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Magnesium in PDB 4r18: Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome

Enzymatic activity of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome

All present enzymatic activity of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome:
3.4.25.1;

Protein crystallography data

The structure of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome, PDB code: 4r18 was solved by C.Dubiella, H.Cui, M.Gersch, A.J.Brouwer, S.A.Sieber, A.Krueger, R.Liskamp, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.580, 300.820, 146.290, 90.00, 113.20, 90.00
R / Rfree (%) 17.7 / 19.5

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome (pdb code 4r18). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome, PDB code: 4r18:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 4r18

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Magnesium binding site 1 out of 11 in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:43.7
occ:1.00
 O G:MET125 2.2 43.2 1.0
O G:TYR119 2.3 35.3 1.0
O G:ARG122 2.3 37.5 1.0
O G:HOH413 2.6 41.5 1.0
OG1 G:THR8 2.7 39.4 1.0
CG2 G:THR8 3.3 35.3 1.0
C G:MET125 3.4 44.6 1.0
C G:TYR119 3.4 34.2 1.0
C G:ARG122 3.4 38.7 1.0
CB G:THR8 3.6 38.1 1.0
O G:ALA123 3.8 43.7 1.0
CA G:ALA123 3.9 39.5 1.0
C G:ALA123 3.9 41.6 1.0
N G:ALA123 4.1 38.7 1.0
N G:MET125 4.2 47.8 1.0
CA G:TYR119 4.2 32.7 1.0
CA G:MET125 4.3 50.1 1.0
N G:ARG126 4.3 40.6 1.0
CA G:ARG126 4.4 38.9 1.0
N G:THR120 4.4 34.5 1.0
N G:ARG122 4.5 38.0 1.0
N G:THR8 4.5 40.9 1.0
CA G:THR120 4.6 35.1 1.0
CA G:ARG122 4.6 40.4 1.0
O G:HOH412 4.6 46.3 1.0
CD G:PRO127 4.6 34.1 1.0
N G:TYR124 4.7 42.4 1.0
C G:THR120 4.7 35.9 1.0
CA G:THR8 4.7 40.0 1.0
CB G:MET125 4.7 57.0 1.0
CB G:TYR119 4.8 31.3 1.0
C G:ARG126 4.8 36.7 1.0
N G:GLN121 4.9 34.0 1.0
N G:PRO127 5.0 34.9 1.0

Magnesium binding site 2 out of 11 in 4r18

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Magnesium binding site 2 out of 11 in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:83.5
occ:1.00
 O N:HOH332 3.1 55.5 1.0
OD1 N:ASP51 3.2 44.5 1.0
O H:HOH417 3.2 42.5 1.0
NE2 H:GLN91 3.3 61.6 1.0
OD2 N:ASP51 3.9 43.7 1.0
CG N:ASP51 4.0 43.6 1.0
ND1 H:HIS116 4.2 41.5 1.0
O N:ASN92 4.2 53.6 1.0
CD H:GLN91 4.4 57.2 1.0
OG N:SER48 4.7 40.4 1.0
OE1 H:GLN91 4.8 67.5 1.0
CE1 H:HIS116 4.9 42.9 1.0

Magnesium binding site 3 out of 11 in 4r18

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Magnesium binding site 3 out of 11 in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:45.1
occ:1.00
 O I:SER180 2.3 48.6 1.0
O I:ASP177 2.3 38.8 1.0
O I:ALA174 2.3 37.8 1.0
O I:HOH411 2.4 59.7 1.0
O I:HOH405 2.5 46.6 1.0
C I:ALA174 3.4 36.8 1.0
C I:SER180 3.4 45.4 1.0
C I:ASP177 3.4 36.0 1.0
O Y:HOH403 3.9 61.5 1.0
CA I:ASP175 4.1 39.8 1.0
N I:ASP175 4.2 39.2 1.0
N I:ASP177 4.2 38.5 1.0
N I:SER180 4.2 43.5 1.0
CA I:SER180 4.3 45.9 1.0
O I:ALA178 4.3 40.8 1.0
CA I:ASP177 4.3 38.6 1.0
N I:ALA178 4.3 34.8 1.0
C I:ASP175 4.3 39.7 1.0
N I:GLY181 4.4 42.5 1.0
C I:ALA178 4.4 37.3 1.0
CA I:ALA178 4.4 34.6 1.0
CA I:ALA174 4.5 33.6 1.0
CA I:GLY181 4.5 40.9 1.0
O I:HOH408 4.5 49.7 1.0
OXT I:ASP204 4.5 47.3 1.0
O I:ASP175 4.6 42.2 1.0
MG I:MG302 4.7 79.4 1.0
CB I:SER180 4.7 49.9 1.0
CB I:ALA174 4.8 31.2 1.0
CB I:ASP177 4.8 42.9 1.0
N I:ARG176 4.9 38.8 1.0
OD1 I:ASP175 4.9 48.5 1.0

Magnesium binding site 4 out of 11 in 4r18

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Magnesium binding site 4 out of 11 in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:79.4
occ:1.00
 O Y:HOH402 3.0 35.5 1.0
OXT I:ASP204 3.0 47.3 1.0
O I:HOH411 3.2 59.7 1.0
CD I:ARG27 3.6 38.3 1.0
NE I:ARG27 3.6 38.0 1.0
C I:ASP204 3.7 47.0 1.0
O I:HOH404 3.7 44.4 1.0
O I:ALA178 3.7 40.8 1.0
CD1 I:TRP182 3.8 39.1 1.0
O I:ASP204 3.8 48.7 1.0
NE1 I:TRP182 4.1 39.4 1.0
O I:HOH408 4.2 49.7 1.0
O I:SER180 4.2 48.6 1.0
CG I:TRP182 4.3 39.0 1.0
MG Y:MG302 4.6 37.3 1.0
CE2 I:TRP182 4.7 38.6 1.0
MG I:MG301 4.7 45.1 1.0
CZ I:ARG27 4.7 36.4 1.0
CG I:ARG27 4.7 38.1 1.0
C I:SER180 4.8 45.4 1.0
CA Y:ALA169 4.8 36.9 1.0
CD2 I:TRP182 4.8 37.9 1.0
N I:TRP182 4.8 40.1 1.0
CA I:ASP204 4.8 44.2 1.0
CB I:TRP182 4.9 37.8 1.0
C I:ALA178 4.9 37.3 1.0

Magnesium binding site 5 out of 11 in 4r18

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Magnesium binding site 5 out of 11 in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:56.3
occ:1.00
 OE1 J:GLN118 3.3 39.2 1.0
O J:THR124 3.4 36.7 1.0
CB J:ASP120 3.7 36.6 1.0
N J:ASP120 3.8 32.8 1.0
CG J:ASP120 3.8 40.0 1.0
OD2 J:ASP120 3.8 43.9 1.0
CB J:THR124 4.0 36.2 1.0
CG J:GLN118 4.1 35.4 1.0
CD J:GLN118 4.1 36.4 1.0
CE1 J:HIS133 4.2 32.2 1.0
O J:GLN118 4.2 34.2 1.0
CG2 J:THR124 4.3 35.5 1.0
CA J:ASP120 4.3 34.5 1.0
C J:THR124 4.3 36.0 1.0
OD1 J:ASP120 4.4 42.3 1.0
C J:ILE119 4.4 33.1 1.0
C J:GLN118 4.6 34.3 1.0
CA J:ILE119 4.6 32.5 1.0
N J:ILE119 4.8 33.1 1.0
CA J:THR124 4.8 36.5 1.0
CG1 I:VAL35 4.8 37.7 1.0
O I:HOH473 4.8 49.3 1.0
CB J:GLN118 4.9 34.5 1.0
ND1 J:HIS133 4.9 32.4 1.0
OG1 J:THR124 5.0 36.1 1.0

Magnesium binding site 6 out of 11 in 4r18

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Magnesium binding site 6 out of 11 in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:42.7
occ:1.00
 O W:ASP204 2.3 51.1 1.0
O K:ALA165 2.3 40.5 1.0
O K:SER171 2.3 41.6 1.0
O K:ASP168 2.3 40.9 1.0
O K:HOH406 2.4 46.6 1.0
C W:ASP204 3.1 49.5 1.0
C K:ASP168 3.4 38.7 1.0
C K:ALA165 3.4 41.9 1.0
C K:SER171 3.5 43.2 1.0
CA W:ASP204 3.6 45.0 1.0
NH1 K:ARG19 3.6 54.9 1.0
O K:ALA169 3.8 41.3 1.0
CB W:ASP204 3.8 43.5 1.0
CA K:ALA169 3.9 40.6 1.0
C K:ALA169 3.9 41.5 1.0
OXT W:ASP204 4.0 52.5 1.0
N K:ALA169 4.0 38.9 1.0
CA K:ALA165 4.0 44.6 1.0
N K:SER171 4.1 42.6 1.0
CA K:SER171 4.4 41.9 1.0
CZ K:ARG19 4.4 55.4 1.0
O K:HIS166 4.4 39.3 1.0
N K:HIS166 4.5 40.3 1.0
N K:GLY172 4.5 43.3 1.0
CA K:ASP168 4.5 37.8 1.0
N K:ASP168 4.5 39.1 1.0
C K:HIS166 4.6 40.0 1.0
O K:ALA164 4.6 43.4 1.0
CA K:GLY172 4.6 43.7 1.0
N K:TYR170 4.6 41.7 1.0
NH2 K:ARG19 4.8 59.6 1.0
CA K:HIS166 4.8 40.6 1.0
CG W:ASP204 4.8 46.0 1.0
CB K:SER171 4.8 41.4 1.0
CB K:ALA165 4.9 48.2 1.0
O W:HOH309 5.0 65.5 1.0

Magnesium binding site 7 out of 11 in 4r18

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Magnesium binding site 7 out of 11 in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg303

b:48.4
occ:1.00
 O K:HOH462 2.6 52.0 1.0
O K:ILE82 2.8 36.5 1.0
O K:HOH434 2.9 47.8 1.0
C K:ILE82 3.6 35.7 1.0
CA K:ILE82 3.6 36.2 1.0
CG2 K:ILE82 3.7 34.9 1.0
CB K:ASN85 3.8 34.2 1.0
N K:LEU86 3.9 35.0 1.0
CB K:ILE82 4.2 37.1 1.0
CB K:LEU86 4.3 34.9 1.0
C K:ASN85 4.4 34.9 1.0
CH2 K:TRP58 4.4 30.0 1.0
CA K:LEU86 4.4 34.5 1.0
O K:LYS81 4.6 36.2 1.0
CA K:ASN85 4.6 34.6 1.0
CG1 K:ILE82 4.7 39.1 1.0
O K:HOH435 4.7 40.5 1.0
N K:ILE82 4.8 35.2 1.0
N K:LEU83 4.9 35.4 1.0
OD1 K:ASN85 4.9 38.4 1.0
CG K:ASN85 4.9 35.1 1.0

Magnesium binding site 8 out of 11 in 4r18

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Magnesium binding site 8 out of 11 in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:43.3
occ:1.00
 O N:SER169 2.5 39.2 1.0
O N:ILE163 2.5 35.7 1.0
O N:ASP166 2.9 41.9 1.0
O N:HOH340 2.9 52.9 1.0
NH1 N:ARG19 3.5 46.8 1.0
C N:ILE163 3.6 37.8 1.0
C N:SER169 3.7 38.5 1.0
CD1 a:LEU34 3.8 43.8 1.0
C N:ASP166 3.9 37.7 1.0
CG2 N:ILE163 3.9 35.1 1.0
CA N:GLY167 4.1 37.1 1.0
CZ N:ARG19 4.2 48.3 1.0
CA N:ILE163 4.3 36.3 1.0
O N:GLY167 4.3 41.1 1.0
CA N:GLY170 4.3 40.5 1.0
N N:GLY167 4.4 36.9 1.0
C N:GLY167 4.4 38.7 1.0
N N:GLY170 4.4 39.9 1.0
NH2 N:ARG19 4.5 49.2 1.0
N N:SER169 4.7 38.3 1.0
CA N:SER169 4.7 36.8 1.0
CB N:ILE163 4.7 35.6 1.0
N N:LYS164 4.7 39.6 1.0
O N:LYS164 4.9 44.0 1.0
C N:LYS164 4.9 42.2 1.0
N N:ASP166 4.9 37.4 1.0

Magnesium binding site 9 out of 11 in 4r18

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Magnesium binding site 9 out of 11 in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:52.2
occ:1.00
 O V:ASP166 2.1 44.4 1.0
OXT L:ASP222 2.2 65.6 1.0
O V:SER169 2.2 45.0 1.0
O V:ILE163 2.2 43.9 1.0
O V:HOH404 2.5 52.1 1.0
C L:ASP222 3.1 66.5 1.0
C V:ASP166 3.2 43.9 1.0
C V:ILE163 3.3 44.1 1.0
C V:SER169 3.4 44.0 1.0
O V:GLY162 3.8 44.3 1.0
CA V:LEU167 3.8 48.2 1.0
CA L:ASP222 3.8 63.9 1.0
N V:LEU167 3.9 45.9 1.0
NH1 V:ARG19 4.0 54.1 1.0
CA V:ILE163 4.0 42.9 1.0
O L:ASP222 4.0 70.3 1.0
N V:ASP166 4.1 44.5 1.0
C V:LEU167 4.1 47.7 1.0
N V:SER169 4.2 44.0 1.0
CB L:ASP222 4.2 64.7 1.0
CA V:ASP166 4.2 43.1 1.0
CA V:SER169 4.2 43.5 1.0
O V:LEU167 4.2 44.9 1.0
N V:GLY170 4.3 45.6 1.0
N V:TRP164 4.3 45.2 1.0
CA V:GLY170 4.4 48.6 1.0
C V:TRP164 4.4 48.6 1.0
CZ V:ARG19 4.5 53.6 1.0
O V:TRP164 4.6 48.5 1.0
CA V:TRP164 4.6 47.6 1.0
CB V:SER169 4.6 44.1 1.0
N V:ASN165 4.7 47.0 1.0
C V:GLY162 4.7 43.5 1.0
NH2 V:ARG19 4.7 54.8 1.0
N V:GLY168 4.9 48.7 1.0
N V:ILE163 4.9 43.8 1.0
C V:ASN165 4.9 45.1 1.0
CB V:ASP166 4.9 43.0 1.0

Magnesium binding site 10 out of 11 in 4r18

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Magnesium binding site 10 out of 11 in the Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Ligand-Induced LYS33-THR1 Crosslinking at Subunit BETA5 of the Yeast 20S Proteasome within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:37.3
occ:1.00
 O Y:ASP168 2.3 37.6 1.0
O Y:ALA165 2.3 36.3 1.0
O Y:SER171 2.3 39.2 1.0
O I:ASP204 2.3 48.7 1.0
O Y:HOH402 2.4 35.5 1.0
C I:ASP204 3.2 47.0 1.0
C Y:ASP168 3.3 36.3 1.0
C Y:ALA165 3.4 34.3 1.0
C Y:SER171 3.5 40.0 1.0
NH1 Y:ARG19 3.7 48.4 1.0
CA I:ASP204 3.7 44.2 1.0
O Y:ALA169 3.8 38.9 1.0
CA Y:ALA169 3.8 36.9 1.0
C Y:ALA169 3.8 38.9 1.0
CB I:ASP204 4.0 44.2 1.0
N Y:ALA169 4.0 36.8 1.0
OXT I:ASP204 4.1 47.3 1.0
CA Y:ALA165 4.1 34.1 1.0
N Y:SER171 4.1 42.0 1.0
CA Y:SER171 4.4 40.7 1.0
O Y:HIS166 4.4 40.3 1.0
CZ Y:ARG19 4.5 49.5 1.0
CA Y:ASP168 4.5 35.7 1.0
N Y:ASP168 4.5 36.8 1.0
N Y:HIS166 4.5 34.4 1.0
N Y:GLY172 4.5 39.8 1.0
N Y:TYR170 4.5 39.8 1.0
O Y:ALA164 4.6 36.2 1.0
C Y:HIS166 4.6 37.0 1.0
MG I:MG302 4.6 79.4 1.0
CA Y:GLY172 4.7 38.8 1.0
O I:HOH411 4.7 59.7 1.0
CA Y:HIS166 4.8 34.8 1.0
NH2 Y:ARG19 4.8 51.4 1.0
CB Y:SER171 4.8 40.3 1.0
CB Y:ALA165 4.9 34.0 1.0
CG I:ASP204 4.9 47.0 1.0
O I:HOH404 5.0 44.4 1.0

Reference:

C.Dubiella, H.Cui, M.Gersch, A.J.Brouwer, S.A.Sieber, A.Kruger, R.M.Liskamp, M.Groll. Selective Inhibition of the Immunoproteasome By Ligand-Induced Crosslinking of the Active Site. Angew.Chem.Int.Ed.Engl. V. 53 11969 2014.
ISSN: ISSN 1433-7851
PubMed: 25244435
DOI: 10.1002/ANIE.201406964
Page generated: Tue Aug 20 02:45:57 2024

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