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Magnesium in PDB 5lai: Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters

Enzymatic activity of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters

All present enzymatic activity of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters:
3.4.25.1;

Protein crystallography data

The structure of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters, PDB code: 5lai was solved by M.Groll, C.Dubiella, H.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.150, 300.750, 145.660, 90.00, 112.80, 90.00
R / Rfree (%) 20.2 / 21.9

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters (pdb code 5lai). 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 Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters, PDB code: 5lai:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 5lai

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Magnesium binding site 1 out of 11 in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:41.2
occ:1.00
 O G:MET125 2.0 41.0 1.0
O G:TYR119 2.3 33.9 1.0
O G:ARG122 2.3 36.6 1.0
O G:HOH425 2.6 40.7 1.0
OG1 G:THR8 2.7 38.9 1.0
C G:MET125 3.2 41.4 1.0
CG2 G:THR8 3.3 38.5 1.0
C G:TYR119 3.4 35.3 1.0
C G:ARG122 3.4 39.2 1.0
CB G:THR8 3.6 39.3 1.0
O G:ALA123 3.8 41.5 1.0
CA G:ALA123 3.9 39.0 1.0
C G:ALA123 3.9 40.2 1.0
N G:MET125 4.1 43.7 1.0
N G:ALA123 4.1 38.9 1.0
CA G:MET125 4.1 44.9 1.0
CA G:TYR119 4.2 36.0 1.0
N G:ARG126 4.2 39.1 1.0
CA G:ARG126 4.3 37.8 1.0
N G:THR120 4.4 34.8 1.0
CB G:MET125 4.5 49.2 1.0
N G:ARG122 4.5 38.1 1.0
CD G:PRO127 4.5 34.6 1.0
N G:THR8 4.5 40.2 1.0
CA G:ARG122 4.6 41.4 1.0
CA G:THR120 4.6 34.4 1.0
CA G:THR8 4.7 39.9 1.0
CB G:TYR119 4.7 37.0 1.0
N G:TYR124 4.7 40.7 1.0
C G:THR120 4.7 35.4 1.0
C G:ARG126 4.8 36.7 1.0
N G:PRO127 4.9 35.3 1.0
N G:GLN121 5.0 35.5 1.0

Magnesium binding site 2 out of 11 in 5lai

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Magnesium binding site 2 out of 11 in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:74.5
occ:1.00
 O N:HOH310 2.6 48.6 1.0
O N:HOH306 3.1 45.0 1.0
NE2 H:GLN91 3.3 58.7 1.0
CD H:GLN91 3.8 56.9 1.0
OE1 H:GLN91 3.9 69.7 1.0
OD1 N:ASP51 4.0 44.6 1.0
O N:ASN92 4.0 49.9 1.0
OD2 N:ASP51 4.2 45.5 1.0
ND1 H:HIS116 4.5 42.2 1.0
CG N:ASP51 4.5 43.4 1.0
O N:HOH327 4.8 52.8 1.0
CE1 H:HIS116 5.0 42.6 1.0

Magnesium binding site 3 out of 11 in 5lai

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Magnesium binding site 3 out of 11 in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:53.7
occ:1.00
 O I:SER180 2.3 41.7 1.0
O I:ASP177 2.4 41.9 1.0
O I:ALA174 2.4 41.8 1.0
C I:ALA174 3.4 41.1 1.0
C I:SER180 3.5 43.5 1.0
C I:ASP177 3.5 40.0 1.0
CA I:ASP175 4.0 43.8 1.0
N I:ASP175 4.1 42.3 1.0
OXT I:ASP204 4.2 49.4 1.0
N I:ASP177 4.3 41.6 1.0
N I:SER180 4.3 44.1 1.0
N I:GLY181 4.4 42.2 1.0
CA I:SER180 4.4 44.4 1.0
C I:ASP175 4.4 43.7 1.0
CA I:GLY181 4.4 41.6 1.0
O I:ALA178 4.4 40.9 1.0
CA I:ASP177 4.4 41.2 1.0
N I:ALA178 4.5 39.1 1.0
C I:ALA178 4.5 41.5 1.0
CA I:ALA174 4.5 39.0 1.0
CA I:ALA178 4.5 40.0 1.0
OD1 I:ASP175 4.6 51.2 1.0
O I:ASP175 4.7 45.3 1.0
CB I:ALA174 4.8 37.3 1.0
CB I:SER180 4.8 45.6 1.0
CB I:ASP177 4.9 42.1 1.0
N I:ARG176 4.9 42.6 1.0

