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Magnesium in PDB 5fhs: Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with Carfilzomib

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with Carfilzomib, PDB code: 5fhs 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 (°) 136.350, 300.770, 145.010, 90.00, 113.16, 90.00
R / Rfree (%) 18.7 / 21.2

Other elements in 5fhs:

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

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with Carfilzomib (pdb code 5fhs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with Carfilzomib, PDB code: 5fhs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5fhs

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with Carfilzomib


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) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:64.1
occ:1.00
 O G:MET125 2.3 53.3 1.0
OG1 G:THR8 2.7 38.6 1.0
O G:ARG122 2.7 47.9 1.0
O G:TYR119 2.9 42.2 1.0
O G:ALA123 3.1 56.4 1.0
CG2 G:THR8 3.3 46.4 1.0
C G:MET125 3.4 51.2 1.0
CB G:THR8 3.5 45.0 1.0
C G:ALA123 3.6 52.4 1.0
CA G:ALA123 3.7 49.0 1.0
C G:ARG122 3.8 48.3 1.0
N G:THR8 4.1 50.6 1.0
CA G:ARG126 4.1 45.0 1.0
C G:TYR119 4.1 42.3 1.0
N G:ARG126 4.2 48.2 1.0
N G:ALA123 4.2 48.3 1.0
N G:MET125 4.3 50.8 1.0
CA G:THR8 4.4 47.6 1.0
CA G:MET125 4.4 53.3 1.0
CD G:PRO127 4.5 41.0 1.0
N G:TYR124 4.6 53.0 1.0
C G:ARG126 4.8 44.5 1.0
CA G:TYR119 4.9 41.1 1.0
C G:TYR124 4.9 51.5 1.0
N G:PRO127 5.0 41.9 1.0
CB G:ALA123 5.0 48.1 1.0

Magnesium binding site 2 out of 7 in 5fhs

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with Carfilzomib


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) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:74.4
occ:1.00
 O I:ASP177 2.8 52.7 1.0
O I:SER180 2.8 56.3 1.0
OXT I:ASP204 3.2 73.6 1.0
O I:ALA174 3.2 58.4 1.0
C I:ASP177 3.9 52.8 1.0
NH1 Y:ARG19 4.0 63.9 1.0
O I:ALA178 4.0 56.1 1.0
C I:SER180 4.0 54.8 1.0
C I:ASP204 4.1 74.3 1.0
O I:ASP204 4.2 71.7 1.0
C I:ALA174 4.3 56.8 1.0
CA I:ALA178 4.3 53.1 1.0
C I:ALA178 4.3 55.4 1.0
CA I:ASP175 4.5 58.0 1.0
N I:ALA178 4.6 51.5 1.0
CZ Y:ARG19 4.7 61.4 1.0
CA I:GLY181 4.7 54.3 1.0
NH2 Y:ARG19 4.7 62.8 1.0
O I:ASP175 4.8 63.5 1.0
C I:ASP175 4.8 59.0 1.0
N I:SER180 4.8 51.4 1.0
N I:GLY181 4.8 53.6 1.0
N I:ASP175 4.8 56.5 1.0
N I:ASP177 4.9 52.0 1.0

Magnesium binding site 3 out of 7 in 5fhs

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with Carfilzomib


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) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:61.9
occ:1.00
 O Y:ASP168 2.2 51.2 1.0
O I:ASP204 2.2 71.7 1.0
O Y:ALA165 2.3 48.4 1.0
O Y:SER171 2.7 50.7 1.0
C I:ASP204 3.1 74.3 1.0
C Y:ASP168 3.2 49.6 1.0
C Y:ALA165 3.5 49.7 1.0
CA Y:ALA169 3.6 51.6 1.0
O Y:ALA169 3.7 51.3 1.0
CA I:ASP204 3.7 70.4 1.0
N Y:ALA169 3.8 50.1 1.0
C Y:ALA169 3.8 52.0 1.0
O Y:HIS166 3.8 51.9 1.0
NH1 Y:ARG19 3.9 63.9 1.0
C Y:SER171 3.9 52.5 1.0
OXT I:ASP204 4.1 73.6 1.0
CB I:ASP204 4.1 70.7 1.0
C Y:HIS166 4.2 50.0 1.0
N Y:SER171 4.3 50.8 1.0
CA Y:ALA165 4.3 50.2 1.0
N Y:ASP168 4.4 50.2 1.0
CA Y:ASP168 4.4 48.9 1.0
N Y:HIS166 4.4 48.4 1.0
CA Y:HIS166 4.6 48.1 1.0
O Y:ALA164 4.6 52.1 1.0
CA Y:SER171 4.6 50.9 1.0
C Y:ARG167 4.6 51.0 1.0
N Y:TYR170 4.7 52.4 1.0
CZ Y:ARG19 4.7 61.4 1.0
N Y:ARG167 4.8 49.5 1.0
O Y:ARG167 4.9 54.8 1.0
CB Y:ALA169 4.9 51.9 1.0
N Y:GLY172 4.9 53.0 1.0

Magnesium binding site 4 out of 7 in 5fhs

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with Carfilzomib


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) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:64.4
occ:1.00
 O K:ASP168 2.1 55.1 1.0
O K:ALA165 2.2 52.3 1.0
O W:ASP204 2.3 77.8 1.0
O K:SER171 2.7 53.2 1.0
C K:ASP168 3.1 55.4 1.0
C W:ASP204 3.1 72.2 1.0
C K:ALA165 3.4 53.8 1.0
CA K:ALA169 3.6 56.7 1.0
CA W:ASP204 3.6 67.7 1.0
O K:HIS166 3.7 55.6 1.0
N K:ALA169 3.7 56.3 1.0
O K:ALA169 3.8 56.0 1.0
C K:ALA169 3.8 57.7 1.0
NH1 K:ARG19 3.9 71.0 1.0
C K:SER171 3.9 53.7 1.0
C K:HIS166 4.1 55.5 1.0
OXT W:ASP204 4.1 75.2 1.0
CB W:ASP204 4.1 66.2 1.0
CA K:ALA165 4.2 54.8 1.0
N K:ASP168 4.3 54.2 1.0
N K:SER171 4.3 55.5 1.0
CA K:ASP168 4.3 54.5 1.0
N K:HIS166 4.3 51.7 1.0
O K:ALA164 4.4 49.8 1.0
CA K:HIS166 4.5 54.3 1.0
C K:ARG167 4.5 55.4 1.0
CA K:SER171 4.6 53.7 1.0
N K:ARG167 4.7 55.1 1.0
N K:TYR170 4.7 57.6 1.0
CZ K:ARG19 4.7 66.9 1.0
O K:ARG167 4.8 59.0 1.0
N K:GLY172 4.9 55.4 1.0
CB K:SER171 4.9 52.2 1.0
CB K:ALA169 5.0 55.8 1.0
N W:ASP204 5.0 68.8 1.0

Magnesium binding site 5 out of 7 in 5fhs

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with Carfilzomib


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) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:70.0
occ:1.00
 OXT L:ASP222 2.1 81.0 1.0
O V:ILE163 2.2 51.6 1.0
O V:ASP166 2.2 46.2 1.0
O V:SER169 2.9 53.7 1.0
C L:ASP222 3.0 76.4 1.0
C V:ASP166 3.1 50.5 1.0
C V:ILE163 3.3 54.5 1.0
O V:TRP164 3.6 60.5 1.0
CA L:ASP222 3.6 72.8 1.0
C V:TRP164 3.7 55.1 1.0
N V:LEU167 3.8 51.2 1.0
CA V:LEU167 3.9 51.8 1.0
N V:ASP166 3.9 49.5 1.0
O V:GLY162 3.9 51.6 1.0
O L:ASP222 4.0 74.5 1.0
CA V:ASP166 4.1 50.2 1.0
N V:TRP164 4.1 54.5 1.0
C V:SER169 4.1 51.1 1.0
CA V:TRP164 4.1 55.6 1.0
N V:ASN165 4.3 54.3 1.0
CA V:ILE163 4.3 55.3 1.0
CB L:ASP222 4.3 72.5 1.0
NH1 V:ARG19 4.3 63.8 1.0
C V:ASN165 4.4 49.9 1.0
C V:LEU167 4.5 51.8 1.0
O L:ARG221 4.6 63.2 1.0
CD2 V:LEU167 4.7 49.3 1.0
N V:SER169 4.8 50.2 1.0
O V:LEU167 4.8 54.6 1.0
N L:ASP222 4.8 70.3 1.0
CA V:ASN165 4.8 52.0 1.0
C V:GLY162 4.9 54.1 1.0
CA V:GLY170 4.9 54.4 1.0
CZ V:ARG19 5.0 59.5 1.0
CA V:SER169 5.0 49.8 1.0
N V:GLY170 5.0 51.2 1.0
NH2 V:ARG19 5.0 60.0 1.0

Magnesium binding site 6 out of 7 in 5fhs

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with Carfilzomib


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) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:46.9
occ:1.00
 O N:SER169 2.4 45.1 1.0
O N:ILE163 2.7 43.8 1.0
O N:ASP166 2.9 46.0 1.0
NH1 N:ARG19 3.5 47.6 1.0
C N:SER169 3.6 41.9 1.0
CD1 a:LEU34 3.8 47.5 1.0
C N:ILE163 3.8 44.2 1.0
C N:ASP166 3.9 43.6 1.0
CG2 N:ILE163 4.0 43.4 1.0
CA N:GLY167 4.1 43.9 1.0
CZ N:ARG19 4.2 45.7 1.0
O N:GLY167 4.3 44.2 1.0
CA N:GLY170 4.3 43.1 1.0
C N:GLY167 4.4 43.8 1.0
NH2 N:ARG19 4.4 46.0 1.0
N N:GLY170 4.4 41.8 1.0
CA N:ILE163 4.4 43.9 1.0
N N:GLY167 4.5 42.8 1.0
N N:SER169 4.6 40.5 1.0
CA N:SER169 4.7 39.2 1.0
CB N:ILE163 4.8 42.9 1.0
N N:LYS164 4.9 43.6 1.0

Magnesium binding site 7 out of 7 in 5fhs

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


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) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:74.3
occ:1.00
 O Z:VAL198 2.5 54.8 1.0
O Z:THR192 2.6 61.2 1.0
O Z:HIS195 3.2 48.8 1.0
O Z:ASP222 3.4 78.7 1.0
CG2 Z:THR192 3.5 63.1 1.0
C Z:THR192 3.6 61.6 1.0
NH2 Z:ARG28 3.7 64.2 1.0
C Z:VAL198 3.7 56.4 1.0
CA Z:THR192 3.9 61.3 1.0
OD1 Z:ASP222 4.1 70.3 1.0
O Z:ILE196 4.2 53.6 1.0
C Z:HIS195 4.2 51.0 1.0
CB Z:THR192 4.3 61.5 1.0
CA Z:ILE196 4.4 50.4 1.0
C Z:ILE196 4.4 49.8 1.0
C Z:ASP222 4.5 74.9 1.0
CA Z:GLY199 4.5 57.3 1.0
NH2 H:ARG19 4.5 66.3 1.0
N Z:GLY199 4.5 56.6 1.0
N Z:VAL198 4.6 50.5 1.0
CZ Z:ARG28 4.7 64.5 1.0
CA Z:VAL198 4.7 53.9 1.0
O Z:LYS220 4.8 66.1 1.0
N Z:ILE196 4.8 50.2 1.0
N Z:GLU193 4.8 59.8 1.0
NH1 Z:ARG28 4.8 67.5 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 04:15:57 2024

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