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Magnesium in PDB 5cz9: Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans

Enzymatic activity of Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans

All present enzymatic activity of Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans, PDB code: 5cz9 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.720, 300.900, 145.070, 90.00, 112.94, 90.00
R / Rfree (%) 19.9 / 22.3

Other elements in 5cz9:

The structure of Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans 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-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans (pdb code 5cz9). 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-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans, PDB code: 5cz9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5cz9

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; 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-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:41.1
occ:1.00
 O G:MET125 2.3 39.1 1.0
O G:ARG122 2.5 37.9 1.0
OG1 G:THR8 2.6 35.6 1.0
O G:TYR119 2.7 30.4 1.0
CG2 G:THR8 3.2 37.8 1.0
O G:ALA123 3.3 44.1 1.0
C G:MET125 3.4 39.2 1.0
CB G:THR8 3.5 37.1 1.0
C G:ARG122 3.6 39.5 1.0
C G:ALA123 3.7 41.4 1.0
CA G:ALA123 3.7 40.0 1.0
C G:TYR119 3.9 31.6 1.0
N G:ALA123 4.1 38.9 1.0
N G:THR8 4.1 40.5 1.0
CA G:ARG126 4.2 34.8 1.0
N G:ARG126 4.3 36.6 1.0
N G:MET125 4.3 41.1 1.0
CA G:MET125 4.4 43.3 1.0
CA G:THR8 4.4 38.8 1.0
CD G:PRO127 4.6 31.2 1.0
CA G:TYR119 4.6 31.2 1.0
N G:TYR124 4.6 43.2 1.0
N G:THR120 4.9 31.9 1.0
C G:ARG126 4.9 34.0 1.0
CA G:ARG122 4.9 41.8 1.0
N G:ARG122 5.0 38.9 1.0
CA G:THR120 5.0 32.0 1.0
C G:TYR124 5.0 40.8 1.0

Magnesium binding site 2 out of 7 in 5cz9

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; 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-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:48.4
occ:1.00
 O I:ASP177 2.6 50.8 1.0
O I:ALA174 2.9 53.0 1.0
O I:SER180 2.9 48.3 1.0
OXT I:ASP204 3.5 72.9 1.0
C I:ASP177 3.7 48.5 1.0
C I:ALA174 4.0 51.8 1.0
C I:SER180 4.1 47.8 1.0
CA I:ASP175 4.2 53.2 1.0
O I:ALA178 4.3 56.0 1.0
CA I:ALA178 4.3 49.5 1.0
O I:ASP204 4.3 73.4 1.0
C I:ASP204 4.3 72.3 1.0
NH2 Y:ARG19 4.4 72.0 1.0
C I:ALA178 4.4 51.2 1.0
N I:ALA178 4.4 47.4 1.0
C I:ASP175 4.5 51.9 1.0
O I:ASP175 4.5 52.2 1.0
N I:ASP175 4.6 51.8 1.0
N I:ASP177 4.6 48.9 1.0
CA I:ASP177 4.7 48.7 1.0
N I:SER180 4.8 46.4 1.0
NH1 Y:ARG19 4.9 74.2 1.0
CA I:GLY181 4.9 47.5 1.0
N I:GLY181 5.0 46.8 1.0
CZ Y:ARG19 5.0 71.2 1.0

Magnesium binding site 3 out of 7 in 5cz9

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; 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-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:48.0
occ:1.00
 O Y:ASP168 2.3 53.3 1.0
O I:ASP204 2.4 73.4 1.0
O Y:ALA165 2.5 49.8 1.0
O Y:SER171 2.9 54.6 1.0
C I:ASP204 3.1 72.3 1.0
C Y:ASP168 3.3 52.4 1.0
CA Y:ALA169 3.6 53.2 1.0
O Y:HIS166 3.6 49.5 1.0
C Y:ALA165 3.7 51.5 1.0
CA I:ASP204 3.7 71.0 1.0
NH1 Y:ARG19 3.7 74.2 1.0
O Y:ALA169 3.8 53.1 1.0
N Y:ALA169 3.8 52.7 1.0
C Y:ALA169 3.9 52.5 1.0
OXT I:ASP204 4.0 72.9 1.0
C Y:HIS166 4.1 51.7 1.0
C Y:SER171 4.1 54.6 1.0
CB I:ASP204 4.1 72.3 1.0
N Y:ASP168 4.5 51.6 1.0
CA Y:ASP168 4.5 51.7 1.0
CA Y:HIS166 4.5 52.0 1.0
N Y:HIS166 4.5 50.9 1.0
N Y:SER171 4.5 52.8 1.0
CA Y:ALA165 4.6 52.7 1.0
C Y:ARG167 4.6 51.5 1.0
O Y:ALA164 4.8 50.2 1.0
N Y:ARG167 4.8 51.0 1.0
N Y:TYR170 4.8 52.8 1.0
CZ Y:ARG19 4.8 71.2 1.0
O Y:ARG167 4.8 50.5 1.0
CA Y:SER171 4.9 53.0 1.0
CB Y:ALA169 4.9 54.0 1.0

