Atomistry » Magnesium » PDB 5lcf-5lmm » 5lex
Atomistry »
  Magnesium »
    PDB 5lcf-5lmm »
      5lex »

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

Go back to Magnesium Binding Sites List in 5lex
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

Go back to Magnesium Binding Sites List in 5lex
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

Go back to Magnesium Binding Sites List in 5lex
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

Go back to Magnesium Binding Sites List in 5lex
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

Go back to Magnesium Binding Sites List in 5lex
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

Go back to Magnesium Binding Sites List in 5lex
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

Go back to Magnesium Binding Sites List in 5lex
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

Go back to Magnesium Binding Sites List in 5lex
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

Go back to Magnesium Binding Sites List in 5lex
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy