Atomistry » Magnesium » PDB 5f8h-5fjo » 5fg7
Atomistry »
  Magnesium »
    PDB 5f8h-5fjo »
      5fg7 »

Magnesium in PDB 5fg7: Yeast 20S Proteasome BETA2-T1A Mutant

Enzymatic activity of Yeast 20S Proteasome BETA2-T1A Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA2-T1A Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-T1A Mutant, PDB code: 5fg7 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.000, 301.730, 144.020, 90.00, 113.06, 90.00
R / Rfree (%) 20.6 / 23.1

Other elements in 5fg7:

The structure of Yeast 20S Proteasome BETA2-T1A 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-T1A Mutant (pdb code 5fg7). 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-T1A Mutant, PDB code: 5fg7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5fg7

Go back to Magnesium Binding Sites List in 5fg7
Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA2-T1A 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-T1A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:44.7
occ:1.00
O G:MET125 2.2 45.5 1.0
O G:ARG122 2.4 41.1 1.0
OG1 G:THR8 2.6 42.3 1.0
O G:TYR119 2.6 37.4 1.0
CG2 G:THR8 3.2 41.3 1.0
C G:MET125 3.4 44.4 1.0
CB G:THR8 3.4 41.4 1.0
C G:ARG122 3.5 42.1 1.0
O G:ALA123 3.5 47.8 1.0
CA G:ALA123 3.7 42.9 1.0
C G:ALA123 3.7 44.5 1.0
C G:TYR119 3.8 36.8 1.0
N G:ALA123 4.0 42.1 1.0
N G:MET125 4.2 47.5 1.0
N G:ARG126 4.2 40.1 1.0
N G:THR8 4.2 42.7 1.0
CA G:ARG126 4.2 39.7 1.0
CA G:MET125 4.3 48.2 1.0
CA G:THR8 4.5 42.3 1.0
CD G:PRO127 4.6 37.1 1.0
CA G:TYR119 4.6 37.0 1.0
N G:TYR124 4.6 45.5 1.0
CA G:ARG122 4.7 43.6 1.0
N G:ARG122 4.7 39.9 1.0
N G:THR120 4.8 36.3 1.0
C G:ARG126 4.8 38.6 1.0
CB G:MET125 4.8 53.2 1.0
CA G:THR120 4.9 36.8 1.0
C G:THR120 5.0 37.9 1.0
C G:TYR124 5.0 47.0 1.0

Magnesium binding site 2 out of 8 in 5fg7

Go back to Magnesium Binding Sites List in 5fg7
Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA2-T1A 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-T1A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:54.4
occ:1.00
O I:ALA174 2.3 42.4 1.0
O Y:HOH409 2.5 32.4 1.0
O I:SER180 2.5 41.7 1.0
O I:ASP177 2.5 42.4 1.0
C I:ALA174 3.4 40.8 1.0
C I:SER180 3.6 42.7 1.0
C I:ASP177 3.7 41.1 1.0
CA I:ASP175 3.8 43.7 1.0
N I:ASP175 4.0 42.1 1.0
OXT I:ASP204 4.1 50.1 1.0
O I:HOH408 4.2 39.8 1.0
C I:ASP175 4.2 45.0 1.0
N I:ASP177 4.3 41.1 1.0
CA I:GLY181 4.5 42.0 1.0
N I:GLY181 4.5 41.7 1.0
CA I:ALA174 4.5 39.0 1.0
O I:ASP175 4.5 46.6 1.0
OD1 I:ASP175 4.5 45.1 1.0
N I:SER180 4.5 42.0 1.0
CA I:ASP177 4.5 40.8 1.0
CA I:SER180 4.6 42.8 1.0
O I:ALA178 4.6 43.1 1.0
N I:ALA178 4.6 39.6 1.0
CB I:ALA174 4.7 35.7 1.0
CA I:ALA178 4.7 41.1 1.0
C I:ALA178 4.7 43.0 1.0
N I:ARG176 4.9 43.5 1.0
NH1 Y:ARG19 4.9 46.5 1.0
CB I:SER180 4.9 45.1 1.0
CB I:ASP177 5.0 41.7 1.0

