Atomistry » Magnesium » PDB 4y8o-4yf4 » 4ya4
Atomistry »
  Magnesium »
    PDB 4y8o-4yf4 »
      4ya4 »

Magnesium in PDB 4ya4: Yeast 20S Proteasome BETA2-H114D Mutant

Enzymatic activity of Yeast 20S Proteasome BETA2-H114D Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA2-H114D Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA2-H114D Mutant, PDB code: 4ya4 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.180, 300.900, 144.310, 90.00, 112.80, 90.00
R / Rfree (%) 21.4 / 23.2

Other elements in 4ya4:

The structure of Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant (pdb code 4ya4). 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-H114D Mutant, PDB code: 4ya4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4ya4

Go back to Magnesium Binding Sites List in 4ya4
Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:42.5
occ:1.00
O G:MET125 2.2 60.1 1.0
O G:ARG122 2.4 54.3 1.0
OG1 G:THR8 2.5 55.7 1.0
O G:TYR119 2.5 48.8 1.0
CG2 G:THR8 3.2 54.2 1.0
C G:MET125 3.4 57.4 1.0
CB G:THR8 3.4 54.5 1.0
C G:ARG122 3.5 54.5 1.0
O G:ALA123 3.5 56.8 1.0
CA G:ALA123 3.7 55.5 1.0
C G:TYR119 3.7 48.8 1.0
C G:ALA123 3.7 55.5 1.0
N G:ALA123 4.1 55.0 1.0
N G:MET125 4.2 59.6 1.0
N G:THR8 4.2 56.7 1.0
N G:ARG126 4.2 53.3 1.0
CA G:ARG126 4.2 51.9 1.0
CA G:MET125 4.3 61.0 1.0
CA G:THR8 4.4 55.4 1.0
CD G:PRO127 4.5 48.7 1.0
CA G:TYR119 4.5 48.4 1.0
N G:TYR124 4.6 56.6 1.0
N G:THR120 4.7 48.8 1.0
CA G:ARG122 4.7 55.8 1.0
N G:ARG122 4.8 53.5 1.0
CA G:THR120 4.8 48.6 1.0
C G:ARG126 4.8 51.0 1.0
CB G:MET125 4.9 65.0 1.0
C G:THR120 4.9 50.0 1.0
N G:PRO127 5.0 49.2 1.0

Magnesium binding site 2 out of 8 in 4ya4

Go back to Magnesium Binding Sites List in 4ya4
Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:67.4
occ:1.00
O I:ASP177 2.3 50.2 1.0
O I:SER180 2.6 53.3 1.0
O I:ALA174 3.0 58.0 1.0
C I:ASP177 3.5 50.2 1.0
C I:SER180 3.8 52.3 1.0
OXT I:ASP204 3.8 60.8 1.0
O I:ALA178 3.9 54.5 1.0
C I:ALA178 4.0 51.9 1.0
CA I:ALA178 4.0 50.6 1.0
C I:ALA174 4.1 51.8 1.0
N I:ALA178 4.2 49.8 1.0
N I:SER180 4.4 50.2 1.0
NH1 Y:ARG19 4.4 55.3 1.0
CA I:ASP175 4.4 54.1 1.0
O I:ASP204 4.5 62.8 1.0
N I:ASP177 4.5 49.8 1.0
CA I:ASP177 4.6 49.8 1.0
C I:ASP204 4.6 60.2 1.0
CA I:SER180 4.6 51.2 1.0
C I:ASP175 4.7 52.5 1.0
N I:GLY181 4.7 52.2 1.0
N I:ASP175 4.7 52.9 1.0
NH2 Y:ARG19 4.7 57.0 1.0
CA I:GLY181 4.7 51.9 1.0
O I:ASP175 4.8 54.9 1.0
N I:LEU179 4.8 51.3 1.0
CZ Y:ARG19 5.0 55.9 1.0

Magnesium binding site 3 out of 8 in 4ya4

Go back to Magnesium Binding Sites List in 4ya4
Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:38.1
occ:1.00
O Y:ASP168 2.1 46.5 1.0
O I:ASP204 2.5 62.8 1.0
O Y:ALA165 2.6 47.7 1.0
O Y:SER171 2.6 45.4 1.0
C Y:ASP168 3.2 46.8 1.0
C I:ASP204 3.3 60.2 1.0
CA Y:ALA169 3.5 46.4 1.0
O Y:ALA169 3.5 48.0 1.0
C Y:ALA169 3.6 47.2 1.0
NH1 Y:ARG19 3.6 55.3 1.0
C Y:ALA165 3.7 47.0 1.0
N Y:ALA169 3.7 47.1 1.0
C Y:SER171 3.8 47.2 1.0
CA I:ASP204 3.8 59.2 1.0
CB I:ASP204 4.1 60.8 1.0
O Y:HIS166 4.1 46.0 1.0
N Y:SER171 4.1 46.5 1.0
OXT I:ASP204 4.2 60.8 1.0
CZ Y:ARG19 4.4 55.9 1.0
N Y:TYR170 4.4 47.8 1.0
CA Y:ASP168 4.4 46.7 1.0
CA Y:ALA165 4.4 46.8 1.0
N Y:ASP168 4.5 45.9 1.0
CA Y:SER171 4.5 47.0 1.0
C Y:HIS166 4.5 46.2 1.0
N Y:HIS166 4.7 47.7 1.0
NH2 Y:ARG19 4.8 57.0 1.0
N Y:GLY172 4.8 47.9 1.0
O Y:ALA164 4.8 47.6 1.0
CB Y:ALA169 4.8 45.8 1.0
C Y:ARG167 4.9 45.0 1.0
CA Y:HIS166 4.9 46.8 1.0
CA Y:GLY172 4.9 48.9 1.0

Magnesium binding site 4 out of 8 in 4ya4

Go back to Magnesium Binding Sites List in 4ya4
Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:41.4
occ:1.00
O K:ASP168 2.0 51.0 1.0
O K:ALA165 2.2 51.4 1.0
O W:ASP204 2.7 59.5 1.0
O K:SER171 2.7 56.1 1.0
C K:ASP168 3.0 48.9 1.0
C K:ALA165 3.4 49.8 1.0
C W:ASP204 3.4 60.8 1.0
CA K:ALA169 3.6 49.4 1.0
N K:ALA169 3.6 49.3 1.0
O W:HOH413 3.7 42.2 1.0
O K:HIS166 3.7 49.9 1.0
C K:ALA169 3.8 50.2 1.0
CA W:ASP204 3.8 59.8 1.0
O K:ALA169 3.9 50.4 1.0
C K:SER171 3.9 52.3 1.0
N K:ASP168 4.0 46.8 1.0
C K:HIS166 4.0 49.5 1.0
CA K:ASP168 4.1 47.7 1.0
NH1 K:ARG19 4.1 57.5 1.0
CA K:ALA165 4.1 50.2 1.0
CB W:ASP204 4.1 58.7 1.0
N K:SER171 4.3 50.2 1.0
OXT W:ASP204 4.3 66.1 1.0
N K:HIS166 4.3 48.7 1.0
O K:ALA164 4.4 50.2 1.0
C K:ARG167 4.4 47.8 1.0
CA K:HIS166 4.5 49.2 1.0
N K:TYR170 4.5 50.9 1.0
CA K:SER171 4.6 50.3 1.0
N K:ARG167 4.6 49.3 1.0
O K:ARG167 4.8 46.8 1.0
CB K:ASP168 4.8 48.0 1.0
CZ K:ARG19 4.8 57.2 1.0
CB K:SER171 4.9 49.4 1.0
CB K:ALA169 5.0 48.8 1.0
N K:GLY172 5.0 51.8 1.0
O W:HOH411 5.0 42.3 1.0

Magnesium binding site 5 out of 8 in 4ya4

Go back to Magnesium Binding Sites List in 4ya4
Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:66.6
occ:1.00
O V:ASP166 2.0 54.5 1.0
OXT L:ASP222 2.2 66.5 1.0
O V:ILE163 2.2 47.8 1.0
O V:SER169 2.5 54.9 1.0
C V:ASP166 3.0 54.3 1.0
C L:ASP222 3.1 67.3 1.0
C V:ILE163 3.3 53.6 1.0
C V:SER169 3.6 56.0 1.0
N V:LEU167 3.7 54.2 1.0
CA V:LEU167 3.7 53.8 1.0
CA L:ASP222 3.8 67.8 1.0
O V:GLY162 3.8 55.7 1.0
O L:ASP222 3.9 67.3 1.0
N V:ASP166 4.0 52.7 1.0
NH1 V:ARG19 4.0 59.4 1.0
CA V:ASP166 4.1 52.5 1.0
O V:TRP164 4.1 55.5 1.0
C V:TRP164 4.1 56.0 1.0
CA V:ILE163 4.2 54.5 1.0
C V:LEU167 4.2 53.5 1.0
N V:TRP164 4.3 55.9 1.0
N V:SER169 4.3 53.5 1.0
CB L:ASP222 4.4 68.2 1.0
CA V:TRP164 4.4 56.1 1.0
O V:LEU167 4.5 53.8 1.0
CA V:SER169 4.5 54.8 1.0
N V:ASN165 4.5 54.1 1.0
N V:GLY170 4.5 58.8 1.0
CA V:GLY170 4.6 60.7 1.0
C V:ASN165 4.6 53.2 1.0
CZ V:ARG19 4.6 59.3 1.0
C V:GLY162 4.8 54.9 1.0
CB V:SER169 4.8 54.8 1.0
NH2 V:ARG19 4.9 60.6 1.0
CB V:ASP166 4.9 51.5 1.0
N V:GLY168 4.9 53.1 1.0
CD2 V:LEU167 4.9 53.9 1.0
O L:ARG221 5.0 66.4 1.0

Magnesium binding site 6 out of 8 in 4ya4

Go back to Magnesium Binding Sites List in 4ya4
Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:42.9
occ:1.00
O N:SER169 2.5 42.1 1.0
O N:ILE163 2.8 42.7 1.0
O N:ASP166 2.8 45.5 1.0
NH1 N:ARG19 3.3 45.9 1.0
CD1 a:LEU34 3.5 52.9 1.0
C N:SER169 3.7 44.6 1.0
C N:ASP166 3.8 44.4 1.0
C N:ILE163 3.9 44.8 1.0
CA N:GLY167 4.0 43.5 1.0
CZ N:ARG19 4.0 46.2 1.0
CG2 N:ILE163 4.1 44.6 1.0
O N:GLY167 4.2 43.0 1.0
C N:GLY167 4.3 42.5 1.0
N N:GLY167 4.3 44.1 1.0
NH2 N:ARG19 4.3 48.5 1.0
CA N:GLY170 4.4 48.0 1.0
CA N:ILE163 4.5 44.6 1.0
N N:GLY170 4.5 46.5 1.0
N N:SER169 4.6 43.7 1.0
CA N:SER169 4.7 43.5 1.0
CG a:LEU34 4.7 51.7 1.0
NE N:ARG19 4.9 46.5 1.0
CB N:ILE163 4.9 44.3 1.0
N N:LYS164 5.0 47.2 1.0

Magnesium binding site 7 out of 8 in 4ya4

Go back to Magnesium Binding Sites List in 4ya4
Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:45.0
occ:1.00
O W:ASP177 2.1 52.7 1.0
O W:SER180 2.4 52.2 1.0
O W:ALA174 2.8 50.2 1.0
C W:ASP177 3.3 53.0 1.0
O W:HOH411 3.5 42.3 1.0
C W:SER180 3.6 52.7 1.0
C W:ALA174 3.9 52.0 1.0
O W:ALA178 3.9 52.8 1.0
C W:ALA178 4.0 52.4 1.0
OXT W:ASP204 4.0 66.1 1.0
CA W:ALA178 4.1 52.4 1.0
N W:ALA178 4.1 51.8 1.0
N W:SER180 4.2 54.0 1.0
N W:ASP177 4.3 53.3 1.0
CA W:ASP175 4.3 56.9 1.0
CA W:ASP177 4.4 52.8 1.0
CA W:SER180 4.4 53.7 1.0
N W:GLY181 4.5 52.2 1.0
N W:ASP175 4.6 55.2 1.0
NH1 K:ARG19 4.6 57.5 1.0
C W:ASP175 4.6 56.1 1.0
CA W:GLY181 4.6 53.4 1.0
N W:LEU179 4.7 52.0 1.0
O W:ASP175 4.8 57.5 1.0
O W:ASP204 4.8 59.5 1.0
CB W:ASP177 4.9 53.9 1.0
C W:ASP204 4.9 60.8 1.0
CA W:ALA174 4.9 49.9 1.0
CB W:SER180 4.9 53.8 1.0
NH2 K:ARG19 5.0 58.9 1.0

Magnesium binding site 8 out of 8 in 4ya4

Go back to Magnesium Binding Sites List in 4ya4
Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA2-H114D 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-H114D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:53.8
occ:1.00
O Z:VAL198 2.4 58.6 1.0
O Z:HIS195 2.6 52.7 1.0
O Z:THR192 3.0 61.1 1.0
O Z:ILE196 3.4 55.3 1.0
NH2 Z:ARG28 3.5 63.2 1.0
CA Z:ILE196 3.5 53.6 1.0
C Z:ILE196 3.6 53.9 1.0
C Z:VAL198 3.6 57.8 1.0
C Z:HIS195 3.6 53.8 1.0
O Z:ASP222 3.8 74.6 1.0
N Z:ILE196 4.0 53.1 1.0
N Z:VAL198 4.0 54.2 1.0
C Z:THR192 4.0 62.0 1.0
CG2 Z:THR192 4.2 65.7 1.0
CA Z:THR192 4.3 62.8 1.0
CA Z:VAL198 4.3 56.0 1.0
NH2 H:ARG19 4.4 65.0 1.0
N Z:GLN197 4.4 53.0 1.0
CZ Z:ARG28 4.5 61.6 1.0
N Z:GLY199 4.6 58.3 1.0
CA Z:GLY199 4.7 59.1 1.0
C Z:ASP222 4.8 74.3 1.0
NH1 Z:ARG28 4.8 62.9 1.0
OD1 Z:ASP222 4.8 70.4 1.0
CB Z:ILE196 4.9 53.6 1.0
CB Z:VAL198 4.9 55.5 1.0
CB Z:THR192 4.9 64.4 1.0
NH1 H:ARG19 4.9 62.1 1.0
CA Z:HIS195 4.9 53.9 1.0
C Z:GLN197 4.9 53.1 1.0
CZ H:ARG19 5.0 62.9 1.0

Reference:

E.M.Huber, G.De Bruin, W.Heinemeyer, G.Paniagua Soriano, H.S.Overkleeft, M.Groll. Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors. J.Am.Chem.Soc. V. 137 7835 2015.
ISSN: ESSN 1520-5126
PubMed: 26020686
DOI: 10.1021/JACS.5B03688
Page generated: Sat Sep 28 23:06:52 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