Atomistry » Magnesium » PDB 5btm-5c25 » 5bxn
Atomistry »
  Magnesium »
    PDB 5btm-5c25 »
      5bxn »

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

Go back to Magnesium Binding Sites List in 5bxn
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

Go back to Magnesium Binding Sites List in 5bxn
Magnesium binding site 2 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 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

Go back to Magnesium Binding Sites List in 5bxn
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

Go back to Magnesium Binding Sites List in 5bxn
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

Go back to Magnesium Binding Sites List in 5bxn
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

Go back to Magnesium Binding Sites List in 5bxn
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

Go back to Magnesium Binding Sites List in 5bxn
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

Go back to Magnesium Binding Sites List in 5bxn
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

Go back to Magnesium Binding Sites List in 5bxn
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy