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Magnesium in PDB 4z1l: Yeast 20S Proteasome in Complex with Belactosin C Derivative 3

Enzymatic activity of Yeast 20S Proteasome in Complex with Belactosin C Derivative 3

All present enzymatic activity of Yeast 20S Proteasome in Complex with Belactosin C Derivative 3:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Belactosin C Derivative 3, PDB code: 4z1l 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 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.085, 301.299, 144.582, 90.00, 113.33, 90.00
R / Rfree (%) 20.4 / 22.9

Other elements in 4z1l:

The structure of Yeast 20S Proteasome in Complex with Belactosin C Derivative 3 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Belactosin C Derivative 3 (pdb code 4z1l). 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 in Complex with Belactosin C Derivative 3, PDB code: 4z1l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4z1l

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with Belactosin C Derivative 3


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 in Complex with Belactosin C Derivative 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:59.6
occ:1.00
O G:MET125 2.1 48.9 1.0
O G:ARG122 2.4 43.2 1.0
O G:TYR119 2.4 41.0 1.0
OG1 G:THR8 2.6 42.0 1.0
CG2 G:THR8 3.2 45.7 1.0
C G:MET125 3.3 48.7 1.0
CB G:THR8 3.4 45.0 1.0
C G:ARG122 3.5 46.2 1.0
O G:ALA123 3.6 50.0 1.0
C G:TYR119 3.6 40.5 1.0
CA G:ALA123 3.8 47.5 1.0
C G:ALA123 3.8 48.3 1.0
N G:ALA123 4.1 46.8 1.0
N G:ARG126 4.2 45.1 1.0
CA G:ARG126 4.2 44.0 1.0
N G:MET125 4.2 52.5 1.0
CA G:MET125 4.3 53.1 1.0
N G:THR8 4.3 49.2 1.0
CA G:TYR119 4.4 40.2 1.0
CD G:PRO127 4.5 41.3 1.0
CA G:THR8 4.5 46.9 1.0
N G:THR120 4.6 40.4 1.0
CA G:ARG122 4.7 48.1 1.0
N G:TYR124 4.7 50.9 1.0
N G:ARG122 4.7 46.8 1.0
C G:ARG126 4.8 43.1 1.0
CA G:THR120 4.8 40.0 1.0
CB G:MET125 4.8 57.7 1.0
C G:THR120 4.9 39.7 1.0
CB G:TYR119 4.9 40.8 1.0
N G:PRO127 4.9 42.0 1.0

Magnesium binding site 2 out of 8 in 4z1l

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with Belactosin C Derivative 3


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 in Complex with Belactosin C Derivative 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:52.3
occ:1.00
O I:ASP177 2.5 46.2 1.0
O I:SER180 2.8 45.7 1.0
O I:ALA174 2.8 47.3 1.0
C I:ASP177 3.7 44.4 1.0
OXT I:ASP204 3.8 64.6 1.0
C I:ALA174 3.8 44.8 1.0
CA I:ASP175 4.0 46.5 1.0
C I:SER180 4.0 45.7 1.0
C I:ASP175 4.3 45.7 1.0
O I:ASP175 4.3 46.6 1.0
N I:ASP175 4.3 45.6 1.0
N I:ASP177 4.4 44.0 1.0
O I:ALA178 4.4 46.2 1.0
CA I:ALA178 4.4 44.4 1.0
NH1 Y:ARG19 4.4 52.4 1.0
N I:ALA178 4.5 43.2 1.0
C I:ALA178 4.5 45.5 1.0
O I:ASP204 4.5 57.2 1.0
NH2 Y:ARG19 4.5 54.2 1.0
CA I:ASP177 4.6 44.0 1.0
C I:ASP204 4.6 57.1 1.0
N I:SER180 4.7 44.7 1.0
OD1 I:ASP175 4.8 49.4 1.0
CA I:GLY181 4.8 45.9 1.0
CZ Y:ARG19 4.9 51.8 1.0
N I:GLY181 4.9 45.5 1.0
CA I:SER180 4.9 45.6 1.0
N I:ARG176 5.0 44.1 1.0

Magnesium binding site 3 out of 8 in 4z1l

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with Belactosin C Derivative 3


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 in Complex with Belactosin C Derivative 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:45.7
occ:1.00
O I:ASP204 2.3 57.2 1.0
O Y:ASP168 2.4 44.3 1.0
O Y:ALA165 2.4 42.8 1.0
O Y:SER171 2.8 46.8 1.0
C I:ASP204 3.1 57.1 1.0
C Y:ASP168 3.3 43.2 1.0
CA Y:ALA169 3.6 42.5 1.0
C Y:ALA165 3.6 43.2 1.0
CA I:ASP204 3.6 55.0 1.0
NH1 Y:ARG19 3.7 52.4 1.0
O Y:ALA169 3.8 43.3 1.0
C Y:ALA169 3.8 42.5 1.0
N Y:ALA169 3.8 43.8 1.0
CB I:ASP204 3.9 55.2 1.0
O Y:HIS166 3.9 39.6 1.0
OXT I:ASP204 3.9 64.6 1.0
C Y:SER171 4.0 44.8 1.0
C Y:HIS166 4.3 41.7 1.0
N Y:SER171 4.4 43.6 1.0
CA Y:ALA165 4.4 42.8 1.0
CA Y:ASP168 4.5 42.3 1.0
N Y:ASP168 4.5 42.1 1.0
CZ Y:ARG19 4.5 51.8 1.0
N Y:HIS166 4.6 43.9 1.0
N Y:TYR170 4.6 41.8 1.0
CA Y:HIS166 4.7 42.5 1.0
CA Y:SER171 4.7 43.1 1.0
O Y:ALA164 4.8 43.9 1.0
C Y:ARG167 4.8 42.3 1.0
NH2 Y:ARG19 4.9 54.2 1.0
CB Y:ALA169 4.9 41.9 1.0
CG I:ASP204 4.9 55.9 1.0
N Y:ARG167 5.0 40.6 1.0
N I:ASP204 5.0 52.3 1.0

Magnesium binding site 4 out of 8 in 4z1l

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with Belactosin C Derivative 3


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 in Complex with Belactosin C Derivative 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:41.9
occ:1.00
O K:ALA165 2.3 44.5 1.0
O K:ASP168 2.3 41.1 1.0
O W:ASP204 2.7 52.0 1.0
O K:SER171 3.2 45.7 1.0
C K:ASP168 3.2 41.4 1.0
C W:ASP204 3.2 53.2 1.0
O K:HIS166 3.4 44.7 1.0
C K:ALA165 3.5 43.5 1.0
CA K:ALA169 3.6 43.6 1.0
CA W:ASP204 3.6 51.8 1.0
N K:ALA169 3.7 42.6 1.0
C K:HIS166 3.9 43.8 1.0
C K:ALA169 4.0 44.9 1.0
OXT W:ASP204 4.1 58.3 1.0
CB W:ASP204 4.1 51.2 1.0
O K:ALA169 4.1 47.8 1.0
NH1 K:ARG19 4.1 53.2 1.0
N K:ASP168 4.2 40.6 1.0
CA K:ASP168 4.3 40.7 1.0
N K:HIS166 4.3 43.0 1.0
C K:SER171 4.4 44.6 1.0
CA K:HIS166 4.4 42.9 1.0
CA K:ALA165 4.4 43.3 1.0
C K:ARG167 4.4 41.3 1.0
N K:ARG167 4.5 42.7 1.0
O K:ALA164 4.6 42.3 1.0
N K:SER171 4.7 42.7 1.0
O K:ARG167 4.7 41.5 1.0
N K:TYR170 4.8 44.2 1.0
CB K:ALA169 4.9 43.5 1.0
N W:ASP204 5.0 51.2 1.0
CZ K:ARG19 5.0 51.8 1.0

Magnesium binding site 5 out of 8 in 4z1l

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with Belactosin C Derivative 3


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 in Complex with Belactosin C Derivative 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:50.2
occ:1.00
OXT L:ASP222 2.1 62.5 1.0
O V:ASP166 2.1 44.2 1.0
O V:ILE163 2.2 43.4 1.0
O V:SER169 2.6 44.4 1.0
C L:ASP222 3.1 59.7 1.0
C V:ASP166 3.1 43.8 1.0
C V:ILE163 3.4 44.7 1.0
C V:SER169 3.7 44.9 1.0
CA V:LEU167 3.8 44.4 1.0
CA L:ASP222 3.8 58.9 1.0
N V:LEU167 3.8 44.5 1.0
O L:ASP222 3.9 62.8 1.0
NH1 V:ARG19 3.9 54.7 1.0
O V:GLY162 4.0 46.9 1.0
N V:ASP166 4.1 42.9 1.0
O V:TRP164 4.1 43.7 1.0
C V:TRP164 4.1 46.0 1.0
CA V:ASP166 4.2 42.6 1.0
C V:LEU167 4.2 44.7 1.0
CA V:ILE163 4.3 45.0 1.0
N V:TRP164 4.3 45.4 1.0
CB L:ASP222 4.4 57.4 1.0
O V:LEU167 4.4 45.2 1.0
CA V:TRP164 4.4 46.4 1.0
N V:SER169 4.5 43.0 1.0
N V:ASN165 4.5 46.1 1.0
CZ V:ARG19 4.6 52.7 1.0
CA V:SER169 4.6 43.8 1.0
N V:GLY170 4.6 47.0 1.0
CA V:GLY170 4.6 50.0 1.0
C V:ASN165 4.6 43.6 1.0
NH2 V:ARG19 4.8 54.2 1.0
CD2 V:LEU167 4.9 42.9 1.0
C V:GLY162 4.9 45.3 1.0
CB V:SER169 4.9 44.4 1.0
O L:ARG221 4.9 58.5 1.0
N V:GLY168 5.0 44.5 1.0

Magnesium binding site 6 out of 8 in 4z1l

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with Belactosin C Derivative 3


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 in Complex with Belactosin C Derivative 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:35.2
occ:1.00
O N:ILE163 2.6 48.4 1.0
O N:SER169 2.7 44.5 1.0
O N:ASP166 3.2 45.3 1.0
NH1 N:ARG19 3.6 49.3 1.0
C N:ILE163 3.7 46.9 1.0
CG2 N:ILE163 3.7 44.6 1.0
CD1 a:LEU34 3.8 61.6 1.0
C N:SER169 3.8 45.0 1.0
C N:ASP166 4.1 43.8 1.0
CZ N:ARG19 4.2 47.8 1.0
CA N:GLY167 4.3 43.0 1.0
CA N:ILE163 4.3 45.4 1.0
CA N:GLY170 4.3 47.2 1.0
NH2 N:ARG19 4.4 48.3 1.0
O N:GLY167 4.5 42.5 1.0
N N:GLY170 4.5 46.2 1.0
N N:GLY167 4.6 43.7 1.0
C N:GLY167 4.6 42.6 1.0
CB N:ILE163 4.7 44.5 1.0
N N:LYS164 4.7 48.0 1.0
CA N:SER169 4.9 43.2 1.0
O N:LYS164 4.9 54.4 1.0
N N:SER169 4.9 43.0 1.0
C N:LYS164 5.0 51.3 1.0
CA N:LYS164 5.0 50.4 1.0

Magnesium binding site 7 out of 8 in 4z1l

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with Belactosin C Derivative 3


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 in Complex with Belactosin C Derivative 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:49.4
occ:1.00
O W:ASP177 2.3 43.0 1.0
O W:SER180 2.5 43.6 1.0
O W:ALA174 2.9 42.5 1.0
C W:ASP177 3.5 43.1 1.0
C W:SER180 3.7 44.7 1.0
OXT W:ASP204 3.9 58.3 1.0
C W:ALA174 4.0 42.9 1.0
O W:ALA178 4.1 45.1 1.0
CA W:ALA178 4.2 43.0 1.0
C W:ALA178 4.2 42.9 1.0
N W:ALA178 4.3 42.4 1.0
CA W:ASP175 4.3 46.1 1.0
N W:ASP177 4.4 44.3 1.0
N W:SER180 4.4 45.4 1.0
CA W:ASP177 4.5 43.3 1.0
NH1 K:ARG19 4.5 53.2 1.0
C W:ASP175 4.5 46.4 1.0
N W:ASP175 4.6 44.9 1.0
O W:ASP204 4.6 52.0 1.0
CA W:SER180 4.6 45.1 1.0
N W:GLY181 4.7 44.5 1.0
O W:ASP175 4.7 48.1 1.0
C W:ASP204 4.7 53.2 1.0
CA W:GLY181 4.7 44.4 1.0
NH2 K:ARG19 4.8 53.8 1.0
N W:LEU179 4.9 42.0 1.0
CZ K:ARG19 5.0 51.8 1.0

Magnesium binding site 8 out of 8 in 4z1l

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with Belactosin C Derivative 3


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 in Complex with Belactosin C Derivative 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:45.0
occ:1.00
O Z:HIS195 2.5 42.2 1.0
O Z:VAL198 2.5 46.6 1.0
O Z:THR192 2.8 51.1 1.0
C Z:HIS195 3.5 43.9 1.0
O Z:ILE196 3.6 46.3 1.0
CA Z:ILE196 3.6 43.2 1.0
C Z:ILE196 3.7 44.5 1.0
C Z:VAL198 3.7 46.5 1.0
C Z:THR192 3.8 53.6 1.0
NH2 Z:ARG28 3.8 50.1 1.0
N Z:ILE196 3.9 43.2 1.0
O Z:ASP222 4.0 62.9 1.0
CA Z:THR192 4.1 52.8 1.0
CG2 Z:THR192 4.1 54.2 1.0
N Z:VAL198 4.1 44.3 1.0
NH2 H:ARG19 4.4 58.7 1.0
CA Z:VAL198 4.4 45.8 1.0
N Z:GLN197 4.6 44.8 1.0
CA Z:HIS195 4.7 44.0 1.0
OD1 Z:ASP222 4.7 62.3 1.0
N Z:GLY199 4.7 46.1 1.0
N Z:HIS195 4.7 46.2 1.0
CB Z:THR192 4.8 52.7 1.0
CB Z:VAL198 4.8 45.8 1.0
CZ Z:ARG28 4.8 49.2 1.0
CB Z:ILE196 4.9 42.6 1.0
CA Z:GLY199 4.9 47.9 1.0
C Z:ASP222 4.9 63.4 1.0
O Z:ALA191 5.0 53.1 1.0
N Z:GLU193 5.0 54.7 1.0
NH1 H:ARG19 5.0 56.3 1.0

Reference:

M.Groll, V.S.Korotkov, E.M.Huber, A.De Meijere, A.Ludwig. A Minimal Beta-Lactone Fragment For Selective Beta 5C or Beta 5I Proteasome Inhibitors. Angew.Chem.Int.Ed.Engl. 2015.
ISSN: ESSN 1521-3773
PubMed: 25973989
DOI: 10.1002/ANIE.201502931
Page generated: Mon Dec 14 19:55:49 2020

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