Magnesium binding site 4 out of 7 in 5cz9

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; 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-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:41.0
occ:1.00
 O K:ASP168 2.0 51.3 1.0
O K:ALA165 2.4 50.8 1.0
O W:ASP204 2.6 66.0 1.0
O K:SER171 2.8 53.3 1.0
C K:ASP168 3.1 52.3 1.0
C W:ASP204 3.3 63.4 1.0
C K:ALA165 3.5 52.0 1.0
CA K:ALA169 3.6 53.8 1.0
O K:HIS166 3.6 49.8 1.0
CA W:ASP204 3.7 62.9 1.0
N K:ALA169 3.7 52.7 1.0
O K:ALA169 3.8 52.3 1.0
NH1 K:ARG19 3.8 66.7 1.0
C K:ALA169 3.8 54.0 1.0
C K:HIS166 4.0 51.5 1.0
C K:SER171 4.0 54.5 1.0
CB W:ASP204 4.2 63.4 1.0
OXT W:ASP204 4.2 60.1 1.0
N K:ASP168 4.2 52.2 1.0
CA K:ASP168 4.3 52.6 1.0
N K:HIS166 4.4 51.0 1.0
N K:SER171 4.4 51.5 1.0
CA K:HIS166 4.4 51.7 1.0
CA K:ALA165 4.5 52.9 1.0
C K:ARG167 4.5 51.9 1.0
O K:ALA164 4.5 51.0 1.0
N K:ARG167 4.6 50.9 1.0
N K:TYR170 4.7 54.0 1.0
O K:ARG167 4.7 51.8 1.0
CA K:SER171 4.7 52.5 1.0
CZ K:ARG19 4.9 66.4 1.0
CB K:ALA169 4.9 54.3 1.0

Magnesium binding site 5 out of 7 in 5cz9

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; 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-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:61.8
occ:1.00
 OXT L:ASP222 2.1 74.5 1.0
O V:ILE163 2.3 48.6 1.0
O V:ASP166 2.4 40.5 1.0
C L:ASP222 3.0 71.5 1.0
O V:SER169 3.2 40.2 1.0
C V:ASP166 3.2 42.4 1.0
O V:TRP164 3.4 51.4 1.0
C V:ILE163 3.4 49.3 1.0
CA L:ASP222 3.6 67.1 1.0
C V:TRP164 3.6 49.2 1.0
N V:LEU167 3.8 43.0 1.0
O L:ASP222 3.9 72.6 1.0
CA V:LEU167 3.9 43.6 1.0
N V:ASP166 3.9 42.0 1.0
O V:GLY162 4.0 49.0 1.0
CA V:TRP164 4.0 49.1 1.0
N V:TRP164 4.1 49.0 1.0
CA V:ASP166 4.2 42.2 1.0
N V:ASN165 4.2 46.9 1.0
C V:SER169 4.3 42.7 1.0
CB L:ASP222 4.4 65.2 1.0
O L:ARG221 4.4 59.6 1.0
C V:ASN165 4.4 43.2 1.0
NH1 V:ARG19 4.4 57.5 1.0
CA V:ILE163 4.4 49.6 1.0
C V:LEU167 4.5 43.4 1.0
CD2 V:LEU167 4.6 43.2 1.0
N L:ASP222 4.7 63.6 1.0
CA V:ASN165 4.8 45.3 1.0
O V:LEU167 4.8 44.7 1.0
CD1 L:ILE35 4.9 52.6 1.0
N V:SER169 5.0 43.3 1.0

Magnesium binding site 6 out of 7 in 5cz9

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; 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-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:44.0
occ:1.00
 O N:SER169 2.5 36.5 1.0
O N:ILE163 2.8 39.1 1.0
O N:ASP166 3.0 38.5 1.0
NH1 N:ARG19 3.4 40.0 1.0
C N:SER169 3.7 35.2 1.0
CD1 a:LEU34 3.8 40.5 1.0
C N:ILE163 3.9 38.5 1.0
CZ N:ARG19 4.1 38.2 1.0
C N:ASP166 4.1 37.3 1.0
CG2 N:ILE163 4.1 37.2 1.0
CA N:GLY167 4.2 37.4 1.0
CA N:GLY170 4.3 36.8 1.0
O N:GLY167 4.3 37.1 1.0
NH2 N:ARG19 4.3 38.4 1.0
N N:GLY170 4.4 36.0 1.0
C N:GLY167 4.5 36.5 1.0
CA N:ILE163 4.6 37.2 1.0
N N:GLY167 4.6 37.2 1.0
N N:SER169 4.7 33.8 1.0
CA N:SER169 4.8 33.1 1.0
CB N:ILE163 5.0 36.5 1.0
N N:LYS164 5.0 38.9 1.0

Magnesium binding site 7 out of 7 in 5cz9

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome BETA5-D17N Mutant in Complex with Carfilzomib; 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-D17N Mutant in Complex with Carfilzomib; Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:50.1
occ:1.00
 O Z:VAL198 2.5 50.6 1.0
O Z:THR192 2.7 54.9 1.0
O Z:HIS195 3.0 44.3 1.0
O Z:ASP222 3.4 66.1 1.0
NH2 Z:ARG28 3.6 58.3 1.0
CG2 Z:THR192 3.6 56.4 1.0
C Z:THR192 3.7 56.5 1.0
C Z:VAL198 3.7 50.7 1.0
O Z:ILE196 4.0 44.8 1.0
CA Z:THR192 4.1 56.0 1.0
C Z:HIS195 4.1 45.9 1.0
CA Z:ILE196 4.2 45.2 1.0
OD1 Z:ASP222 4.2 63.5 1.0
C Z:ILE196 4.3 43.5 1.0
NH2 H:ARG19 4.4 60.0 1.0
CB Z:THR192 4.5 56.7 1.0
C Z:ASP222 4.5 65.5 1.0
N Z:VAL198 4.5 47.5 1.0
CA Z:GLY199 4.6 51.5 1.0
N Z:GLY199 4.6 51.2 1.0
CZ Z:ARG28 4.6 56.3 1.0
N Z:ILE196 4.6 45.4 1.0
CA Z:VAL198 4.7 49.1 1.0
NH1 Z:ARG28 4.8 59.6 1.0
O Z:LYS220 4.9 59.3 1.0
N Z:GLU193 4.9 55.8 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 02:21:15 2024

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