Atomistry » Magnesium » PDB 4r0d-4rcr » 4r18
Atomistry »
  Magnesium »
    PDB 4r0d-4rcr »
      4r18 »

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

Go back to Magnesium Binding Sites List in 4r18
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

Go back to Magnesium Binding Sites List in 4r18
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

Go back to Magnesium Binding Sites List in 4r18
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

Go back to Magnesium Binding Sites List in 4r18
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

Go back to Magnesium Binding Sites List in 4r18
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

Go back to Magnesium Binding Sites List in 4r18
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

Go back to Magnesium Binding Sites List in 4r18
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

Go back to Magnesium Binding Sites List in 4r18
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

Go back to Magnesium Binding Sites List in 4r18
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

Go back to Magnesium Binding Sites List in 4r18
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy