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Magnesium in PDB 6hwf: Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914

Enzymatic activity of Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914

All present enzymatic activity of Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914, PDB code: 6hwf 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 (°) 136.630, 299.660, 145.150, 90.00, 113.39, 90.00
R / Rfree (%) 18.9 / 21.6

Other elements in 6hwf:

The structure of Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914 (pdb code 6hwf). 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 BETA2-G45A Mutant in Complex with Onx 0914, PDB code: 6hwf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6hwf

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914


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 BETA2-G45A Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:52.5
occ:1.00
 O G:MET125 2.3 42.9 1.0
O G:ARG122 2.4 41.1 1.0
OG1 G:THR8 2.5 41.3 1.0
O G:TYR119 2.5 40.9 1.0
CG2 G:THR8 3.3 42.3 1.0
CB G:THR8 3.4 41.8 1.0
C G:ARG122 3.5 41.7 1.0
C G:MET125 3.5 46.1 1.0
O G:ALA123 3.6 48.7 1.0
C G:TYR119 3.7 38.5 1.0
CA G:ALA123 3.7 42.6 1.0
C G:ALA123 3.8 45.6 1.0
N G:ALA123 4.0 41.0 1.0
N G:MET125 4.2 45.7 1.0
N G:THR8 4.2 40.9 1.0
N G:ARG126 4.4 45.2 1.0
CA G:MET125 4.4 50.2 1.0
CA G:ARG126 4.4 44.3 1.0
CA G:THR8 4.4 41.0 1.0
CA G:TYR119 4.5 38.8 1.0
N G:ARG122 4.6 42.5 1.0
CD G:PRO127 4.6 40.1 1.0
CA G:ARG122 4.7 44.8 1.0
N G:THR120 4.7 37.9 1.0
N G:TYR124 4.7 47.9 1.0
CA G:THR120 4.8 40.1 1.0
CB G:MET125 4.8 59.3 1.0
C G:THR120 4.9 41.6 1.0
C G:ARG126 4.9 42.5 1.0

Magnesium binding site 2 out of 8 in 6hwf

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914


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 BETA2-G45A Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:59.4
occ:1.00
 O I:SER180 2.4 47.1 1.0
O I:ASP177 2.5 43.0 1.0
O I:ALA174 2.6 45.9 1.0
C I:SER180 3.6 45.1 1.0
C I:ALA174 3.6 43.5 1.0
C I:ASP177 3.7 41.7 1.0
O I:HOH406 3.7 49.7 1.0
OXT I:ASP204 3.9 62.8 1.0
CA I:ASP175 4.2 44.7 1.0
N I:ASP175 4.3 44.0 1.0
O I:ALA178 4.4 39.6 1.0
N I:SER180 4.4 42.9 1.0
C I:ALA178 4.5 39.5 1.0
N I:GLY181 4.5 43.3 1.0
N I:ASP177 4.5 42.1 1.0
CA I:GLY181 4.5 44.4 1.0
C I:ASP175 4.5 42.6 1.0
CA I:ALA178 4.5 38.9 1.0
N I:ALA178 4.5 39.0 1.0
CA I:SER180 4.5 44.7 1.0
O I:ASP175 4.6 47.5 1.0
CA I:ASP177 4.6 42.8 1.0
CA I:ALA174 4.7 41.1 1.0
O I:ASP204 4.7 59.2 1.0
C I:ASP204 4.7 57.3 1.0
OD1 I:ASP175 4.9 52.3 1.0
CB I:ALA174 4.9 39.8 1.0

Magnesium binding site 3 out of 8 in 6hwf

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914


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 BETA2-G45A Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:59.0
occ:1.00
 O Y:ASP168 2.2 46.2 1.0
O Y:SER171 2.3 46.4 1.0
O Y:ALA165 2.4 44.8 1.0
O I:ASP204 2.6 59.2 1.0
O Y:HOH417 2.9 50.1 1.0
C I:ASP204 3.3 57.3 1.0
C Y:ASP168 3.4 42.2 1.0
C Y:SER171 3.5 44.9 1.0
C Y:ALA165 3.5 44.4 1.0
NH1 Y:ARG19 3.7 63.6 1.0
CA I:ASP204 3.7 54.0 1.0
O Y:ALA169 3.8 42.1 1.0
CA Y:ALA169 3.8 39.2 1.0
C Y:ALA169 3.8 40.0 1.0
CB I:ASP204 4.0 54.5 1.0
N Y:ALA169 4.0 40.3 1.0
N Y:SER171 4.0 43.0 1.0
OXT I:ASP204 4.2 62.8 1.0
CA Y:ALA165 4.2 43.0 1.0
O Y:HIS166 4.3 43.9 1.0
CA Y:SER171 4.3 43.2 1.0
CZ Y:ARG19 4.3 58.4 1.0
N Y:GLY172 4.5 45.6 1.0
CA Y:ASP168 4.5 40.9 1.0
NH2 Y:ARG19 4.6 59.2 1.0
N Y:ASP168 4.6 40.1 1.0
N Y:HIS166 4.6 43.7 1.0
C Y:HIS166 4.6 42.7 1.0
O Y:ALA164 4.6 41.3 1.0
N Y:TYR170 4.6 39.9 1.0
CA Y:GLY172 4.6 45.9 1.0
CA Y:HIS166 4.8 43.3 1.0
CB Y:SER171 4.9 42.6 1.0
CG I:ASP204 4.9 55.3 1.0

