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Magnesium in PDB 5bxl: Yeast 20S Proteasome BETA2-G170A Mutant

Enzymatic activity of Yeast 20S Proteasome BETA2-G170A Mutant

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

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-G170A Mutant, PDB code: 5bxl 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 (°) 134.800, 300.940, 144.490, 90.00, 112.71, 90.00
R / Rfree (%) 18.9 / 21.4

Other elements in 5bxl:

The structure of Yeast 20S Proteasome BETA2-G170A Mutant 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-G170A Mutant (pdb code 5bxl). 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, PDB code: 5bxl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5bxl

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:51.6
occ:1.00
 O G:MET125 2.1 51.2 1.0
O G:ARG122 2.4 44.5 1.0
O G:TYR119 2.4 41.5 1.0
OG1 G:THR8 2.6 46.2 1.0
CG2 G:THR8 3.2 45.8 1.0
C G:MET125 3.3 49.0 1.0
CB G:THR8 3.5 45.9 1.0
C G:ARG122 3.5 46.2 1.0
O G:ALA123 3.6 49.2 1.0
C G:TYR119 3.6 41.1 1.0
CA G:ALA123 3.8 46.9 1.0
C G:ALA123 3.8 47.8 1.0
N G:ALA123 4.1 46.4 1.0
N G:MET125 4.2 52.4 1.0
N G:ARG126 4.2 45.1 1.0
CA G:ARG126 4.2 43.7 1.0
CA G:MET125 4.3 52.8 1.0
N G:THR8 4.4 47.7 1.0
CA G:TYR119 4.4 41.0 1.0
CD G:PRO127 4.5 40.8 1.0
CA G:THR8 4.6 46.8 1.0
N G:THR120 4.6 41.0 1.0
N G:TYR124 4.7 49.5 1.0
N G:ARG122 4.7 45.9 1.0
CA G:ARG122 4.7 47.9 1.0
C G:ARG126 4.7 43.1 1.0
CB G:MET125 4.8 56.3 1.0
CA G:THR120 4.8 41.1 1.0
C G:THR120 4.9 42.5 1.0
N G:PRO127 4.9 41.5 1.0
CB G:TYR119 4.9 41.5 1.0

Magnesium binding site 2 out of 9 in 5bxl

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


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-G170A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:30.0
occ:1.00
 OXT Z:ASP222 1.8 72.3 1.0
O H:ILE163 1.9 47.1 1.0
O H:ASP166 2.3 48.4 1.0
O H:SER169 2.4 46.8 1.0
C Z:ASP222 2.8 67.3 1.0
C H:ILE163 3.1 52.5 1.0
CA Z:ASP222 3.2 61.9 1.0
C H:ASP166 3.4 48.8 1.0
C H:SER169 3.7 49.4 1.0
CB Z:ASP222 3.7 61.6 1.0
O Z:ASP222 3.8 66.4 1.0
O H:TRP164 3.9 53.1 1.0
CA H:ILE163 4.0 50.2 1.0
O H:GLY162 4.0 44.9 1.0
N H:TRP164 4.0 53.0 1.0
C H:TRP164 4.0 52.9 1.0
CA H:LEU167 4.1 48.5 1.0
N H:LEU167 4.1 47.3 1.0
N H:ASP166 4.2 50.4 1.0
CA H:TRP164 4.2 51.5 1.0
CB H:ALA170 4.3 47.2 1.0
CA H:ASP166 4.4 47.2 1.0
C H:LEU167 4.4 48.2 1.0
CA H:ALA170 4.4 49.0 1.0
O H:LEU167 4.5 49.1 1.0
N H:ALA170 4.5 49.7 1.0
N Z:ASP222 4.5 62.1 1.0
N H:SER169 4.5 45.9 1.0
O Z:ARG221 4.6 59.2 1.0
NH1 H:ARG19 4.6 59.0 1.0
CA H:SER169 4.6 47.0 1.0
N H:ASN165 4.7 50.9 1.0
CG2 H:ILE163 4.7 49.8 1.0
C H:GLY162 4.9 45.8 1.0
N H:ILE163 4.9 46.5 1.0
C H:ASN165 5.0 50.4 1.0
CB H:SER169 5.0 45.1 1.0
CB H:ILE163 5.0 50.8 1.0

Magnesium binding site 3 out of 9 in 5bxl

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.0
occ:1.00
 O I:ASP177 2.4 47.8 1.0
O I:HOH418 2.7 44.3 1.0
O I:SER180 2.7 49.0 1.0
O I:ALA174 2.8 48.6 1.0
O Y:HOH408 3.5 39.0 1.0
C I:ASP177 3.5 47.0 1.0
OXT I:ASP204 3.9 59.1 1.0
C I:ALA174 3.9 47.4 1.0
C I:SER180 3.9 49.3 1.0
CA I:ASP175 4.1 50.0 1.0
O I:ALA178 4.2 49.4 1.0
CA I:ALA178 4.3 47.5 1.0
N I:ALA178 4.3 46.5 1.0
C I:ALA178 4.3 48.5 1.0
N I:ASP177 4.4 47.3 1.0
C I:ASP175 4.4 49.8 1.0
NH1 Y:ARG19 4.4 52.4 1.0
N I:ASP175 4.4 48.8 1.0
CA I:ASP177 4.5 47.3 1.0
O I:ASP175 4.6 50.8 1.0
O I:ASP204 4.6 56.5 1.0
N I:SER180 4.6 48.6 1.0
NH2 Y:ARG19 4.6 53.1 1.0
C I:ASP204 4.7 55.5 1.0
OD1 I:ASP175 4.8 49.4 1.0
CA I:SER180 4.8 49.3 1.0
CA I:GLY181 4.8 48.8 1.0
N I:GLY181 4.8 49.0 1.0
CZ Y:ARG19 4.9 52.3 1.0

Magnesium binding site 4 out of 9 in 5bxl

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:52.9
occ:1.00
 O Y:ASP168 2.2 47.2 1.0
O I:ASP204 2.3 56.5 1.0
O Y:ALA165 2.4 45.1 1.0
O Y:SER171 2.6 42.9 1.0
C I:ASP204 3.1 55.5 1.0
C Y:ASP168 3.3 44.4 1.0
C Y:ALA165 3.5 43.4 1.0
CA I:ASP204 3.6 54.1 1.0
NH1 Y:ARG19 3.7 52.4 1.0
CA Y:ALA169 3.7 42.9 1.0
O Y:ALA169 3.7 44.7 1.0
C Y:SER171 3.8 45.2 1.0
C Y:ALA169 3.8 44.5 1.0
CB I:ASP204 3.9 54.9 1.0
N Y:ALA169 3.9 43.9 1.0
OXT I:ASP204 4.0 59.1 1.0
O Y:HIS166 4.1 41.5 1.0
CA Y:ALA165 4.3 43.3 1.0
N Y:SER171 4.3 43.4 1.0
CZ Y:ARG19 4.4 52.3 1.0
C Y:HIS166 4.5 42.4 1.0
CA Y:ASP168 4.5 43.8 1.0
N Y:ASP168 4.5 43.4 1.0
N Y:HIS166 4.5 43.1 1.0
CA Y:SER171 4.6 44.0 1.0
N Y:TYR170 4.7 44.6 1.0
NH2 Y:ARG19 4.7 53.1 1.0
CA Y:HIS166 4.7 42.6 1.0
N Y:GLY172 4.8 46.0 1.0
O Y:ALA164 4.8 45.0 1.0
CG I:ASP204 4.8 56.6 1.0
CA Y:GLY172 4.9 45.4 1.0
C Y:ARG167 4.9 42.9 1.0
N I:ASP204 5.0 52.6 1.0

Magnesium binding site 5 out of 9 in 5bxl

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:46.5
occ:1.00
 O W:ASP204 2.2 53.7 1.0
O K:ASP168 2.2 41.3 1.0
O K:ALA165 2.4 44.4 1.0
O K:SER171 2.5 45.1 1.0
C W:ASP204 3.0 53.0 1.0
C K:ASP168 3.3 40.8 1.0
CA W:ASP204 3.5 50.8 1.0
NH1 K:ARG19 3.6 50.4 1.0
C K:ALA165 3.6 42.3 1.0
O K:ALA169 3.7 44.0 1.0
C K:SER171 3.7 44.5 1.0
CA K:ALA169 3.7 41.0 1.0
C K:ALA169 3.8 42.3 1.0
CB W:ASP204 3.8 50.0 1.0
N K:ALA169 3.9 40.6 1.0
OXT W:ASP204 3.9 58.6 1.0
N K:SER171 4.2 44.0 1.0
O K:HIS166 4.3 44.8 1.0
CA K:ALA165 4.3 42.4 1.0
CZ K:ARG19 4.3 48.5 1.0
CA K:SER171 4.5 42.9 1.0
CA K:ASP168 4.5 40.3 1.0
C K:HIS166 4.6 41.1 1.0
N K:ASP168 4.6 41.5 1.0
N K:TYR170 4.6 43.0 1.0
N K:HIS166 4.6 40.9 1.0
NH2 K:ARG19 4.6 50.9 1.0
N K:GLY172 4.7 44.7 1.0
CG W:ASP204 4.8 49.9 1.0
CA K:GLY172 4.8 45.6 1.0
O K:ALA164 4.8 43.1 1.0
CA K:HIS166 4.8 41.0 1.0
CB K:SER171 4.9 42.2 1.0
N W:ASP204 4.9 50.4 1.0

Magnesium binding site 6 out of 9 in 5bxl

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:61.9
occ:1.00
 O V:ILE163 2.0 52.2 1.0
OXT L:ASP222 2.0 65.7 1.0
O V:ASP166 2.1 50.7 1.0
O V:SER169 2.3 52.1 1.0
C L:ASP222 3.1 62.9 1.0
C V:ASP166 3.2 48.4 1.0
C V:ILE163 3.2 54.1 1.0
C V:SER169 3.5 50.2 1.0
CA L:ASP222 3.6 62.1 1.0
CA V:LEU167 3.9 46.8 1.0
N V:LEU167 3.9 47.3 1.0
O V:GLY162 4.0 49.7 1.0
O V:TRP164 4.0 56.9 1.0
CA V:ILE163 4.0 52.6 1.0
O L:ASP222 4.1 62.6 1.0
N V:ASP166 4.1 50.5 1.0
CB L:ASP222 4.1 63.0 1.0
C V:TRP164 4.2 53.4 1.0
N V:TRP164 4.2 53.9 1.0
C V:LEU167 4.2 44.5 1.0
CA V:ASP166 4.2 48.8 1.0
CB V:ALA170 4.3 50.1 1.0
O V:LEU167 4.3 46.0 1.0
N V:SER169 4.3 46.8 1.0
CA V:TRP164 4.4 52.3 1.0
CA V:ALA170 4.4 52.0 1.0
N V:ALA170 4.4 51.4 1.0
CA V:SER169 4.4 47.2 1.0
NH1 V:ARG19 4.5 54.6 1.0
N V:ASN165 4.7 51.6 1.0
CB V:SER169 4.8 47.2 1.0
O L:ARG221 4.8 58.3 1.0
CG2 V:ILE163 4.9 52.6 1.0
C V:GLY162 4.9 49.0 1.0
N L:ASP222 4.9 61.1 1.0
N V:GLY168 4.9 44.3 1.0
C V:ASN165 4.9 51.7 1.0
N V:ILE163 4.9 49.5 1.0

Magnesium binding site 7 out of 9 in 5bxl

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:48.4
occ:1.00
 O N:ILE163 2.6 43.7 1.0
O N:SER169 2.7 41.9 1.0
O N:ASP166 3.1 45.4 1.0
CD1 a:LEU34 3.6 49.9 1.0
C N:ILE163 3.7 43.5 1.0
NH1 N:ARG19 3.7 44.8 1.0
CG2 N:ILE163 3.8 42.7 1.0
C N:SER169 3.9 43.7 1.0
C N:ASP166 4.1 42.4 1.0
CZ N:ARG19 4.2 45.2 1.0
CA N:GLY167 4.2 41.0 1.0
CA N:ILE163 4.4 42.9 1.0
NH2 N:ARG19 4.4 47.0 1.0
CA N:GLY170 4.4 46.2 1.0
O N:GLY167 4.5 39.9 1.0
N N:GLY167 4.6 41.3 1.0
N N:GLY170 4.6 45.3 1.0
C N:GLY167 4.6 41.1 1.0
CB N:ILE163 4.7 42.5 1.0
N N:LYS164 4.8 45.0 1.0
CG a:LEU34 4.9 49.3 1.0
CA N:SER169 4.9 42.6 1.0
N N:SER169 4.9 43.5 1.0
O N:LYS164 5.0 50.7 1.0

Magnesium binding site 8 out of 9 in 5bxl

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:62.9
occ:1.00
 O W:ASP177 2.3 45.7 1.0
O W:SER180 2.6 47.4 1.0
O W:ALA174 2.8 43.0 1.0
C W:ASP177 3.4 44.4 1.0
C W:SER180 3.8 46.5 1.0
C W:ALA174 3.9 43.9 1.0
OXT W:ASP204 3.9 58.6 1.0
O W:ALA178 4.1 47.6 1.0
CA W:ALA178 4.1 43.3 1.0
C W:ALA178 4.2 44.5 1.0
N W:ALA178 4.2 43.4 1.0
CA W:ASP175 4.2 47.1 1.0
N W:ASP177 4.3 45.1 1.0
NH1 K:ARG19 4.4 50.4 1.0
N W:SER180 4.4 46.5 1.0
CA W:ASP177 4.4 44.4 1.0
C W:ASP175 4.5 46.0 1.0
N W:ASP175 4.5 45.9 1.0
O W:ASP204 4.7 53.7 1.0
CA W:SER180 4.7 46.1 1.0
O W:ASP175 4.7 47.9 1.0
NH2 K:ARG19 4.7 50.9 1.0
N W:GLY181 4.7 46.0 1.0
C W:ASP204 4.7 53.0 1.0
CA W:GLY181 4.8 45.8 1.0
N W:LEU179 4.9 43.7 1.0
CZ K:ARG19 4.9 48.5 1.0
OD1 W:ASP175 5.0 52.0 1.0

Magnesium binding site 9 out of 9 in 5bxl

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:59.4
occ:1.00
 O Z:VAL198 2.5 47.1 1.0
O Z:HIS195 2.8 40.7 1.0
O Z:THR192 3.0 51.8 1.0
O Z:ASP222 3.3 66.4 1.0
NH2 Z:ARG28 3.5 54.2 1.0
O Z:ILE196 3.5 47.1 1.0
C Z:VAL198 3.7 48.6 1.0
CA Z:ILE196 3.7 45.3 1.0
C Z:ILE196 3.7 46.0 1.0
C Z:HIS195 3.8 45.5 1.0
NH2 H:ARG19 4.0 54.6 1.0
C Z:THR192 4.0 54.2 1.0
CG2 Z:THR192 4.1 55.6 1.0
N Z:ILE196 4.2 45.6 1.0
NH1 H:ARG19 4.2 59.0 1.0
N Z:VAL198 4.2 46.8 1.0
CA Z:THR192 4.4 54.5 1.0
C Z:ASP222 4.5 67.3 1.0
CA Z:VAL198 4.5 48.2 1.0
CZ H:ARG19 4.6 56.1 1.0
CZ Z:ARG28 4.6 53.6 1.0
N Z:GLN197 4.6 46.3 1.0
N Z:GLY199 4.6 49.4 1.0
CA Z:GLY199 4.7 51.1 1.0
NH1 Z:ARG28 4.8 54.9 1.0
OXT Z:ASP222 4.9 72.3 1.0
CB Z:THR192 4.9 55.3 1.0
CB Z:ILE196 4.9 45.3 1.0
C Z:GLN197 5.0 46.8 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 01:45:46 2024

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