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Magnesium in PDB 5lex: Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom

Enzymatic activity of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom

All present enzymatic activity of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom:
3.4.25.1;

Protein crystallography data

The structure of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom, PDB code: 5lex was solved by J.Schrader, F.Henneberg, R.Mata, K.Tittmann, T.R.Schneider, H.Stark, G.Bourenkov, A.Chari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 170.89 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.860, 203.150, 316.020, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.1

Other elements in 5lex:

The structure of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom also contains other interesting chemical elements:

Potassium (K) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom (pdb code 5lex). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom, PDB code: 5lex:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5lex

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Magnesium binding site 1 out of 9 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:47.5
occ:1.00
 O H:ILE163 2.2 51.7 1.0
O H:ASP166 2.2 47.1 1.0
O H:SER169 2.2 51.2 1.0
O Z:ASP213 2.2 56.8 1.0
O H:HOH486 2.6 54.5 1.0
C Z:ASP213 3.2 56.9 1.0
C H:ILE163 3.2 48.0 1.0
C H:SER169 3.3 44.8 1.0
C H:ASP166 3.3 44.8 1.0
CA Z:ASP213 3.7 55.6 1.0
N H:SER169 4.0 43.2 1.0
CA H:ILE163 4.0 46.7 1.0
NH1 H:ARG19 4.0 47.1 1.0
CA H:SER169 4.0 44.8 1.0
CA H:LEU167 4.0 44.8 1.0
CB Z:ASP213 4.1 54.4 1.0
N H:LEU167 4.1 44.1 1.0
N H:ASP166 4.1 46.0 1.0
O H:GLY162 4.1 43.2 1.0
N H:GLY170 4.2 45.5 1.0
OXT Z:ASP213 4.2 59.1 1.0
N H:PHE164 4.2 47.3 1.0
C H:LEU167 4.3 42.1 1.0
CA H:ASP166 4.3 45.5 1.0
CA H:GLY170 4.4 46.5 1.0
O Z:HOH468 4.4 63.2 1.0
CB H:SER169 4.4 44.3 1.0
O H:LEU167 4.5 40.7 1.0
CZ H:ARG19 4.5 47.3 1.0
CA H:PHE164 4.5 48.7 1.0
C H:PHE164 4.6 47.6 1.0
NH2 H:ARG19 4.6 46.7 1.0
N H:ASN165 4.8 46.6 1.0
O H:PHE164 4.8 46.9 1.0
N H:GLY168 4.9 42.1 1.0
CG2 H:ILE163 4.9 47.3 1.0
CB H:ASP166 4.9 45.3 1.0
C H:GLY162 5.0 43.7 1.0
N H:ILE163 5.0 44.8 1.0

Magnesium binding site 2 out of 9 in 5lex

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Magnesium binding site 2 out of 9 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:46.8
occ:1.00
 O I:VAL174 2.2 47.5 1.0
O I:ASP177 2.2 52.1 1.0
O I:SER180 2.2 50.7 1.0
O I:HOH458 2.4 47.5 1.0
O I:HOH456 2.6 46.8 1.0
C I:VAL174 3.3 47.8 1.0
C I:SER180 3.4 49.9 1.0
C I:ASP177 3.4 46.8 1.0
O I:HOH422 3.4 67.4 1.0
O Y:HOH465 4.0 51.3 1.0
O I:HOH416 4.0 46.0 1.0
N I:SER180 4.1 48.4 1.0
N I:ASP177 4.1 47.6 1.0
N I:ASP175 4.1 48.6 1.0
CA I:ASP177 4.2 47.2 1.0
CA I:ASP175 4.2 50.3 1.0
CA I:SER180 4.2 49.4 1.0
CA I:VAL174 4.2 46.4 1.0
O I:ALA178 4.3 47.5 1.0
C I:ALA178 4.3 47.6 1.0
N I:GLY181 4.3 48.9 1.0
N I:ALA178 4.3 46.3 1.0
CB I:VAL174 4.3 47.0 1.0
CA I:GLY181 4.4 48.5 1.0
CA I:ALA178 4.4 47.1 1.0
CD1 Y:ILE26 4.5 45.8 1.0
CB I:ASP177 4.5 47.4 1.0
OXT I:ASP204 4.5 55.6 1.0
CB I:SER180 4.6 50.5 1.0
CG2 I:VAL174 4.6 48.4 1.0
OD2 I:ASP175 4.6 50.4 1.0
C I:ASP175 4.7 48.9 1.0
N I:VAL179 4.8 47.3 1.0

Magnesium binding site 3 out of 9 in 5lex

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Magnesium binding site 3 out of 9 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg303

b:45.7
occ:1.00
 O Y:ASP167 2.2 44.8 1.0
O I:ASP204 2.2 57.5 1.0
O Y:SER170 2.2 48.9 1.0
O Y:THR164 2.2 48.0 1.0
O Y:HOH492 2.8 52.0 1.0
C I:ASP204 3.2 55.5 1.0
C Y:THR164 3.2 45.1 1.0
C Y:ASP167 3.3 43.2 1.0
C Y:SER170 3.4 44.8 1.0
CA I:ASP204 3.7 53.7 1.0
CA Y:THR164 3.7 43.9 1.0
CA Y:ALA168 3.9 42.0 1.0
NH1 Y:ARG19 3.9 45.6 1.0
CB I:ASP204 3.9 51.8 1.0
C Y:ALA168 3.9 41.8 1.0
N Y:SER170 4.0 40.9 1.0
N Y:ALA168 4.0 42.1 1.0
O Y:ALA168 4.0 41.2 1.0
CA Y:SER170 4.2 42.4 1.0
CB Y:THR164 4.2 43.4 1.0
OXT I:ASP204 4.3 55.6 1.0
N Y:ASP167 4.4 45.2 1.0
CA Y:ASP167 4.4 43.3 1.0
N Y:TYR165 4.4 45.2 1.0
N Y:GLY171 4.4 42.6 1.0
CZ Y:ARG19 4.5 46.6 1.0
CB Y:SER170 4.6 41.5 1.0
CA Y:GLY171 4.6 43.1 1.0
O Y:ALA163 4.6 42.6 1.0
N Y:TYR169 4.6 41.7 1.0
O Y:TYR165 4.7 45.9 1.0
C Y:TYR165 4.8 45.2 1.0
O I:HOH440 4.8 54.6 1.0
CA Y:TYR165 4.9 47.3 1.0
NH2 Y:ARG19 4.9 46.8 1.0
CB Y:ASP167 4.9 44.1 1.0

Magnesium binding site 4 out of 9 in 5lex

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Magnesium binding site 4 out of 9 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg301

b:65.5
occ:1.00
 O J:HOH513 2.2 65.5 1.0
O J:HOH503 2.2 66.5 1.0
O K:HOH476 2.2 62.5 1.0
O J:HOH426 2.2 61.2 1.0
O J:HOH407 2.2 61.5 1.0
O J:HOH466 2.2 64.1 1.0
O J:PRO97 4.0 52.9 1.0
O J:HOH485 4.0 61.4 1.0
O K:HOH452 4.1 53.9 1.0
OE2 J:GLU49 4.3 64.4 1.0
O J:HOH456 4.3 73.9 1.0
OD1 J:ASP52 4.4 51.5 1.0
OD2 J:ASP52 4.4 49.4 1.0
O K:HOH415 4.4 66.0 1.0
CE K:LYS91 4.6 62.5 1.0
CE1 J:HIS99 4.6 48.3 0.5
O J:HOH514 4.8 66.8 1.0
CD J:PRO97 4.8 49.9 1.0
CG J:ASP52 4.8 49.8 1.0
ND1 J:HIS99 4.9 48.5 0.5
CG J:PRO97 5.0 48.7 1.0

Magnesium binding site 5 out of 9 in 5lex

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Magnesium binding site 5 out of 9 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:53.5
occ:1.00
 O W:ASP204 2.2 71.7 1.0
O K:ASP167 2.2 65.3 1.0
O K:THR164 2.2 65.0 1.0
O K:SER170 2.2 68.4 1.0
O K:HOH443 2.7 54.1 1.0
C W:ASP204 3.2 71.1 1.0
C K:THR164 3.3 60.1 1.0
C K:ASP167 3.3 60.1 1.0
C K:SER170 3.5 62.4 1.0
CA W:ASP204 3.6 72.6 1.0
CB W:ASP204 3.7 71.9 1.0
CA K:THR164 3.8 59.2 1.0
CA K:ALA168 3.8 59.1 1.0
NH1 K:ARG19 3.9 64.1 1.0
C K:ALA168 3.9 58.8 1.0
N K:ALA168 4.0 58.2 1.0
O K:ALA168 4.0 58.6 1.0
N K:SER170 4.0 60.2 1.0
CA K:SER170 4.2 60.1 1.0
OXT W:ASP204 4.3 67.6 1.0
CB K:THR164 4.3 59.0 1.0
N K:TYR165 4.4 60.7 1.0
CA K:ASP167 4.4 59.8 1.0
N K:ASP167 4.4 60.1 1.0
N K:GLY171 4.5 62.1 1.0
O K:TYR165 4.6 60.6 1.0
CZ K:ARG19 4.6 65.0 1.0
CA K:GLY171 4.7 63.4 1.0
O K:ALA163 4.7 57.9 1.0
C K:TYR165 4.7 61.3 1.0
N K:TYR169 4.7 59.1 1.0
CB K:SER170 4.7 59.1 1.0
CA K:TYR165 4.8 62.2 1.0
CG W:ASP204 4.9 72.9 1.0
NH2 K:ARG19 4.9 68.0 1.0
CB K:ASP167 5.0 60.4 1.0
N W:ASP204 5.0 72.4 1.0

Magnesium binding site 6 out of 9 in 5lex

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Magnesium binding site 6 out of 9 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg303

b:53.0
occ:1.00
 O V:SER169 2.2 67.7 1.0
O V:ASP166 2.2 64.0 1.0
O V:ILE163 2.2 67.5 1.0
O L:ASP213 2.2 79.0 1.0
O V:HOH457 2.8 57.8 1.0
C L:ASP213 3.2 75.0 1.0
C V:ILE163 3.3 62.8 1.0
C V:SER169 3.3 61.0 1.0
C V:ASP166 3.3 58.5 1.0
CA L:ASP213 3.7 74.5 1.0
NH1 V:ARG19 4.0 63.7 1.0
CB L:ASP213 4.0 74.3 1.0
N V:SER169 4.0 58.0 1.0
O L:HOH417 4.0 58.7 1.0
CA V:ILE163 4.0 61.5 1.0
CA V:LEU167 4.1 57.6 1.0
N V:ASP166 4.1 59.1 1.0
CA V:SER169 4.1 59.0 1.0
N V:LEU167 4.1 57.1 1.0
O V:GLY162 4.1 58.3 1.0
N V:GLY170 4.2 61.3 1.0
OXT L:ASP213 4.3 76.5 1.0
N V:PHE164 4.3 62.1 1.0
CA V:ASP166 4.3 58.5 1.0
C V:LEU167 4.3 56.4 1.0
CA V:GLY170 4.4 62.1 1.0
CB V:SER169 4.4 59.2 1.0
CZ V:ARG19 4.5 64.7 1.0
O V:LEU167 4.5 56.2 1.0
CA V:PHE164 4.6 63.9 1.0
C V:PHE164 4.6 63.5 1.0
NH2 V:ARG19 4.6 66.0 1.0
N V:ASN165 4.8 61.9 1.0
O V:PHE164 4.8 64.8 1.0
N V:GLY168 4.9 55.6 1.0
CB V:ASP166 4.9 58.0 1.0
CG2 V:ILE163 4.9 63.7 1.0
C V:GLY162 5.0 58.1 1.0