Magnesium binding site 4 out of 8 in 6hwf

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914


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 BETA2-G45A Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:58.0
occ:1.00
 O K:ASP168 2.2 42.6 1.0
O K:ALA165 2.3 41.2 1.0
O K:SER171 2.5 50.2 1.0
O W:ASP204 2.5 78.0 1.0
C W:ASP204 3.2 59.8 1.0
C K:ASP168 3.3 42.2 1.0
C K:ALA165 3.5 42.1 1.0
CA W:ASP204 3.7 54.3 1.0
C K:SER171 3.7 48.6 1.0
CA K:ALA169 3.8 40.8 1.0
NH1 K:ARG19 3.9 58.4 1.0
O K:ALA169 3.9 44.7 1.0
C K:ALA169 3.9 42.0 1.0
CB W:ASP204 4.0 51.6 1.0
N K:ALA169 4.0 41.2 1.0
O K:HIS166 4.1 41.5 1.0
OXT W:ASP204 4.2 70.0 1.0
N K:SER171 4.2 46.3 1.0
CA K:ALA165 4.3 41.1 1.0
C K:HIS166 4.4 41.1 1.0
CA K:SER171 4.5 46.6 1.0
N K:HIS166 4.5 41.2 1.0
CZ K:ARG19 4.5 57.0 1.0
CA K:ASP168 4.5 42.2 1.0
N K:ASP168 4.5 41.7 1.0
O K:ALA164 4.6 44.0 1.0
N K:GLY172 4.6 49.4 1.0
NH2 K:ARG19 4.7 62.6 1.0
N K:TYR170 4.7 41.7 1.0
CA K:HIS166 4.7 40.8 1.0
CA K:GLY172 4.7 51.5 1.0
CG W:ASP204 4.9 52.4 1.0

Magnesium binding site 5 out of 8 in 6hwf

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914


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 BETA2-G45A Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:54.5
occ:1.00
 O V:ASP166 2.1 45.0 1.0
OXT L:ASP222 2.2 57.0 1.0
O V:SER169 2.2 47.6 1.0
O V:ILE163 2.3 45.5 1.0
C V:ASP166 3.1 45.2 1.0
C L:ASP222 3.1 59.2 1.0
C V:ILE163 3.3 47.1 1.0
C V:SER169 3.4 45.5 1.0
O V:GLY162 3.8 47.5 1.0
CA L:ASP222 3.8 56.3 1.0
N V:LEU167 3.9 45.9 1.0
CA V:LEU167 3.9 45.3 1.0
O L:ASP222 4.0 63.7 1.0
NH1 V:ARG19 4.0 56.1 1.0
N V:ASP166 4.0 45.2 1.0
CA V:ILE163 4.0 46.8 1.0
N V:SER169 4.1 41.2 1.0
CA V:ASP166 4.1 45.0 1.0
CA V:SER169 4.2 43.1 1.0
N V:TRP164 4.3 49.5 1.0
O V:TRP164 4.3 53.7 1.0
C V:TRP164 4.3 52.1 1.0
C V:LEU167 4.3 45.2 1.0
CB L:ASP222 4.3 55.3 1.0
N V:GLY170 4.4 46.1 1.0
CA V:GLY170 4.5 48.3 1.0
CA V:TRP164 4.5 51.0 1.0
O V:LEU167 4.5 44.8 1.0
CZ V:ARG19 4.6 53.3 1.0
CB V:SER169 4.6 43.4 1.0
N V:ASN165 4.7 49.8 1.0
C V:GLY162 4.7 45.5 1.0
NH2 V:ARG19 4.8 53.3 1.0
C V:ASN165 4.8 45.1 1.0
N V:ILE163 4.9 46.0 1.0
CB V:ASP166 4.9 44.6 1.0
N V:GLY168 4.9 45.2 1.0