Magnesium binding site 4 out of 11 in 5lai

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Magnesium binding site 4 out of 11 in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:81.6
occ:1.00
 NE I:ARG27 3.3 37.4 1.0
OXT I:ASP204 3.4 49.4 1.0
O I:ALA178 3.5 40.9 1.0
CD I:ARG27 3.6 36.2 1.0
C I:ASP204 3.8 49.2 1.0
O I:ASP204 3.8 47.1 1.0
CD1 I:TRP182 4.0 40.7 1.0
NE1 I:TRP182 4.1 41.0 1.0
CZ I:ARG27 4.3 37.1 1.0
CA Y:ALA169 4.3 36.7 1.0
MG Y:MG302 4.4 47.3 1.0
O I:SER180 4.4 41.7 1.0
CG I:TRP182 4.5 41.1 1.0
CB Y:ALA169 4.6 35.5 1.0
NH2 I:ARG27 4.6 37.4 1.0
CE2 I:TRP182 4.6 41.1 1.0
C I:ALA178 4.7 41.5 1.0
CG I:ARG27 4.7 35.7 1.0
O Y:HIS166 4.8 38.5 1.0
CD2 I:TRP182 4.8 41.0 1.0
CA I:ASP204 4.9 48.1 1.0

Magnesium binding site 5 out of 11 in 5lai

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Magnesium binding site 5 out of 11 in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:55.9
occ:1.00
 OE1 J:GLN118 3.2 37.8 1.0
O J:THR124 3.5 37.0 1.0
CB J:ASP120 3.7 37.6 1.0
OD2 J:ASP120 3.7 41.9 1.0
N J:ASP120 3.7 35.3 1.0
CG J:ASP120 3.8 39.6 1.0
CG J:GLN118 4.0 34.2 1.0
CD J:GLN118 4.0 36.0 1.0
CE1 J:HIS133 4.1 34.9 1.0
CB J:THR124 4.2 38.8 1.0
O J:GLN118 4.3 32.3 1.0
CA J:ASP120 4.3 36.3 1.0
C J:ILE119 4.4 34.3 1.0
CG2 J:THR124 4.4 37.8 1.0
C J:THR124 4.4 37.3 1.0
CA J:ILE119 4.6 33.1 1.0
C J:GLN118 4.6 32.5 1.0
OD1 J:ASP120 4.6 42.2 1.0
N J:ILE119 4.7 32.2 1.0
ND1 J:HIS133 4.8 34.9 1.0
CB J:GLN118 4.8 33.1 1.0
CG1 I:VAL35 4.9 42.6 1.0
CA J:THR124 5.0 38.5 1.0

Magnesium binding site 6 out of 11 in 5lai

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Magnesium binding site 6 out of 11 in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:51.8
occ:1.00
 O K:ASP168 2.2 42.3 1.0
O K:ALA165 2.2 41.8 1.0
O W:ASP204 2.2 49.7 1.0
O K:SER171 2.3 45.7 1.0
C W:ASP204 3.2 48.1 1.0
C K:ASP168 3.3 39.3 1.0
C K:ALA165 3.3 40.2 1.0
C K:SER171 3.5 43.4 1.0
CA W:ASP204 3.7 47.3 1.0
NH1 K:ARG19 3.8 49.4 1.0
CA K:ALA169 3.8 38.7 1.0
CB W:ASP204 3.9 46.4 1.0
O K:ALA169 3.9 41.2 1.0
C K:ALA169 3.9 40.3 1.0
N K:ALA169 3.9 38.4 1.0
CA K:ALA165 4.0 39.7 1.0
N K:SER171 4.0 42.4 1.0
OXT W:ASP204 4.1 48.9 1.0
CA K:SER171 4.3 42.4 1.0
O K:HIS166 4.4 38.7 1.0
N K:ASP168 4.4 38.4 1.0
CA K:ASP168 4.4 38.5 1.0
N K:HIS166 4.4 39.6 1.0
N K:GLY172 4.5 44.5 1.0
C K:HIS166 4.5 38.2 1.0
CZ K:ARG19 4.5 47.4 1.0
O K:ALA164 4.6 39.8 1.0
N K:TYR170 4.6 40.9 1.0
CB K:SER171 4.6 41.3 1.0
CA K:GLY172 4.6 44.5 1.0
CA K:HIS166 4.8 38.9 1.0
CB K:ALA165 4.8 38.5 1.0
CG W:ASP204 4.8 47.2 1.0
NH2 K:ARG19 4.9 48.4 1.0
C K:ARG167 5.0 38.6 1.0
N K:ARG167 5.0 37.8 1.0

Magnesium binding site 7 out of 11 in 5lai

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Magnesium binding site 7 out of 11 in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg303

b:45.9
occ:1.00
 O K:HOH415 2.5 45.3 1.0
O K:ILE82 2.7 38.2 1.0
O K:HOH424 2.8 46.8 1.0
C K:ILE82 3.5 38.7 1.0
CA K:ILE82 3.6 37.7 1.0
CG2 K:ILE82 3.8 36.3 1.0
CB K:ASN85 3.9 38.5 1.0
N K:LEU86 3.9 35.5 1.0
CB K:LEU86 4.2 35.4 1.0
CB K:ILE82 4.2 37.1 1.0
CH2 K:TRP58 4.3 33.4 1.0
CA K:LEU86 4.3 35.3 1.0
C K:ASN85 4.4 36.5 1.0
CG1 K:ILE82 4.6 38.1 1.0
O K:LYS81 4.6 38.3 1.0
CA K:ASN85 4.6 37.5 1.0
O K:HOH435 4.7 51.8 1.0
N K:LEU83 4.8 39.1 1.0
N K:ILE82 4.9 37.4 1.0
CG K:ASN85 5.0 40.1 1.0

Magnesium binding site 8 out of 11 in 5lai

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Magnesium binding site 8 out of 11 in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:48.1
occ:1.00
 O N:SER169 2.5 42.6 1.0
O N:ILE163 2.5 38.3 1.0
O N:ASP166 2.9 39.4 1.0
C N:ILE163 3.6 39.3 1.0
C N:SER169 3.7 40.5 1.0
CD1 a:LEU34 3.7 45.7 1.0
CG2 N:ILE163 3.8 36.0 1.0
NH1 N:ARG19 3.8 43.4 1.0
C N:ASP166 3.9 37.9 1.0
CA N:ILE163 4.2 38.0 1.0
CA N:GLY167 4.2 36.3 1.0
CZ N:ARG19 4.3 43.1 1.0
CA N:GLY170 4.3 42.0 1.0
N N:GLY170 4.5 40.7 1.0
NH2 N:ARG19 4.5 42.2 1.0
N N:GLY167 4.5 36.6 1.0
O N:GLY167 4.5 37.3 1.0
C N:GLY167 4.6 37.3 1.0
CB N:ILE163 4.6 37.2 1.0
N N:LYS164 4.7 41.5 1.0
CA N:SER169 4.7 38.6 1.0
N N:SER169 4.7 38.9 1.0
O N:LYS164 4.9 42.0 1.0
C N:LYS164 4.9 42.3 1.0
N N:ASP166 5.0 38.6 1.0
CA N:LYS164 5.0 43.6 1.0