Magnesium binding site 3 out of 8 in 5fg7

Go back to Magnesium Binding Sites List in 5fg7
Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA2-T1A 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-T1A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:47.2
occ:1.00
O Y:ASP168 2.3 43.0 1.0
O I:ASP204 2.4 47.0 1.0
O Y:ALA165 2.4 38.6 1.0
O Y:SER171 2.7 37.2 1.0
C I:ASP204 3.1 47.2 1.0
C Y:ASP168 3.2 39.4 1.0
C Y:ALA165 3.6 39.3 1.0
CA Y:ALA169 3.6 39.1 1.0
CA I:ASP204 3.6 47.2 1.0
O Y:ALA169 3.8 40.5 1.0
C Y:ALA169 3.8 39.9 1.0
N Y:ALA169 3.8 38.9 1.0
NH1 Y:ARG19 3.9 46.5 1.0
CB I:ASP204 3.9 48.3 1.0
O Y:HIS166 3.9 37.9 1.0
C Y:SER171 3.9 39.9 1.0
OXT I:ASP204 4.0 50.1 1.0
N Y:SER171 4.3 38.6 1.0
C Y:HIS166 4.3 37.5 1.0
CA Y:ALA165 4.4 39.5 1.0
N Y:ASP168 4.4 38.3 1.0
CA Y:ASP168 4.4 39.0 1.0
N Y:HIS166 4.6 40.0 1.0
N Y:TYR170 4.6 38.8 1.0
CZ Y:ARG19 4.6 46.0 1.0
CA Y:SER171 4.7 38.3 1.0
O Y:HOH409 4.7 32.4 1.0
O Y:ALA164 4.7 39.7 1.0
CA Y:HIS166 4.7 37.8 1.0
C Y:ARG167 4.8 38.6 1.0
N Y:ARG167 4.9 36.4 1.0
CG I:ASP204 4.9 47.5 1.0
CB Y:ALA169 4.9 38.3 1.0
N Y:GLY172 5.0 40.2 1.0
N I:ASP204 5.0 47.8 1.0
NH2 Y:ARG19 5.0 46.0 1.0

Magnesium binding site 4 out of 8 in 5fg7

Go back to Magnesium Binding Sites List in 5fg7
Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA2-T1A 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-T1A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:45.5
occ:1.00
O W:ASP204 2.3 51.0 1.0
O K:ASP168 2.3 39.8 1.0
O K:SER171 2.4 43.5 1.0
O K:ALA165 2.5 39.2 1.0
C W:ASP204 3.1 48.8 1.0
C K:ASP168 3.4 37.9 1.0
CA W:ASP204 3.5 46.0 1.0
C K:SER171 3.6 41.3 1.0
NH1 K:ARG19 3.6 48.5 1.0
C K:ALA165 3.6 38.5 1.0
O K:ALA169 3.6 42.8 1.0
CA K:ALA169 3.7 38.5 1.0
C K:ALA169 3.7 39.6 1.0
CB W:ASP204 3.7 45.2 1.0
N K:ALA169 4.0 38.0 1.0
OXT W:ASP204 4.0 54.1 1.0
N K:SER171 4.0 39.9 1.0
O K:HIS166 4.3 43.0 1.0
CA K:ALA165 4.3 38.9 1.0
CZ K:ARG19 4.3 46.2 1.0
CA K:SER171 4.3 39.4 1.0
N K:TYR170 4.5 39.5 1.0
CA K:ASP168 4.6 37.0 1.0
N K:GLY172 4.6 42.0 1.0
C K:HIS166 4.6 38.7 1.0
N K:ASP168 4.6 36.9 1.0
N K:HIS166 4.7 37.8 1.0
NH2 K:ARG19 4.7 49.1 1.0
CA K:GLY172 4.7 42.6 1.0
CG W:ASP204 4.8 44.8 1.0
O K:ALA164 4.8 37.7 1.0
CB K:SER171 4.9 39.1 1.0
CA K:HIS166 4.9 38.4 1.0
N W:ASP204 4.9 45.3 1.0

Magnesium binding site 5 out of 8 in 5fg7

Go back to Magnesium Binding Sites List in 5fg7
Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA2-T1A 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-T1A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:46.5
occ:1.00
OXT L:ASP222 2.1 59.6 1.0
O V:ILE163 2.1 50.4 1.0
O V:SER169 2.2 43.5 1.0
O V:ASP166 2.3 45.3 1.0
O V:HOH409 2.7 28.6 1.0
C L:ASP222 3.1 56.9 1.0
C V:ILE163 3.2 52.5 1.0
C V:ASP166 3.4 48.4 1.0
C V:SER169 3.4 44.5 1.0
CA L:ASP222 3.7 55.5 1.0
NH1 V:ARG19 3.8 55.1 1.0
O V:GLY162 3.9 44.3 1.0
O L:ASP222 4.0 60.8 1.0
CA V:LEU167 4.0 52.8 1.0
CA V:ILE163 4.0 54.2 1.0
N V:LEU167 4.1 50.8 1.0
CB L:ASP222 4.2 57.3 1.0
N V:TRP164 4.2 50.7 1.0
CA V:GLY170 4.2 49.1 1.0
O V:TRP164 4.3 52.6 1.0
N V:GLY170 4.3 44.1 1.0
C V:LEU167 4.3 50.5 1.0
C V:TRP164 4.3 52.7 1.0
N V:SER169 4.3 49.7 1.0
O V:LEU167 4.3 47.6 1.0
CZ V:ARG19 4.4 55.6 1.0
N V:ASP166 4.4 49.4 1.0
CA V:SER169 4.4 47.3 1.0
CA V:TRP164 4.5 54.2 1.0
CA V:ASP166 4.5 48.9 1.0
NH2 V:ARG19 4.5 54.0 1.0
N V:ASN165 4.8 53.0 1.0
C V:GLY162 4.8 48.9 1.0
CB V:SER169 4.9 46.0 1.0
O L:ARG221 4.9 51.0 1.0
N V:ILE163 4.9 50.8 1.0
CG2 V:ILE163 5.0 58.4 1.0
N V:GLY168 5.0 51.3 1.0

Magnesium binding site 6 out of 8 in 5fg7

Go back to Magnesium Binding Sites List in 5fg7
Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA2-T1A 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-T1A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:44.1
occ:1.00
O N:ILE163 2.4 37.0 1.0
O N:SER169 2.5 37.3 1.0
O N:ASP166 2.9 40.3 1.0
C N:ILE163 3.5 36.6 1.0
CD1 a:LEU34 3.6 42.8 1.0
C N:SER169 3.7 37.2 1.0
NH1 N:ARG19 3.7 35.4 1.0
CG2 N:ILE163 3.8 35.5 1.0
C N:ASP166 3.9 36.2 1.0
CA N:ILE163 4.2 36.2 1.0
CA N:GLY167 4.3 36.0 1.0
CZ N:ARG19 4.3 36.6 1.0
CA N:GLY170 4.4 39.5 1.0
N N:GLY167 4.5 35.7 1.0
N N:GLY170 4.5 37.7 1.0
O N:GLY167 4.5 35.4 1.0
C N:GLY167 4.6 35.6 1.0
CB N:ILE163 4.6 35.4 1.0
N N:LYS164 4.6 38.3 1.0
NH2 N:ARG19 4.6 38.6 1.0
CA N:SER169 4.7 35.3 1.0
N N:SER169 4.7 36.3 1.0
O N:LYS164 4.8 42.3 1.0
CG a:LEU34 4.8 42.7 1.0
C N:LYS164 4.8 39.9 1.0
CA N:LYS164 4.9 39.7 1.0
N N:ASP166 4.9 36.4 1.0
CA N:ASP166 5.0 36.2 1.0