Magnesium binding site 7 out of 9 in 5lex

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Magnesium binding site 7 out of 9 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:63.2
occ:1.00
 O b:HOH409 2.2 52.7 1.0
O V:HOH487 2.2 61.3 1.0
O V:HOH432 2.2 61.8 1.0
O b:HOH442 2.2 63.1 1.0
O b:HOH408 2.2 58.6 1.0
OE1 V:GLN91 2.2 62.4 1.0
CD V:GLN91 3.3 57.5 1.0
OD2 b:ASP51 3.6 47.6 1.0
NE2 V:GLN91 3.7 55.6 1.0
O b:ASP93 3.8 52.1 1.0
O V:HOH420 4.0 46.5 1.0
O V:HOH448 4.1 58.3 1.0
OD1 b:ASP51 4.1 47.3 1.0
CG b:ASP51 4.3 45.4 1.0
O b:HOH440 4.5 62.1 1.0
CG V:GLN91 4.6 56.2 1.0
ND1 V:HIS116 4.8 52.6 1.0
C b:ASP93 4.8 49.4 1.0

Magnesium binding site 8 out of 9 in 5lex

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Magnesium binding site 8 out of 9 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:52.8
occ:1.00
 O W:HOH434 2.1 55.0 1.0
O W:ASP177 2.2 66.5 1.0
O W:VAL174 2.2 68.1 1.0
O W:SER180 2.2 70.0 1.0
O W:HOH448 2.4 52.7 1.0
C W:SER180 3.3 63.9 1.0
C W:VAL174 3.3 64.6 1.0
C W:ASP177 3.3 60.9 1.0
O W:HOH455 3.9 64.1 1.0
O W:HOH410 4.1 63.3 1.0
N W:SER180 4.1 60.9 1.0
N W:ASP177 4.1 62.4 1.0
CA W:ASP177 4.1 62.7 1.0
O W:HOH477 4.2 71.1 1.0
CA W:SER180 4.2 62.2 1.0
N W:ASP175 4.2 65.5 1.0
CA W:ASP175 4.3 66.4 1.0
CA W:VAL174 4.3 63.9 1.0
O W:ALA178 4.3 63.8 1.0
N W:GLY181 4.3 63.0 1.0
N W:ALA178 4.3 59.4 1.0
C W:ALA178 4.3 60.8 1.0
CB W:VAL174 4.3 62.9 1.0
CA W:GLY181 4.4 64.8 1.0
CB W:ASP177 4.4 63.3 1.0
CA W:ALA178 4.4 59.4 1.0
CD1 K:ILE26 4.5 62.3 1.0
OXT W:ASP204 4.5 67.6 1.0
CB W:SER180 4.5 62.8 1.0
CG2 W:VAL174 4.6 64.3 1.0
C W:ASP175 4.7 64.4 1.0
OD2 W:ASP175 4.7 72.8 1.0
N W:VAL179 4.8 59.8 1.0

Magnesium binding site 9 out of 9 in 5lex

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Magnesium binding site 9 out of 9 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg301

b:69.6
occ:1.00
 O X:HOH444 2.2 61.5 1.0
O X:HOH403 2.2 67.0 1.0
O X:HOH507 2.2 67.8 1.0
O X:HOH499 2.2 62.9 1.0
O X:HOH401 2.2 63.5 1.0
O Y:HOH512 2.2 69.6 1.0
O X:PRO97 4.0 56.6 1.0
O Y:HOH502 4.1 61.1 1.0
O Y:HOH484 4.1 57.9 1.0
OE2 X:GLU49 4.2 63.6 1.0
CE1 X:HIS99 4.3 46.4 0.5
OD1 X:ASP52 4.3 48.7 1.0
OD2 X:ASP52 4.4 49.8 1.0
ND1 X:HIS99 4.5 46.8 0.5
CE Y:LYS91 4.5 58.0 1.0
CG X:ASP52 4.8 48.8 1.0
CD X:PRO97 4.8 52.9 1.0
CG X:PRO97 5.0 52.8 1.0

Reference:

J.Schrader, F.Henneberg, R.A.Mata, K.Tittmann, T.R.Schneider, H.Stark, G.Bourenkov, A.Chari. The Inhibition Mechanism of Human 20S Proteasomes Enables Next-Generation Inhibitor Design. Science V. 353 594 2016.
ISSN: ESSN 1095-9203
PubMed: 27493187
DOI: 10.1126/SCIENCE.AAF8993
Page generated: Sun Sep 29 20:04:35 2024

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