.6 1.0
CG W:ASP204 4.7 44.5 1.0
CA K:HIS166 4.8 36.8 1.0
NH2 K:ARG19 4.8 46.7 1.0
CB K:SER171 4.8 38.7 1.0
CB K:ALA165 4.9 38.4 1.0
N W:ASP204 4.9 44.2 1.0

Magnesium binding site 4 out of 8 in 5cz4

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome at 2.3 A Resolution


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 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:41.0
occ:1.00
 O N:SER169 2.6 40.5 1.0
O N:ILE163 2.7 37.5 1.0
O N:HOH344 2.9 45.5 1.0
O N:ASP166 3.0 38.8 1.0
NH1 N:ARG19 3.6 40.8 1.0
CD1 a:LEU34 3.7 43.9 1.0
C N:ILE163 3.8 38.8 1.0
C N:SER169 3.8 39.7 1.0
CG2 N:ILE163 3.9 37.2 1.0
C N:ASP166 4.0 37.1 1.0
CA N:GLY167 4.2 36.9 1.0
CZ N:ARG19 4.2 41.2 1.0
O N:GLY167 4.4 37.8 1.0
CA N:ILE163 4.4 37.5 1.0
CA N:GLY170 4.5 41.5 1.0
NH2 N:ARG19 4.5 41.8 1.0
N N:GLY167 4.5 36.5 1.0
C N:GLY167 4.5 37.3 1.0
N N:GLY170 4.6 40.5 1.0
N N:SER169 4.8 37.8 1.0
CB N:ILE163 4.8 37.0 1.0
CA N:SER169 4.8 37.7 1.0
N N:LYS164 4.8 40.4 1.0
CG a:LEU34 4.9 43.2 1.0
O N:LYS164 5.0 41.0 1.0

Magnesium binding site 5 out of 8 in 5cz4

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome at 2.3 A Resolution


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 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:44.9
occ:1.00
 O V:ILE163 2.1 43.1 1.0
O V:ASP166 2.2 43.7 1.0
OXT L:ASP222 2.3 54.6 1.0
O V:SER169 2.3 47.5 1.0
O V:HOH435 2.5 43.6 1.0
C L:ASP222 3.2 54.5 1.0
C V:ILE163 3.2 44.9 1.0
C V:ASP166 3.3 43.6 1.0
C V:SER169 3.4 46.9 1.0
O V:GLY162 3.7 42.3 1.0
CA L:ASP222 3.8 54.5 1.0
CA V:ILE163 3.9 44.4 1.0
O L:ASP222 4.0 55.6 1.0
NH1 V:ARG19 4.0 50.9 1.0
CA V:LEU167 4.0 44.3 1.0
N V:LEU167 4.0 44.1 1.0
N V:ASP166 4.1 43.7 1.0
N V:TRP164 4.2 45.6 1.0
CA V:ASP166 4.3 43.2 1.0
C V:TRP164 4.3 46.1 1.0
N V:GLY170 4.3 48.3 1.0
CB L:ASP222 4.3 55.5 1.0
N V:SER169 4.3 44.9 1.0
CA V:GLY170 4.3 50.5 1.0
CA V:SER169 4.3 45.6 1.0
C V:LEU167 4.4 44.4 1.0
CA V:TRP164 4.4 46.5 1.0
O V:LEU167 4.5 42.8 1.0
N V:ASN165 4.5 46.0 1.0
O V:TRP164 4.5 46.5 1.0
CZ V:ARG19 4.6 50.1 1.0
CB V:SER169 4.7 44.9 1.0
C V:GLY162 4.7 43.9 1.0
C V:ASN165 4.8 44.2 1.0
NH2 V:ARG19 4.8 50.7 1.0
N V:ILE163 4.8 44.3 1.0
CG2 V:ILE163 5.0 44.5 1.0