Magnesium binding site 7 out of 8 in 5fg7

Go back to Magnesium Binding Sites List in 5fg7
Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA2-T1A 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-T1A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:70.8
occ:1.00
O W:ASP177 2.3 42.7 1.0
O W:SER180 2.5 46.1 1.0
O W:ALA174 2.8 39.0 1.0
C W:ASP177 3.4 40.7 1.0
C W:SER180 3.7 43.1 1.0
O W:HOH405 3.8 49.7 1.0
C W:ALA174 3.8 39.5 1.0
OXT W:ASP204 3.9 54.1 1.0
O W:ALA178 4.1 41.2 1.0
CA W:ALA178 4.2 40.1 1.0
C W:ALA178 4.2 40.3 1.0
N W:ALA178 4.2 39.7 1.0
CA W:ASP175 4.3 42.9 1.0
N W:SER180 4.3 43.6 1.0
N W:ASP177 4.3 41.0 1.0
NH1 K:ARG19 4.4 48.5 1.0
CA W:ASP177 4.4 40.8 1.0
N W:ASP175 4.5 41.9 1.0
C W:ASP175 4.5 43.6 1.0
CA W:SER180 4.6 43.1 1.0
N W:GLY181 4.6 42.2 1.0
O W:ASP175 4.7 45.6 1.0
O W:ASP204 4.7 51.0 1.0
CA W:GLY181 4.7 42.6 1.0
C W:ASP204 4.8 48.8 1.0
NH2 K:ARG19 4.8 49.1 1.0
N W:LEU179 4.9 39.2 1.0
CA W:ALA174 4.9 37.8 1.0
CB W:ASP177 5.0 41.0 1.0
CZ K:ARG19 5.0 46.2 1.0

Magnesium binding site 8 out of 8 in 5fg7

Go back to Magnesium Binding Sites List in 5fg7
Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA2-T1A 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-T1A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:56.5
occ:1.00
O Z:VAL198 2.3 44.0 1.0
O Z:THR192 2.9 50.9 1.0
O Z:HIS195 3.1 35.0 1.0
C Z:VAL198 3.5 44.5 1.0
NH2 Z:ARG28 3.6 45.9 1.0
CG2 Z:THR192 3.7 51.4 1.0
O Z:ASP222 3.7 59.9 1.0
O Z:ILE196 3.8 44.2 1.0
C Z:THR192 3.8 51.2 1.0
CA Z:THR192 4.0 50.5 1.0
C Z:HIS195 4.1 39.8 1.0
C Z:ILE196 4.1 41.6 1.0
CA Z:ILE196 4.2 40.9 1.0
N Z:VAL198 4.3 42.1 1.0
N Z:GLY199 4.4 45.4 1.0
CA Z:GLY199 4.4 47.5 1.0
CA Z:VAL198 4.4 43.4 1.0
OD1 Z:ASP222 4.4 56.3 1.0
CZ Z:ARG28 4.5 46.8 1.0
CB Z:THR192 4.5 50.7 1.0
N Z:ILE196 4.6 40.7 1.0
NH2 H:ARG19 4.6 53.9 1.0
NH1 Z:ARG28 4.6 47.2 1.0
C Z:ASP222 4.7 59.0 1.0
O Z:LYS220 4.9 52.4 1.0
CB Z:VAL198 4.9 42.4 1.0
N Z:GLN197 5.0 41.5 1.0

Reference:

E.M.Huber, W.Heinemeyer, X.Li, C.S.Arendt, M.Hochstrasser, M.Groll. A Unified Mechanism For Proteolysis and Autocatalytic Activation in the 20S Proteasome. Nat Commun V. 7 10900 2016.
ISSN: ESSN 2041-1723
PubMed: 26964885
DOI: 10.1038/NCOMMS10900
Page generated: Sun Sep 29 04:09:40 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy