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

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

Go back to Magnesium Binding Sites List in 5bxl
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

Go back to Magnesium Binding Sites List in 5bxl
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

Go back to Magnesium Binding Sites List in 5bxl
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

Go back to Magnesium Binding Sites List in 5bxl
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

Go back to Magnesium Binding Sites List in 5bxl
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

Go back to Magnesium Binding Sites List in 5bxl
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

Go back to Magnesium Binding Sites List in 5bxl
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

Go back to Magnesium Binding Sites List in 5bxl
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

Go back to Magnesium Binding Sites List in 5bxl
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy