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Magnesium in PDB 5cz6: Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans

Enzymatic activity of Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans

All present enzymatic activity of Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans, PDB code: 5cz6 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 (°) 135.040, 301.440, 145.750, 90.00, 113.27, 90.00
R / Rfree (%) 19.4 / 22.6

Other elements in 5cz6:

The structure of Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, 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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans (pdb code 5cz6). 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 BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans, PDB code: 5cz6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5cz6

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, 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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:56.7
occ:1.00
 O G:MET125 2.1 55.5 1.0
O G:TYR119 2.4 50.5 1.0
O G:ARG122 2.4 54.8 1.0
OG1 G:THR8 2.7 43.5 1.0
CG2 G:THR8 3.3 50.2 1.0
C G:MET125 3.3 54.8 1.0
CB G:THR8 3.5 48.8 1.0
C G:TYR119 3.6 46.8 1.0
C G:ARG122 3.6 52.3 1.0
O G:ALA123 3.8 59.7 1.0
CA G:ALA123 3.9 52.4 1.0
C G:ALA123 3.9 55.3 1.0
N G:ARG126 4.2 49.7 1.0
CA G:ARG126 4.2 49.4 1.0
N G:MET125 4.2 56.4 1.0
N G:ALA123 4.2 50.7 1.0
CA G:MET125 4.3 58.3 1.0
CA G:TYR119 4.3 46.3 1.0
CD G:PRO127 4.4 46.7 1.0
N G:THR8 4.4 50.1 1.0
N G:THR120 4.6 45.0 1.0
CA G:THR8 4.6 50.6 1.0
CB G:MET125 4.7 64.0 1.0
C G:ARG126 4.7 48.6 1.0
N G:ARG122 4.7 49.7 1.0
CA G:THR120 4.7 45.6 1.0
CA G:ARG122 4.7 53.5 1.0
N G:TYR124 4.8 56.8 1.0
C G:THR120 4.8 46.0 1.0
CB G:TYR119 4.9 46.6 1.0
N G:PRO127 4.9 46.7 1.0

Magnesium binding site 2 out of 9 in 5cz6

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, 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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:64.1
occ:1.00
 OE1 H:GLN91 2.5 63.6 1.0
OD1 N:ASP51 3.1 45.5 1.0
CD H:GLN91 3.4 60.4 1.0
NE2 H:GLN91 3.5 59.8 1.0
OD2 N:ASP51 3.6 43.4 1.0
O N:ASN92 3.7 46.7 1.0
CG N:ASP51 3.8 41.1 1.0
CG H:GLN91 4.8 56.6 1.0
C N:ASN92 4.8 49.1 1.0
ND1 H:HIS116 4.9 42.9 1.0

Magnesium binding site 3 out of 9 in 5cz6

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, 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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:70.3
occ:1.00
 O I:SER180 2.6 51.0 1.0
O I:ASP177 2.7 51.3 1.0
O I:ALA174 2.8 45.2 1.0
C I:ALA174 3.7 49.8 1.0
OXT I:ASP204 3.8 58.6 1.0
C I:SER180 3.8 52.7 1.0
C I:ASP177 3.9 48.8 1.0
CA I:ASP175 4.0 52.5 1.0
N I:ASP175 4.3 51.7 1.0
C I:ASP175 4.4 53.4 1.0
OD1 I:ASP175 4.4 56.8 1.0
CA I:GLY181 4.6 50.9 1.0
O I:ALA178 4.6 49.5 1.0
O I:ASP204 4.6 55.7 1.0
NH1 Y:ARG19 4.6 57.9 1.0
N I:ASP177 4.6 50.2 1.0
C I:ASP204 4.6 56.2 1.0
N I:GLY181 4.6 51.4 1.0
O I:ASP175 4.6 60.0 1.0
NH2 Y:ARG19 4.6 57.9 1.0
CA I:ALA178 4.7 48.4 1.0
N I:SER180 4.7 47.1 1.0
C I:ALA178 4.7 48.8 1.0
N I:ALA178 4.7 47.2 1.0
CA I:SER180 4.8 50.2 1.0
CA I:ASP177 4.8 48.1 1.0
CA I:ALA174 4.9 47.7 1.0

Magnesium binding site 4 out of 9 in 5cz6

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, 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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:55.6
occ:1.00
 O Y:ASP168 2.3 47.0 1.0
O I:ASP204 2.4 55.7 1.0
O Y:ALA165 2.5 48.7 1.0
O Y:SER171 2.7 51.2 1.0
C I:ASP204 3.1 56.2 1.0
C Y:ASP168 3.2 49.2 1.0
CA Y:ALA169 3.5 49.0 1.0
O Y:ALA169 3.6 53.5 1.0
CA I:ASP204 3.7 55.6 1.0
C Y:ALA169 3.7 51.0 1.0
C Y:ALA165 3.7 47.5 1.0
NH1 Y:ARG19 3.7 57.9 1.0
N Y:ALA169 3.8 49.2 1.0
O Y:HIS166 3.9 53.3 1.0
C Y:SER171 3.9 50.0 1.0
CB I:ASP204 4.0 56.0 1.0
OXT I:ASP204 4.0 58.6 1.0
N Y:SER171 4.3 49.4 1.0
C Y:HIS166 4.4 48.8 1.0
CA Y:ASP168 4.4 49.0 1.0
N Y:ASP168 4.5 51.8 1.0
CA Y:ALA165 4.5 48.2 1.0
CZ Y:ARG19 4.5 56.3 1.0
N Y:TYR170 4.5 48.9 1.0
CA Y:SER171 4.7 48.6 1.0
N Y:HIS166 4.7 47.7 1.0
O Y:ALA164 4.8 46.1 1.0
CA Y:HIS166 4.8 47.0 1.0
C Y:ARG167 4.8 51.6 1.0
NH2 Y:ARG19 4.9 57.9 1.0
CB Y:ALA169 4.9 47.8 1.0
N Y:GLY172 5.0 49.4 1.0
CG I:ASP204 5.0 56.0 1.0

Magnesium binding site 5 out of 9 in 5cz6

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, 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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:53.2
occ:1.00
 O K:ASP168 2.2 48.3 1.0
O K:ALA165 2.4 53.7 1.0
O W:ASP204 2.5 57.0 1.0
O K:SER171 2.6 53.4 1.0
C W:ASP204 3.2 58.7 1.0
C K:ASP168 3.2 50.1 1.0
C K:ALA165 3.5 51.7 1.0
CA W:ASP204 3.5 57.6 1.0
CA K:ALA169 3.7 52.2 1.0
O K:ALA169 3.8 55.8 1.0
C K:SER171 3.8 52.8 1.0
C K:ALA169 3.8 53.8 1.0
NH1 K:ARG19 3.8 61.3 1.0
N K:ALA169 3.8 51.1 1.0
CB W:ASP204 3.9 57.5 1.0
O K:HIS166 3.9 54.6 1.0
OXT W:ASP204 4.1 61.6 1.0
N K:SER171 4.2 54.6 1.0
CA K:ALA165 4.3 52.3 1.0
C K:HIS166 4.3 52.5 1.0
N K:ASP168 4.4 52.1 1.0
CA K:ASP168 4.4 50.1 1.0
CA K:SER171 4.5 51.6 1.0
N K:HIS166 4.5 51.0 1.0
CZ K:ARG19 4.5 58.6 1.0
N K:TYR170 4.6 52.8 1.0
O K:ALA164 4.6 52.2 1.0
CA K:HIS166 4.7 51.6 1.0
C K:ARG167 4.8 53.1 1.0
N K:GLY172 4.8 52.9 1.0
NH2 K:ARG19 4.9 61.9 1.0
N W:ASP204 4.9 57.3 1.0
CG W:ASP204 4.9 57.1 1.0
N K:ARG167 4.9 51.4 1.0
CB K:SER171 4.9 51.2 1.0
CA K:GLY172 5.0 55.0 1.0

Magnesium binding site 6 out of 9 in 5cz6

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, 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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:59.9
occ:1.00
 O V:ASP166 2.2 41.5 1.0
O V:ILE163 2.3 47.4 1.0
OXT L:ASP222 2.4 55.4 1.0
O V:SER169 2.6 57.4 1.0
C L:ASP222 3.1 60.0 1.0
C V:ASP166 3.1 45.6 1.0
C V:ILE163 3.4 49.2 1.0
C V:SER169 3.7 50.9 1.0
CA L:ASP222 3.7 60.5 1.0
CA V:LEU167 3.8 47.6 1.0
N V:LEU167 3.8 46.4 1.0
O L:ASP222 3.9 62.4 1.0
O V:GLY162 3.9 44.4 1.0
N V:ASP166 4.0 46.5 1.0
NH1 V:ARG19 4.0 60.7 1.0
C V:TRP164 4.1 51.4 1.0
O V:TRP164 4.1 56.6 1.0
CA V:ASP166 4.2 46.1 1.0
CA V:ILE163 4.2 47.7 1.0
N V:TRP164 4.2 52.1 1.0
C V:LEU167 4.3 47.9 1.0
CB L:ASP222 4.4 63.0 1.0
CA V:TRP164 4.4 51.1 1.0
N V:SER169 4.4 46.5 1.0
O V:LEU167 4.4 47.4 1.0
N V:ASN165 4.5 49.3 1.0
CA V:SER169 4.5 48.0 1.0
N V:GLY170 4.6 50.5 1.0
CA V:GLY170 4.6 53.2 1.0
C V:ASN165 4.7 45.7 1.0
CZ V:ARG19 4.7 56.5 1.0
O L:ARG221 4.8 60.4 1.0
C V:GLY162 4.9 47.4 1.0
CB V:SER169 4.9 48.7 1.0
CD2 V:LEU167 4.9 45.7 1.0
NH2 V:ARG19 4.9 59.8 1.0
N V:GLY168 5.0 47.3 1.0

Magnesium binding site 7 out of 9 in 5cz6

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, 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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:47.9
occ:1.00
 O N:ILE163 2.6 45.1 1.0
O N:SER169 2.6 42.8 1.0
O N:ASP166 2.8 44.3 1.0
CD1 a:LEU34 3.5 48.0 1.0
C N:ILE163 3.7 43.7 1.0
NH1 N:ARG19 3.7 43.4 1.0
C N:SER169 3.8 42.9 1.0
C N:ASP166 3.8 41.7 1.0
CG2 N:ILE163 4.0 42.5 1.0
CA N:GLY167 4.1 41.0 1.0
CZ N:ARG19 4.3 44.4 1.0
CA N:ILE163 4.3 42.9 1.0
N N:GLY167 4.4 41.2 1.0
O N:GLY167 4.4 37.8 1.0
CA N:GLY170 4.5 44.5 1.0
C N:GLY167 4.5 39.3 1.0
N N:GLY170 4.6 43.0 1.0
NH2 N:ARG19 4.6 46.5 1.0
N N:SER169 4.7 42.1 1.0
CG a:LEU34 4.7 47.0 1.0
N N:LYS164 4.7 45.2 1.0
CA N:SER169 4.8 41.0 1.0
CB N:ILE163 4.8 42.1 1.0
O N:LYS164 4.8 48.2 1.0
C N:LYS164 4.9 47.0 1.0
N N:ASP166 4.9 40.4 1.0
CA N:ASP166 5.0 41.1 1.0
CA N:LYS164 5.0 45.9 1.0

Magnesium binding site 8 out of 9 in 5cz6

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, 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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:76.8
occ:1.00
 O W:ASP177 2.7 51.5 1.0
O W:SER180 2.8 47.6 1.0
O W:ALA174 2.9 48.0 1.0
OXT W:ASP204 3.8 61.6 1.0
C W:ASP177 3.8 48.5 1.0
C W:ALA174 3.9 51.2 1.0
C W:SER180 4.0 52.0 1.0
CA W:ASP175 4.0 54.2 1.0
NH1 K:ARG19 4.3 61.3 1.0
N W:ASP175 4.3 54.1 1.0
C W:ASP175 4.4 53.3 1.0
NH2 K:ARG19 4.4 61.9 1.0
O W:ALA178 4.5 52.0 1.0
O W:ASP204 4.5 57.0 1.0
N W:ASP177 4.5 50.0 1.0
CA W:ALA178 4.5 49.0 1.0
O W:ASP175 4.5 55.2 1.0
C W:ASP204 4.6 58.7 1.0
N W:ALA178 4.6 46.7 1.0
OD1 W:ASP175 4.6 60.4 1.0
C W:ALA178 4.6 51.1 1.0
CZ K:ARG19 4.7 58.6 1.0
CA W:ASP177 4.7 50.0 1.0
N W:SER180 4.8 52.1 1.0
CA W:GLY181 4.8 52.5 1.0
N W:GLY181 4.8 52.1 1.0
CA W:SER180 4.9 52.7 1.0

Magnesium binding site 9 out of 9 in 5cz6

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans


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 BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:69.4
occ:1.00
 O Z:VAL198 2.4 45.5 1.0
O Z:THR192 2.7 54.1 1.0
O Z:HIS195 3.0 46.3 1.0
C Z:VAL198 3.6 48.0 1.0
CG2 Z:THR192 3.6 56.2 1.0
C Z:THR192 3.6 54.4 1.0
NH2 Z:ARG28 3.8 53.0 1.0
O Z:ASP222 3.9 58.6 1.0
CA Z:THR192 4.0 55.0 1.0
O Z:ILE196 4.0 52.8 1.0
C Z:HIS195 4.0 47.6 1.0
CA Z:ILE196 4.2 46.7 1.0
C Z:ILE196 4.2 48.0 1.0
NH2 H:ARG19 4.2 59.7 1.0
CB Z:THR192 4.4 55.5 1.0
N Z:VAL198 4.4 46.3 1.0
OD1 Z:ASP222 4.4 57.9 1.0
N Z:GLY199 4.5 48.6 1.0
CA Z:GLY199 4.5 51.0 1.0
CA Z:VAL198 4.5 47.5 1.0
N Z:ILE196 4.6 46.1 1.0
CZ Z:ARG28 4.7 54.2 1.0
C Z:ASP222 4.7 61.1 1.0
NH1 Z:ARG28 4.9 56.1 1.0
N Z:GLU193 4.9 54.7 1.0
O Z:LYS220 4.9 56.2 1.0
OXT Z:ASP222 5.0 63.8 1.0
CB Z:VAL198 5.0 48.0 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 02:20:37 2024

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