Atomistry » Magnesium » PDB 5f7u-5fjj » 5fg9
Atomistry »
  Magnesium »
    PDB 5f7u-5fjj »
      5fg9 »

Magnesium in PDB 5fg9: Yeast 20S Proteasome BETA2-T(-2)V Mutant

Enzymatic activity of Yeast 20S Proteasome BETA2-T(-2)V Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA2-T(-2)V Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-T(-2)V Mutant, PDB code: 5fg9 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.570, 301.550, 145.130, 90.00, 113.36, 90.00
R / Rfree (%) 20.9 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA2-T(-2)V Mutant (pdb code 5fg9). 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-T(-2)V Mutant, PDB code: 5fg9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5fg9

Go back to Magnesium Binding Sites List in 5fg9
Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:47.4
occ:1.00
 O G:MET125 2.1 43.9 1.0
O G:ARG122 2.5 40.7 1.0
OG1 G:THR8 2.6 39.2 1.0
O G:TYR119 2.7 36.0 1.0
C G:MET125 3.3 43.8 1.0
CG2 G:THR8 3.3 39.8 1.0
O G:ALA123 3.4 43.5 1.0
CB G:THR8 3.5 39.7 1.0
C G:ARG122 3.6 40.9 1.0
C G:ALA123 3.7 43.3 1.0
CA G:ALA123 3.7 41.2 1.0
C G:TYR119 3.9 35.2 1.0
N G:MET125 4.1 44.9 1.0
N G:ALA123 4.1 40.4 1.0
N G:ARG126 4.1 40.1 1.0
CA G:ARG126 4.1 38.2 1.0
CA G:MET125 4.2 47.2 1.0
N G:THR8 4.3 40.6 1.0
CD G:PRO127 4.5 34.9 1.0
CA G:THR8 4.5 40.0 1.0
N G:TYR124 4.6 44.1 1.0
CA G:TYR119 4.6 35.2 1.0
C G:ARG126 4.8 36.4 1.0
CB G:MET125 4.8 52.0 1.0
CA G:ARG122 4.8 42.0 1.0
N G:ARG122 4.9 38.8 1.0
N G:THR120 4.9 34.5 1.0
C G:TYR124 4.9 44.5 1.0
N G:PRO127 5.0 35.2 1.0

Magnesium binding site 2 out of 9 in 5fg9

Go back to Magnesium Binding Sites List in 5fg9
Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:56.2
occ:1.00
 O I:ASP177 2.5 41.7 1.0
O I:SER180 2.6 44.8 1.0
O I:ALA174 2.8 43.6 1.0
C I:ASP177 3.6 41.1 1.0
C I:SER180 3.8 43.9 1.0
C I:ALA174 3.8 42.9 1.0
OXT I:ASP204 3.9 47.8 1.0
CA I:ASP175 4.1 44.7 1.0
O I:ALA178 4.3 43.2 1.0
CA I:ALA178 4.4 41.1 1.0
N I:ASP175 4.4 44.3 1.0
C I:ALA178 4.4 42.6 1.0
N I:ALA178 4.4 40.3 1.0
N I:ASP177 4.5 41.9 1.0
C I:ASP175 4.5 44.3 1.0
N I:SER180 4.6 42.4 1.0
O I:ASP204 4.6 46.1 1.0
NH1 Y:ARG19 4.6 49.3 1.0
CA I:ASP177 4.6 41.0 1.0
CA I:GLY181 4.6 43.1 1.0
C I:ASP204 4.7 46.4 1.0
N I:GLY181 4.7 43.2 1.0
O I:ASP175 4.7 46.6 1.0
NH2 Y:ARG19 4.7 47.8 1.0
OD1 I:ASP175 4.7 45.9 1.0
CA I:SER180 4.7 43.8 1.0
CA I:ALA174 5.0 40.8 1.0

Magnesium binding site 3 out of 9 in 5fg9

Go back to Magnesium Binding Sites List in 5fg9
Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:54.4
occ:1.00
 O J:THR124 3.1 36.3 1.0
N J:ASP120 3.3 33.9 1.0
OE1 J:GLN118 3.3 37.3 1.0
CB J:ASP120 3.5 34.7 1.0
CG J:GLN118 3.7 35.3 1.0
CG J:ASP120 3.7 35.5 1.0
CE1 J:HIS133 3.8 34.1 1.0
OD2 J:ASP120 3.8 36.8 1.0
C J:ILE119 3.9 33.5 1.0
O J:GLN118 3.9 34.0 1.0
CD J:GLN118 4.0 35.8 1.0
CA J:ASP120 4.0 34.4 1.0
CA J:ILE119 4.1 33.0 1.0
CB J:THR124 4.2 37.3 1.0
C J:GLN118 4.2 33.8 1.0
C J:THR124 4.2 36.9 1.0
N J:ILE119 4.3 33.1 1.0
OD1 J:ASP120 4.4 36.5 1.0
CG2 J:THR124 4.6 36.6 1.0
ND1 J:HIS133 4.6 34.7 1.0
CB J:GLN118 4.6 34.4 1.0
NE2 J:HIS133 4.7 33.3 1.0
O J:ILE119 4.8 34.5 1.0
CA J:THR124 4.8 37.1 1.0

Magnesium binding site 4 out of 9 in 5fg9

Go back to Magnesium Binding Sites List in 5fg9
Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:41.3
occ:1.00
 O K:ALA165 2.3 41.7 1.0
O K:ASP168 2.4 37.7 1.0
O K:SER171 2.4 40.3 1.0
O W:ASP204 2.4 47.5 1.0
C W:ASP204 3.1 46.9 1.0
C K:ASP168 3.4 37.7 1.0
C K:ALA165 3.4 40.1 1.0
CA W:ASP204 3.5 46.7 1.0
C K:SER171 3.6 41.6 1.0
NH1 K:ARG19 3.7 45.5 1.0
CB W:ASP204 3.8 46.9 1.0
CA K:ALA169 3.8 38.0 1.0
O K:ALA169 3.9 41.7 1.0
C K:ALA169 3.9 39.8 1.0
OXT W:ASP204 4.0 46.5 1.0
N K:ALA169 4.0 37.6 1.0
CA K:ALA165 4.2 40.5 1.0
O K:HIS166 4.2 40.6 1.0
N K:SER171 4.2 41.0 1.0
CZ K:ARG19 4.4 45.1 1.0
C K:HIS166 4.4 38.4 1.0
CA K:SER171 4.4 40.6 1.0
N K:HIS166 4.5 39.3 1.0
N K:ASP168 4.6 38.0 1.0
CA K:ASP168 4.6 37.2 1.0
N K:GLY172 4.6 42.9 1.0
O K:ALA164 4.6 39.2 1.0
N K:TYR170 4.7 39.7 1.0
NH2 K:ARG19 4.7 47.0 1.0
CA K:GLY172 4.7 44.2 1.0
CA K:HIS166 4.7 39.0 1.0
CG W:ASP204 4.8 47.5 1.0
CB K:SER171 4.9 40.3 1.0
N W:ASP204 4.9 46.5 1.0
CB K:ALA165 5.0 40.3 1.0

Magnesium binding site 5 out of 9 in 5fg9

Go back to Magnesium Binding Sites List in 5fg9
Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:46.9
occ:1.00
 O K:ILE82 2.7 37.5 1.0
O K:HOH405 2.9 36.8 1.0
C K:ILE82 3.5 36.8 1.0
CA K:ILE82 3.6 36.4 1.0
N K:LEU86 3.8 33.0 1.0
CB K:ASN85 3.8 35.0 1.0
CG2 K:ILE82 3.8 36.3 1.0
CB K:LEU86 4.1 33.6 1.0
CB K:ILE82 4.2 36.3 1.0
CA K:LEU86 4.2 33.1 1.0
C K:ASN85 4.3 33.7 1.0
CH2 K:TRP58 4.3 32.2 1.0
CA K:ASN85 4.6 34.5 1.0
O K:LYS81 4.6 35.0 1.0
CG1 K:ILE82 4.7 36.5 1.0
N K:LEU83 4.8 36.5 1.0
N K:ILE82 4.8 36.0 1.0
O K:HOH434 4.9 52.9 1.0
CG K:ASN85 4.9 35.3 1.0
OD1 K:ASN85 4.9 38.0 1.0
N K:ASN85 5.0 34.4 1.0

Magnesium binding site 6 out of 9 in 5fg9

Go back to Magnesium Binding Sites List in 5fg9
Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:40.9
occ:1.00
 O N:ILE163 2.6 37.9 1.0
O N:SER169 2.6 37.2 1.0
O N:ASP166 3.0 40.2 1.0
CD1 a:LEU34 3.6 43.6 1.0
NH1 N:ARG19 3.6 37.7 1.0
C N:ILE163 3.7 37.4 1.0
C N:SER169 3.8 37.2 1.0
CG2 N:ILE163 3.9 35.2 1.0
C N:ASP166 3.9 37.0 1.0
CA N:GLY167 4.2 35.4 1.0
CZ N:ARG19 4.2 37.6 1.0
CA N:ILE163 4.3 36.2 1.0
O N:GLY167 4.4 35.2 1.0
CA N:GLY170 4.4 37.5 1.0
N N:GLY167 4.4 35.9 1.0
NH2 N:ARG19 4.5 37.5 1.0
C N:GLY167 4.5 35.0 1.0
N N:GLY170 4.6 37.1 1.0
N N:LYS164 4.7 39.1 1.0
CB N:ILE163 4.8 35.5 1.0
N N:SER169 4.8 35.4 1.0
CA N:SER169 4.8 35.5 1.0
CG a:LEU34 4.8 43.5 1.0
O N:LYS164 4.9 42.1 1.0
C N:LYS164 4.9 40.8 1.0
CA N:LYS164 5.0 41.4 1.0
N N:ASP166 5.0 36.6 1.0

Magnesium binding site 7 out of 9 in 5fg9

Go back to Magnesium Binding Sites List in 5fg9
Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:52.9
occ:1.00
 O V:ILE163 2.1 42.3 1.0
OXT L:ASP222 2.2 56.2 1.0
O V:ASP166 2.2 41.6 1.0
O V:SER169 2.3 46.0 1.0
C L:ASP222 3.1 57.8 1.0
C V:ILE163 3.2 43.7 1.0
C V:ASP166 3.3 42.0 1.0
C V:SER169 3.4 45.4 1.0
CA L:ASP222 3.7 59.9 1.0
O V:GLY162 3.8 42.0 1.0
O L:ASP222 3.9 55.4 1.0
NH1 V:ARG19 3.9 49.6 1.0
CA V:LEU167 4.0 42.3 1.0
N V:LEU167 4.0 42.3 1.0
CA V:ILE163 4.0 43.0 1.0
N V:ASP166 4.1 41.9 1.0
N V:TRP164 4.2 45.1 1.0
CB L:ASP222 4.2 61.3 1.0
C V:TRP164 4.3 44.9 1.0
N V:SER169 4.3 42.8 1.0
CA V:ASP166 4.3 41.6 1.0
N V:GLY170 4.3 47.6 1.0
CA V:GLY170 4.3 49.3 1.0
C V:LEU167 4.3 42.0 1.0
CA V:SER169 4.4 43.4 1.0
O V:TRP164 4.4 44.6 1.0
CA V:TRP164 4.4 45.6 1.0
O V:LEU167 4.5 40.1 1.0
CZ V:ARG19 4.5 49.7 1.0
N V:ASN165 4.6 44.0 1.0
NH2 V:ARG19 4.7 51.0 1.0
CB V:SER169 4.7 43.2 1.0
C V:GLY162 4.8 42.2 1.0
C V:ASN165 4.9 42.6 1.0
N V:ILE163 4.9 42.4 1.0
O L:ARG221 5.0 55.5 1.0
CG2 V:ILE163 5.0 43.1 1.0

Magnesium binding site 8 out of 9 in 5fg9

Go back to Magnesium Binding Sites List in 5fg9
Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:40.0
occ:1.00
 O Y:ASP168 2.2 41.4 1.0
O Y:SER171 2.5 41.5 1.0
O Y:ALA165 2.5 44.0 1.0
O I:ASP204 2.6 46.1 1.0
C Y:ASP168 3.2 40.7 1.0
C I:ASP204 3.3 46.4 1.0
CA Y:ALA169 3.5 40.3 1.0
C Y:ALA165 3.6 42.0 1.0
O Y:ALA169 3.6 42.8 1.0
NH1 Y:ARG19 3.6 49.3 1.0
C Y:ALA169 3.6 41.2 1.0
C Y:SER171 3.7 42.4 1.0
N Y:ALA169 3.8 40.9 1.0
CA I:ASP204 3.9 46.9 1.0
N Y:SER171 4.1 41.3 1.0
CB I:ASP204 4.1 48.0 1.0
OXT I:ASP204 4.2 47.8 1.0
O Y:HIS166 4.2 40.5 1.0
CA Y:ALA165 4.3 41.0 1.0
CA Y:ASP168 4.4 40.6 1.0
N Y:TYR170 4.4 40.8 1.0
CA Y:SER171 4.4 41.4 1.0
CZ Y:ARG19 4.4 48.4 1.0
N Y:ASP168 4.4 41.7 1.0
C Y:HIS166 4.5 39.8 1.0
N Y:HIS166 4.7 41.6 1.0
O Y:ALA164 4.7 42.9 1.0
N Y:GLY172 4.7 42.9 1.0
NH2 Y:ARG19 4.8 47.8 1.0
CA Y:HIS166 4.9 40.4 1.0
CB Y:SER171 4.9 41.2 1.0
CA Y:GLY172 4.9 42.4 1.0
C Y:ARG167 4.9 41.0 1.0
CB Y:ALA169 4.9 39.9 1.0

Magnesium binding site 9 out of 9 in 5fg9

Go back to Magnesium Binding Sites List in 5fg9
Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome BETA2-T(-2)V 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-T(-2)V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:59.7
occ:1.00
 O Z:VAL198 2.4 47.1 1.0
O Z:THR192 2.8 52.1 1.0
O Z:HIS195 2.8 40.8 1.0
C Z:VAL198 3.6 46.5 1.0
NH2 Z:ARG28 3.7 47.9 1.0
O Z:ILE196 3.8 45.5 1.0
C Z:THR192 3.8 52.1 1.0
C Z:HIS195 3.8 42.9 1.0
O Z:ASP222 3.9 55.4 1.0
CA Z:ILE196 3.9 43.0 1.0
CG2 Z:THR192 3.9 53.1 1.0
C Z:ILE196 4.0 43.1 1.0
CA Z:THR192 4.1 52.1 1.0
N Z:VAL198 4.2 43.9 1.0
NH2 H:ARG19 4.3 53.9 1.0
N Z:ILE196 4.3 43.3 1.0
CA Z:VAL198 4.4 45.2 1.0
N Z:GLY199 4.5 47.0 1.0
OD1 Z:ASP222 4.6 52.6 1.0
CA Z:GLY199 4.6 47.2 1.0
CB Z:THR192 4.7 53.3 1.0
CZ Z:ARG28 4.7 48.9 1.0
C Z:ASP222 4.8 58.6 1.0
N Z:GLN197 4.8 42.6 1.0
CB Z:VAL198 4.9 45.0 1.0
NH1 Z:ARG28 4.9 49.5 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 04:10:02 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