Magnesium binding site 9 out of 11 in 5lai

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Magnesium binding site 9 out of 11 in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:44.8
occ:1.00
 O V:ILE163 2.1 42.2 1.0
O V:ASP166 2.2 43.8 1.0
OXT L:ASP222 2.2 56.6 1.0
O V:SER169 2.3 46.7 1.0
C L:ASP222 3.2 57.9 1.0
C V:ILE163 3.2 43.3 1.0
C V:ASP166 3.2 43.0 1.0
C V:SER169 3.4 45.9 1.0
O V:GLY162 3.7 41.4 1.0
CA L:ASP222 3.8 56.8 1.0
CA V:ILE163 3.9 43.1 1.0
NH1 V:ARG19 3.9 52.6 1.0
CA V:LEU167 4.0 45.0 1.0
N V:LEU167 4.0 44.3 1.0
O L:ASP222 4.0 62.8 1.0
N V:ASP166 4.0 43.0 1.0
N V:TRP164 4.2 44.1 1.0
CA V:ASP166 4.2 41.9 1.0
N V:SER169 4.3 43.7 1.0
N V:GLY170 4.3 47.8 1.0
CA V:SER169 4.3 43.9 1.0
CB L:ASP222 4.3 58.4 1.0
C V:TRP164 4.3 45.7 1.0
C V:LEU167 4.3 44.3 1.0
CA V:GLY170 4.4 49.5 1.0
CA V:TRP164 4.5 45.2 1.0
O V:LEU167 4.5 43.6 1.0
O V:TRP164 4.5 46.8 1.0
N V:ASN165 4.6 44.2 1.0
CZ V:ARG19 4.6 51.2 1.0
CB V:SER169 4.7 42.7 1.0
C V:GLY162 4.7 42.7 1.0
C V:ASN165 4.8 43.6 1.0
N V:ILE163 4.8 42.9 1.0
NH2 V:ARG19 4.8 50.9 1.0
CG2 V:ILE163 4.9 43.5 1.0
CB V:ASP166 5.0 42.2 1.0

Magnesium binding site 10 out of 11 in 5lai

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Magnesium binding site 10 out of 11 in the Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Ligand-Induced Aziridine-Formation at the Yeast Proteasomal Subunit BETA5 By Sulfonate Esters within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:47.3
occ:1.00
 O Y:ASP168 2.2 39.6 1.0
O I:ASP204 2.3 47.1 1.0
O Y:ALA165 2.3 39.3 1.0
O Y:SER171 2.3 40.9 1.0
C I:ASP204 3.2 49.2 1.0
C Y:ASP168 3.3 37.9 1.0
C Y:ALA165 3.4 38.8 1.0
C Y:SER171 3.5 40.2 1.0
CA I:ASP204 3.7 48.1 1.0
NH1 Y:ARG19 3.7 44.8 1.0
CA Y:ALA169 3.8 36.7 1.0
O Y:ALA169 3.8 39.2 1.0
C Y:ALA169 3.9 38.3 1.0
N Y:ALA169 3.9 36.6 1.0
CB I:ASP204 3.9 48.8 1.0
CA Y:ALA165 4.0 38.0 1.0
N Y:SER171 4.1 38.8 1.0
OXT I:ASP204 4.1 49.4 1.0
CA Y:SER171 4.3 39.1 1.0
MG I:MG302 4.4 81.6 1.0
O Y:HIS166 4.4 38.5 1.0
N Y:ASP168 4.4 38.8 1.0
CA Y:ASP168 4.4 38.5 1.0
N Y:HIS166 4.5 38.5 1.0
CZ Y:ARG19 4.5 44.3 1.0
C Y:HIS166 4.5 37.6 1.0
N Y:GLY172 4.6 40.3 1.0
N Y:TYR170 4.6 39.0 1.0
O Y:ALA164 4.6 38.4 1.0
CA Y:GLY172 4.7 40.0 1.0
CB Y:SER171 4.7 39.4 1.0
CA Y:HIS166 4.8 37.9 1.0
CB Y:ALA165 4.8 38.0 1.0
CG I:ASP204 4.9 49.4 1.0
NH2 Y:ARG19 4.9 45.4 1.0
C Y:ARG167 4.9 39.0 1.0

Reference:

C.Dubiella, H.Cui, M.Groll. Tunable Probes with Direct Fluorescence Signals For the Constitutive and Immunoproteasome. Angew. Chem. Int. Ed. Engl. V. 55 13330 2016.
ISSN: ESSN 1521-3773
PubMed: 27709817
DOI: 10.1002/ANIE.201605753
Page generated: Sun Sep 29 19:47:02 2024

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