Magnesium binding site 6 out of 8 in 5cz4

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome at 2.3 A Resolution


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 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:47.9
occ:1.00
 O W:SER180 2.3 42.9 1.0
O W:ASP177 2.3 40.4 1.0
O W:HOH422 2.4 39.2 1.0
O W:ALA174 2.4 38.9 1.0
C W:SER180 3.4 41.9 1.0
C W:ALA174 3.5 39.3 1.0
C W:ASP177 3.5 39.7 1.0
O K:HOH419 3.8 47.3 1.0
CA W:ASP175 4.1 42.7 1.0
N W:ASP175 4.2 41.1 1.0
N W:ASP177 4.2 40.0 1.0
N W:SER180 4.3 41.6 1.0
N W:GLY181 4.3 41.1 1.0
CA W:SER180 4.3 42.2 1.0
O W:HOH416 4.4 35.4 1.0
OXT W:ASP204 4.4 46.4 1.0
O W:ALA178 4.4 42.1 1.0
CA W:ASP177 4.4 40.3 1.0
CA W:GLY181 4.4 41.4 1.0
N W:ALA178 4.4 38.8 1.0
C W:ASP175 4.4 42.0 1.0
C W:ALA178 4.5 39.8 1.0
CA W:ALA178 4.5 39.0 1.0
CA W:ALA174 4.5 37.3 1.0
O W:ASP175 4.7 42.4 1.0
CB W:SER180 4.8 43.1 1.0
CB W:ALA174 4.8 36.6 1.0
OD1 W:ASP175 4.8 47.0 1.0
CB W:ASP177 4.8 41.0 1.0
N W:ARG176 5.0 41.1 1.0
NH1 K:ARG19 5.0 45.8 1.0

Magnesium binding site 7 out of 8 in 5cz4

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome at 2.3 A Resolution


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 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:41.9
occ:1.00
 O Y:SER171 2.2 37.9 1.0
O Y:ALA165 2.3 37.4 1.0
O Y:ASP168 2.3 37.9 1.0
O I:ASP204 2.4 45.6 1.0
O Y:HOH443 2.6 40.0 1.0
C I:ASP204 3.2 46.4 1.0
C Y:ALA165 3.4 36.7 1.0
C Y:ASP168 3.4 37.0 1.0
C Y:SER171 3.5 38.7 1.0
NH1 Y:ARG19 3.7 42.7 1.0
CA I:ASP204 3.7 44.7 1.0
CB I:ASP204 3.8 45.4 1.0
O Y:ALA169 3.8 38.0 1.0
C Y:ALA169 3.9 37.9 1.0
CA Y:ALA169 3.9 36.4 1.0
CA Y:ALA165 4.0 37.0 1.0
N Y:SER171 4.1 37.5 1.0
N Y:ALA169 4.1 36.2 1.0
OXT I:ASP204 4.1 47.7 1.0
CA Y:SER171 4.3 38.0 1.0
CZ Y:ARG19 4.4 43.1 1.0
O Y:HIS166 4.4 37.4 1.0
N Y:GLY172 4.4 38.7 1.0
N Y:HIS166 4.5 36.3 1.0
N Y:ASP168 4.6 36.6 1.0
CA Y:GLY172 4.6 38.7 1.0
CA Y:ASP168 4.6 37.6 1.0
C Y:HIS166 4.6 35.8 1.0
O Y:ALA164 4.6 36.1 1.0
N Y:TYR170 4.6 38.1 1.0
CB Y:SER171 4.7 38.2 1.0
CG I:ASP204 4.7 46.3 1.0
NH2 Y:ARG19 4.8 44.0 1.0
CA Y:HIS166 4.8 35.5 1.0
CB Y:ALA165 4.8 37.5 1.0

Magnesium binding site 8 out of 8 in 5cz4

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome at 2.3 A Resolution


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 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:56.8
occ:1.00
 O Z:VAL198 2.3 43.7 1.0
O Z:HOH440 2.4 44.9 1.0
O Z:THR192 2.4 45.3 1.0
O Z:HIS195 2.6 39.6 1.0
C Z:THR192 3.4 48.2 1.0
C Z:VAL198 3.5 43.7 1.0
CA Z:THR192 3.7 48.1 1.0
C Z:HIS195 3.7 40.2 1.0
CG2 Z:THR192 3.7 49.9 1.0
O Z:ILE196 4.1 39.9 1.0
CA Z:ILE196 4.1 39.5 1.0
NH2 Z:ARG28 4.1 47.4 1.0
C Z:ILE196 4.2 39.3 1.0
N Z:VAL198 4.2 42.2 1.0
CB Z:THR192 4.3 49.0 1.0
CA Z:VAL198 4.3 43.0 1.0
N Z:ILE196 4.3 38.9 1.0
O Z:ASP222 4.5 56.5 1.0
N Z:GLY199 4.5 44.4 1.0
NH2 H:ARG19 4.5 51.5 1.0
CB Z:VAL198 4.6 42.6 1.0
N Z:GLU193 4.6 49.6 1.0
O Z:ALA191 4.6 46.3 1.0
CA Z:GLY199 4.7 45.4 1.0
N Z:HIS195 4.7 42.2 1.0
CA Z:HIS195 4.8 40.7 1.0
N Z:THR192 4.9 47.8 1.0
N Z:GLN197 4.9 39.4 1.0
OD1 Z:ASP222 4.9 56.9 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 02:20:26 2024

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