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Magnesium in PDB 5bxn: Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib

Enzymatic activity of Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib

All present enzymatic activity of Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib, PDB code: 5bxn 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.220, 300.860, 144.100, 90.00, 112.32, 90.00
R / Rfree (%) 19.8 / 21.8

Other elements in 5bxn:

The structure of Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib (pdb code 5bxn). 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 BETA2-G170A Mutant in Complex with Bortezomib, PDB code: 5bxn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5bxn

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib


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-G170A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:54.5
occ:1.00
 O G:MET125 2.3 55.4 1.0
OG1 G:THR8 2.6 52.3 1.0
O G:ARG122 2.6 54.3 1.0
O G:TYR119 3.0 50.7 1.0
O G:ALA123 3.2 58.0 1.0
CG2 G:THR8 3.3 55.2 1.0
C G:MET125 3.4 56.5 1.0
CB G:THR8 3.5 53.6 1.0
C G:ALA123 3.5 57.4 1.0
CA G:ALA123 3.6 56.2 1.0
C G:ARG122 3.7 55.9 1.0
N G:THR8 4.0 55.6 1.0
N G:ALA123 4.1 55.9 1.0
N G:MET125 4.2 59.0 1.0
N G:ARG126 4.2 53.3 1.0
C G:TYR119 4.2 48.9 1.0
CA G:ARG126 4.2 51.7 1.0
CA G:THR8 4.3 54.5 1.0
CA G:MET125 4.4 61.1 1.0
N G:TYR124 4.5 59.5 1.0
CD G:PRO127 4.7 49.4 1.0
CB G:ALA123 4.9 55.8 1.0
C G:TYR124 4.9 58.3 1.0
C G:ARG126 4.9 51.1 1.0
CA G:TYR119 4.9 48.2 1.0
CA G:ARG122 5.0 57.7 1.0

Magnesium binding site 2 out of 9 in 5bxn

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:30.0
occ:1.00
 OXT Z:ASP222 1.6 81.4 1.0
O H:ILE163 2.1 56.6 1.0
O H:ASP166 2.1 59.2 1.0
O H:SER169 2.2 58.5 1.0
C Z:ASP222 2.8 79.5 1.0
C H:ILE163 3.2 60.9 1.0
C H:ASP166 3.2 59.9 1.0
C H:SER169 3.4 61.9 1.0
CA Z:ASP222 3.5 76.7 1.0
O H:GLY162 3.7 60.3 1.0
O Z:ASP222 3.8 76.9 1.0
CB Z:ASP222 3.9 76.0 1.0
CA H:LEU167 3.9 60.9 1.0
CA H:ILE163 3.9 61.4 1.0
N H:LEU167 4.0 59.3 1.0
O H:TRP164 4.1 61.8 1.0
N H:ASP166 4.1 62.2 1.0
N H:TRP164 4.2 60.5 1.0
N H:SER169 4.2 59.1 1.0
CA H:ASP166 4.2 58.8 1.0
C H:TRP164 4.2 60.8 1.0
CA H:SER169 4.2 56.6 1.0
C H:LEU167 4.3 62.9 1.0
N H:ALA170 4.3 64.4 1.0
CA H:ALA170 4.4 68.0 1.0
NH1 H:ARG19 4.4 70.6 1.0
CA H:TRP164 4.4 60.7 1.0
CB H:ALA170 4.4 69.5 1.0
O H:LEU167 4.5 63.0 1.0
CB H:SER169 4.5 51.5 1.0
C H:GLY162 4.7 60.1 1.0
N H:ASN165 4.8 59.9 1.0
N H:ILE163 4.8 59.8 1.0
N H:GLY168 4.8 63.7 1.0
N Z:ASP222 4.9 74.7 1.0
C H:ASN165 4.9 63.8 1.0
CG2 H:ILE163 5.0 64.5 1.0
CB H:ASP166 5.0 55.0 1.0
O Z:ARG221 5.0 71.9 1.0

Magnesium binding site 3 out of 9 in 5bxn

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib


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-G170A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:66.4
occ:1.00
 O I:ASP177 2.3 53.9 1.0
O I:SER180 2.7 49.0 1.0
O I:ALA174 2.9 57.3 1.0
C I:ASP177 3.4 53.6 1.0
OXT I:ASP204 3.7 67.7 1.0
C I:SER180 3.9 53.8 1.0
C I:ALA174 4.0 56.5 1.0
CA I:ALA178 4.1 52.2 1.0
O I:ALA178 4.2 52.0 1.0
C I:ALA178 4.2 52.2 1.0
N I:ALA178 4.2 51.8 1.0
NH1 Y:ARG19 4.3 70.7 1.0
CA I:ASP175 4.4 58.5 1.0
N I:ASP177 4.4 53.3 1.0
N I:SER180 4.4 53.1 1.0
CA I:ASP177 4.5 53.9 1.0
O I:ASP204 4.6 65.6 1.0
C I:ASP204 4.6 64.9 1.0
N I:ASP175 4.6 57.4 1.0
C I:ASP175 4.6 56.8 1.0
NH2 Y:ARG19 4.6 75.7 1.0
CA I:SER180 4.7 53.7 1.0
N I:GLY181 4.8 55.0 1.0
O I:ASP175 4.8 56.4 1.0
CA I:GLY181 4.9 57.4 1.0
CZ Y:ARG19 4.9 69.2 1.0
N I:LEU179 4.9 53.4 1.0

Magnesium binding site 4 out of 9 in 5bxn

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib


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-G170A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:48.4
occ:1.00
 O I:ASP204 2.2 65.6 1.0
O Y:ASP168 2.2 53.5 1.0
O Y:ALA165 2.4 51.9 1.0
O Y:SER171 2.7 49.7 1.0
C I:ASP204 3.1 64.9 1.0
C Y:ASP168 3.3 52.4 1.0
CA I:ASP204 3.5 65.7 1.0
C Y:ALA165 3.6 51.7 1.0
CA Y:ALA169 3.6 53.1 1.0
NH1 Y:ARG19 3.7 70.7 1.0
N Y:ALA169 3.8 53.7 1.0
CB I:ASP204 3.8 67.2 1.0
O Y:ALA169 3.8 53.7 1.0
C Y:ALA169 3.9 53.3 1.0
C Y:SER171 3.9 50.0 1.0
O Y:HIS166 3.9 49.6 1.0
OXT I:ASP204 4.0 67.7 1.0
CZ Y:ARG19 4.3 69.2 1.0
C Y:HIS166 4.4 53.0 1.0
N Y:SER171 4.4 48.7 1.0
CA Y:ALA165 4.4 51.6 1.0
CA Y:ASP168 4.5 51.3 1.0
N Y:ASP168 4.5 53.7 1.0
N Y:HIS166 4.6 53.4 1.0
NH2 Y:ARG19 4.6 75.7 1.0
CA Y:SER171 4.7 48.0 1.0
N Y:TYR170 4.7 51.5 1.0
CA Y:HIS166 4.7 52.8 1.0
O Y:ALA164 4.8 52.5 1.0
CG I:ASP204 4.8 68.5 1.0
N Y:GLY172 4.8 52.3 1.0
C Y:ARG167 4.9 53.9 1.0
N I:ASP204 4.9 64.0 1.0
CA Y:GLY172 4.9 53.7 1.0
CB Y:ALA169 5.0 52.3 1.0

Magnesium binding site 5 out of 9 in 5bxn

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib


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-G170A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:30.7
occ:1.00
 OE1 J:GLN118 3.4 47.2 1.0
OD2 J:ASP120 3.7 48.8 1.0
CB J:ASP120 3.7 43.0 1.0
O J:THR124 3.8 48.7 1.0
CG J:ASP120 3.8 45.0 1.0
N J:ASP120 4.2 40.8 1.0
CD J:GLN118 4.3 45.7 1.0
CB J:THR124 4.3 46.4 1.0
CE1 J:HIS133 4.4 42.3 1.0
CG2 J:THR124 4.4 45.8 1.0
O J:HOH314 4.4 32.7 1.0
CG J:GLN118 4.4 43.8 1.0
CA J:ASP120 4.6 41.9 1.0
OD1 J:ASP120 4.6 49.7 1.0
O J:GLN118 4.7 41.4 1.0
OG I:SER30 4.7 63.9 1.0
C J:THR124 4.8 46.2 1.0
C J:ILE119 4.9 40.4 1.0
CG1 I:VAL35 4.9 54.3 1.0

Magnesium binding site 6 out of 9 in 5bxn

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib


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-G170A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:57.2
occ:1.00
 O K:ASP168 2.1 52.3 1.0
O K:ALA165 2.3 51.9 1.0
O W:ASP204 2.4 55.9 1.0
C K:ASP168 3.0 51.0 1.0
O K:SER171 3.1 53.8 1.0
C W:ASP204 3.2 56.0 1.0
C K:ALA165 3.4 52.4 1.0
O K:HIS166 3.4 54.3 1.0
CA K:ALA169 3.6 53.0 1.0
N K:ALA169 3.7 52.6 1.0
CA W:ASP204 3.7 57.9 1.0
C K:HIS166 3.9 51.9 1.0
C K:ALA169 4.0 52.8 1.0
CB W:ASP204 4.1 58.2 1.0
N K:ASP168 4.1 49.6 1.0
OXT W:ASP204 4.1 58.6 1.0
O K:ALA169 4.1 53.6 1.0
CA K:ASP168 4.1 49.0 1.0
NH1 K:ARG19 4.2 66.6 1.0
C K:SER171 4.2 51.4 1.0
N K:HIS166 4.3 51.7 1.0
CA K:ALA165 4.3 53.8 1.0
C K:ARG167 4.4 50.5 1.0
CA K:HIS166 4.4 51.9 1.0
O K:ALA164 4.5 55.4 1.0
N K:ARG167 4.6 49.9 1.0
N K:SER171 4.6 49.7 1.0
O K:ARG167 4.7 49.3 1.0
N K:TYR170 4.8 52.1 1.0
CZ K:ARG19 4.8 66.5 1.0
CA K:SER171 4.9 48.9 1.0
CB K:ALA169 4.9 52.2 1.0
CB K:ASP168 5.0 47.7 1.0

Magnesium binding site 7 out of 9 in 5bxn

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib


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-G170A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:72.5
occ:1.00
 O V:ASP166 1.9 60.3 1.0
OXT L:ASP222 2.0 73.2 1.0
O V:ILE163 2.1 60.1 1.0
O V:SER169 2.2 55.0 1.0
C V:ASP166 3.0 57.4 1.0
C V:ILE163 3.2 60.7 1.0
C L:ASP222 3.2 73.0 1.0
C V:SER169 3.4 51.4 1.0
O V:GLY162 3.6 53.9 1.0
N V:LEU167 3.8 58.4 1.0
CA V:LEU167 3.8 56.5 1.0
CA L:ASP222 3.8 71.6 1.0
N V:ASP166 3.9 54.0 1.0
CA V:ILE163 3.9 59.4 1.0
O V:TRP164 4.0 62.8 1.0
CA V:ASP166 4.0 54.6 1.0
N V:SER169 4.1 47.4 1.0
O L:ASP222 4.1 69.5 1.0
N V:TRP164 4.1 58.6 1.0
C V:TRP164 4.1 58.7 1.0
C V:LEU167 4.2 54.4 1.0
CA V:SER169 4.2 46.9 1.0
CB L:ASP222 4.3 71.0 1.0
CB V:ALA170 4.3 59.5 1.0
N V:ALA170 4.4 53.3 1.0
CA V:TRP164 4.4 57.1 1.0
O V:LEU167 4.4 54.5 1.0
CA V:ALA170 4.5 57.7 1.0
NH1 V:ARG19 4.5 72.9 1.0
C V:GLY162 4.6 53.3 1.0
CB V:SER169 4.6 45.1 1.0
N V:ASN165 4.7 55.2 1.0
N V:ILE163 4.8 56.0 1.0
C V:ASN165 4.8 53.8 1.0
CB V:ASP166 4.8 53.2 1.0
N V:GLY168 4.8 52.3 1.0

Magnesium binding site 8 out of 9 in 5bxn

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib


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-G170A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:58.0
occ:1.00
 O N:SER169 2.6 45.1 1.0
O N:ILE163 2.6 46.1 1.0
O N:ASP166 2.8 49.3 1.0
CD1 a:LEU34 3.6 53.5 1.0
NH1 N:ARG19 3.6 49.5 1.0
C N:ILE163 3.7 47.4 1.0
C N:SER169 3.8 44.4 1.0
C N:ASP166 3.8 46.4 1.0
CG2 N:ILE163 3.9 46.0 1.0
CA N:GLY167 4.1 46.1 1.0
CZ N:ARG19 4.2 48.6 1.0
CA N:ILE163 4.3 46.8 1.0
N N:GLY167 4.4 45.7 1.0
CA N:GLY170 4.5 46.8 1.0
NH2 N:ARG19 4.5 51.3 1.0
C N:GLY167 4.5 45.9 1.0
O N:GLY167 4.5 46.6 1.0
N N:GLY170 4.6 45.3 1.0
N N:SER169 4.7 44.6 1.0
CA N:SER169 4.7 43.0 1.0
N N:LYS164 4.8 49.3 1.0
CB N:ILE163 4.8 46.3 1.0
CG a:LEU34 4.9 53.5 1.0
O N:LYS164 4.9 53.8 1.0
N N:ASP166 4.9 44.9 1.0
C N:LYS164 4.9 50.7 1.0
CA N:ASP166 5.0 44.9 1.0

Magnesium binding site 9 out of 9 in 5bxn

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome BETA2-G170A Mutant in Complex with Bortezomib


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 BETA2-G170A Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:77.4
occ:1.00
 O Z:VAL198 2.8 56.8 1.0
O Z:THR192 3.2 64.5 1.0
O Z:ASP222 3.2 76.9 1.0
O Z:HIS195 3.3 58.0 1.0
NH2 Z:ARG28 3.4 71.7 1.0
O Z:ILE196 3.7 62.5 1.0
NH2 H:ARG19 3.7 68.2 1.0
CA Z:ILE196 3.9 60.1 1.0
C Z:VAL198 4.0 62.6 1.0
C Z:ILE196 4.0 60.5 1.0
CG2 Z:THR192 4.1 70.4 1.0
C Z:HIS195 4.2 59.7 1.0
C Z:THR192 4.2 68.0 1.0
CZ Z:ARG28 4.3 69.0 1.0
NH1 H:ARG19 4.3 70.6 1.0
C Z:ASP222 4.4 79.5 1.0
NH1 Z:ARG28 4.5 69.2 1.0
CZ H:ARG19 4.5 69.6 1.0
N Z:ILE196 4.5 59.7 1.0
CA Z:THR192 4.6 68.8 1.0
N Z:VAL198 4.6 58.7 1.0
OD1 Z:ASP222 4.7 75.3 1.0
CA Z:GLY199 4.8 65.3 1.0
N Z:GLY199 4.8 63.1 1.0
CA Z:VAL198 4.9 61.2 1.0
N Z:GLN197 5.0 59.0 1.0
CB Z:THR192 5.0 68.6 1.0

Reference:

I.Treise, E.M.Huber, T.Klein-Rodewald, W.Heinemeyer, S.A.Grassmann, M.Basler, T.Adler, B.Rathkolb, L.Helming, C.Andres, M.Klaften, C.Landbrecht, T.Wieland, T.M.Strom, K.D.Mccoy, A.J.Macpherson, E.Wolf, M.Groettrup, M.Ollert, F.Neff, V.Gailus-Durner, H.Fuchs, M.Hrabe De Angelis, M.Groll, D.H.Busch. Defective Immuno- and Thymoproteasome Assembly Causes Severe Immunodeficiency. Sci Rep V. 8 5975 2018.
ISSN: ESSN 2045-2322
PubMed: 29654304
DOI: 10.1038/S41598-018-24199-0
Page generated: Sun Sep 29 01:45:53 2024

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