Magnesium binding site 6 out of 8 in 6hwf

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914


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 BETA2-G45A Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:51.1
occ:1.00
 O N:SER169 2.4 43.5 1.0
O N:ILE163 2.5 40.8 1.0
O N:ASP166 2.7 45.1 1.0
C N:SER169 3.6 42.5 1.0
CD1 a:LEU34 3.6 43.2 1.0
C N:ILE163 3.6 44.0 1.0
NH1 N:ARG19 3.7 50.8 1.0
C N:ASP166 3.8 43.3 1.0
CG2 N:ILE163 3.9 40.6 1.0
CA N:GLY167 4.1 43.2 1.0
CA N:ILE163 4.3 42.3 1.0
CZ N:ARG19 4.3 48.2 1.0
CA N:GLY170 4.3 44.5 1.0
N N:GLY167 4.4 43.5 1.0
O N:GLY167 4.4 40.9 1.0
N N:GLY170 4.4 42.7 1.0
C N:GLY167 4.4 41.9 1.0
N N:SER169 4.6 42.3 1.0
NH2 N:ARG19 4.6 47.4 1.0
CA N:SER169 4.6 40.7 1.0
CB N:ILE163 4.7 41.4 1.0
N N:LYS164 4.7 46.8 1.0
N N:ASP166 4.9 44.1 1.0
O N:LYS164 4.9 43.6 1.0
CG a:LEU34 4.9 42.8 1.0
CA N:ASP166 5.0 43.6 1.0
C N:LYS164 5.0 45.0 1.0

Magnesium binding site 7 out of 8 in 6hwf

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914


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 BETA2-G45A Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:57.2
occ:1.00
 O W:ASP177 2.5 41.8 1.0
O W:SER180 2.5 47.4 1.0
O W:ALA174 2.9 47.3 1.0
C W:ASP177 3.6 42.6 1.0
OXT W:ASP204 3.7 70.0 1.0
C W:SER180 3.8 47.2 1.0
C W:ALA174 4.0 46.7 1.0
O W:ALA178 4.1 42.2 1.0
C W:ALA178 4.2 42.5 1.0
CA W:ALA178 4.2 42.1 1.0
O W:ASP204 4.3 78.0 1.0
N W:ALA178 4.4 41.2 1.0
N W:SER180 4.4 47.9 1.0
C W:ASP204 4.5 59.8 1.0
CA W:ASP175 4.5 50.9 1.0
N W:ASP177 4.6 47.7 1.0
N W:GLY181 4.7 45.3 1.0
CA W:SER180 4.7 48.7 1.0
O W:ASP175 4.7 50.7 1.0
CA W:ASP177 4.7 47.2 1.0
N W:ASP175 4.7 47.6 1.0
C W:ASP175 4.7 48.8 1.0
CA W:GLY181 4.7 44.4 1.0
NH1 K:ARG19 4.8 58.4 1.0
N W:LEU179 4.9 43.8 1.0

Magnesium binding site 8 out of 8 in 6hwf

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA2-G45A Mutant in Complex with Onx 0914


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 BETA2-G45A Mutant in Complex with Onx 0914 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:70.0
occ:1.00
 O Z:VAL198 2.5 47.1 1.0
O Z:THR192 2.9 44.2 1.0
O Z:HIS195 3.4 39.6 1.0
NH2 Z:ARG28 3.5 53.9 1.0
O Z:ASP222 3.5 64.3 1.0
CG2 Z:THR192 3.5 42.5 1.0
C Z:VAL198 3.7 47.7 1.0
C Z:THR192 3.8 45.4 1.0
OD1 Z:ASP222 3.9 53.8 1.0
O Z:ILE196 4.0 43.5 1.0
CA Z:THR192 4.1 43.7 1.0
CA Z:GLY199 4.3 50.2 1.0
NH2 H:ARG19 4.4 49.9 1.0
CA Z:ILE196 4.4 39.2 1.0
C Z:HIS195 4.4 39.6 1.0
C Z:ILE196 4.4 39.8 1.0
C Z:ASP222 4.4 61.4 1.0
CB Z:THR192 4.5 43.4 1.0
N Z:GLY199 4.5 49.0 1.0
CZ Z:ARG28 4.5 55.0 1.0
O Z:LYS220 4.6 49.7 1.0
N Z:VAL198 4.7 45.7 1.0
CA Z:VAL198 4.8 47.4 1.0
NH1 Z:ARG28 4.8 58.4 1.0
N Z:ILE196 4.9 39.0 1.0
CG Z:ASP222 5.0 53.1 1.0
OXT Z:ASP222 5.0 62.5 1.0

Reference:

B.T.Xin, E.M.Huber, G.De Bruin, W.Heinemeyer, E.Maurits, C.Espinal, Y.Du, M.Janssens, E.S.Weyburne, A.F.Kisselev, B.I.Florea, C.Driessen, G.A.Van Der Marel, M.Groll, H.S.Overkleeft. Structure-Based Design of Inhibitors Selective For Human Proteasome Beta 2C or Beta 2I Subunits. J.Med.Chem. V. 62 1626 2019.
ISSN: ISSN 0022-2623
PubMed: 30657666
DOI: 10.1021/ACS.JMEDCHEM.8B01884
Page generated: Tue Oct 1 02:46:23 2024

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