Atomistry » Magnesium » PDB 6hvy-6i1k » 6hw3
Atomistry »
  Magnesium »
    PDB 6hvy-6i1k »
      6hw3 »

Magnesium in PDB 6hw3: Yeast 20S Proteasome in Complex with 13

Enzymatic activity of Yeast 20S Proteasome in Complex with 13

All present enzymatic activity of Yeast 20S Proteasome in Complex with 13:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with 13, PDB code: 6hw3 was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.510, 299.280, 145.420, 90.00, 112.95, 90.00
R / Rfree (%) 19.1 / 21.5

Other elements in 6hw3:

The structure of Yeast 20S Proteasome in Complex with 13 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with 13 (pdb code 6hw3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with 13, PDB code: 6hw3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6hw3

Go back to Magnesium Binding Sites List in 6hw3
Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with 13


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast 20S Proteasome in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:52.5
occ:1.00
 O G:MET125 2.3 55.3 1.0
OG1 G:THR8 2.5 49.3 1.0
O G:ARG122 2.5 50.4 1.0
O G:TYR119 2.7 46.4 1.0
CG2 G:THR8 3.2 50.5 1.0
O G:ALA123 3.2 55.0 1.0
CB G:THR8 3.4 50.0 1.0
C G:MET125 3.4 54.5 1.0
C G:ALA123 3.6 53.6 1.0
C G:ARG122 3.6 50.7 1.0
CA G:ALA123 3.7 51.6 1.0
C G:TYR119 3.9 44.9 1.0
N G:THR8 4.1 54.6 1.0
N G:ALA123 4.1 49.9 1.0
CA G:ARG126 4.3 48.7 1.0
N G:ARG126 4.3 51.0 1.0
N G:MET125 4.3 52.8 1.0
CA G:THR8 4.4 51.8 1.0
CA G:MET125 4.4 57.1 1.0
CD G:PRO127 4.6 46.5 1.0
N G:TYR124 4.6 56.6 1.0
CA G:TYR119 4.7 42.4 1.0
N G:THR120 4.9 44.9 1.0
C G:ARG126 4.9 47.9 1.0
CA G:ARG122 4.9 54.3 1.0
C G:TYR124 5.0 51.2 1.0
N G:ARG122 5.0 52.4 1.0

Magnesium binding site 2 out of 8 in 6hw3

Go back to Magnesium Binding Sites List in 6hw3
Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with 13


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast 20S Proteasome in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:67.3
occ:1.00
 O I:ASP177 2.5 52.6 1.0
O I:SER180 2.5 55.4 1.0
O I:ALA174 2.9 56.6 1.0
OXT I:ASP204 3.4 74.2 1.0
C I:ASP177 3.6 53.0 1.0
C I:SER180 3.7 53.7 1.0
O I:ALA178 4.0 55.7 1.0
C I:ALA174 4.0 56.9 1.0
CA I:ALA178 4.2 52.6 1.0
C I:ALA178 4.2 53.9 1.0
C I:ASP204 4.4 73.5 1.0
CA I:ASP175 4.4 58.3 1.0
N I:ALA178 4.4 52.6 1.0
O I:ASP204 4.5 75.6 1.0
N I:SER180 4.5 51.1 1.0
CA I:GLY181 4.6 55.3 1.0
N I:GLY181 4.6 53.8 1.0
N I:ASP175 4.6 57.2 1.0
C I:ASP175 4.7 56.7 1.0
NH1 Y:ARG19 4.7 68.6 1.0
N I:ASP177 4.7 51.2 1.0
CA I:SER180 4.7 52.7 1.0
O I:ASP175 4.7 59.9 1.0
CA I:ASP177 4.7 52.7 1.0
NH2 Y:ARG19 4.8 67.9 1.0
OD1 I:ASP175 5.0 61.0 1.0

Magnesium binding site 3 out of 8 in 6hw3

Go back to Magnesium Binding Sites List in 6hw3
Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with 13


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast 20S Proteasome in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:56.0
occ:1.00
 O Y:ASP168 2.2 53.4 1.0
O I:ASP204 2.3 75.6 1.0
O Y:ALA165 2.4 53.1 1.0
O Y:SER171 2.6 56.1 1.0
O Y:HOH403 2.6 46.4 1.0
C I:ASP204 3.2 73.5 1.0
C Y:ASP168 3.2 52.9 1.0
CA Y:ALA169 3.5 53.1 1.0
C Y:ALA165 3.6 54.0 1.0
CA I:ASP204 3.6 72.2 1.0
O Y:ALA169 3.7 53.8 1.0
C Y:ALA169 3.7 53.1 1.0
N Y:ALA169 3.8 53.4 1.0
C Y:SER171 3.8 52.2 1.0
NH1 Y:ARG19 3.8 68.6 1.0
O Y:HIS166 4.0 54.8 1.0
CB I:ASP204 4.0 72.4 1.0
OXT I:ASP204 4.2 74.2 1.0
N Y:SER171 4.2 49.3 1.0
C Y:HIS166 4.3 54.0 1.0
CA Y:ALA165 4.4 53.8 1.0
CA Y:ASP168 4.5 51.9 1.0
CZ Y:ARG19 4.5 66.5 1.0
N Y:ASP168 4.5 53.1 1.0
N Y:HIS166 4.5 54.2 1.0
CA Y:SER171 4.6 49.2 1.0
N Y:TYR170 4.6 53.3 1.0
CA Y:HIS166 4.7 53.7 1.0
O Y:ALA164 4.7 53.5 1.0
NH2 Y:ARG19 4.7 67.9 1.0
N Y:GLY172 4.8 54.7 1.0
C Y:ARG167 4.8 53.9 1.0
CA Y:GLY172 4.9 55.8 1.0
CB Y:ALA169 4.9 53.8 1.0
N Y:ARG167 5.0 53.6 1.0
CB Y:SER171 5.0 47.6 1.0

Magnesium binding site 4 out of 8 in 6hw3

Go back to Magnesium Binding Sites List in 6hw3
Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with 13


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast 20S Proteasome in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:71.5
occ:1.00
 O K:ASP168 2.2 56.2 1.0
O K:ALA165 2.3 55.1 1.0
O W:ASP204 2.3 72.3 1.0
O K:SER171 2.9 57.0 1.0
C K:ASP168 3.1 56.0 1.0
C W:ASP204 3.2 71.0 1.0
C K:ALA165 3.4 57.2 1.0
O K:HIS166 3.6 56.2 1.0
CA K:ALA169 3.6 58.8 1.0
CA W:ASP204 3.6 68.1 1.0
N K:ALA169 3.7 57.5 1.0
O K:ALA169 3.9 57.4 1.0
C K:ALA169 3.9 58.0 1.0
C K:HIS166 3.9 56.6 1.0
CB W:ASP204 4.1 67.0 1.0
OXT W:ASP204 4.1 73.7 1.0
C K:SER171 4.1 56.4 1.0
NH1 K:ARG19 4.2 68.6 1.0
N K:ASP168 4.2 56.1 1.0
CA K:ASP168 4.3 55.0 1.0
N K:HIS166 4.3 56.1 1.0
CA K:HIS166 4.4 56.7 1.0
CA K:ALA165 4.4 57.5 1.0
C K:ARG167 4.5 57.0 1.0
O K:ALA164 4.5 58.0 1.0
N K:SER171 4.5 55.7 1.0
N K:ARG167 4.6 55.5 1.0
O K:ARG167 4.7 54.2 1.0
N K:TYR170 4.8 57.1 1.0
CA K:SER171 4.9 55.1 1.0
CZ K:ARG19 4.9 68.6 1.0
CB K:ALA169 4.9 59.3 1.0
N W:ASP204 5.0 67.0 1.0

Magnesium binding site 5 out of 8 in 6hw3

Go back to Magnesium Binding Sites List in 6hw3
Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with 13


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast 20S Proteasome in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:72.3
occ:1.00
 O V:ASP166 2.0 57.7 1.0
O V:ILE163 2.1 59.9 1.0
OXT L:ASP222 2.1 75.5 1.0
O V:SER169 2.7 58.1 1.0
C V:ASP166 3.0 59.5 1.0
C L:ASP222 3.1 78.5 1.0
C V:ILE163 3.2 64.9 1.0
O V:TRP164 3.7 66.4 1.0
O V:GLY162 3.7 63.2 1.0
CA L:ASP222 3.7 76.3 1.0
N V:LEU167 3.7 61.0 1.0
CA V:LEU167 3.8 62.9 1.0
N V:ASP166 3.8 57.4 1.0
C V:TRP164 3.8 64.1 1.0
C V:SER169 3.8 57.7 1.0
O L:ASP222 4.0 84.4 1.0
CA V:ASP166 4.0 58.3 1.0
N V:TRP164 4.0 64.6 1.0
CA V:ILE163 4.1 66.2 1.0
CA V:TRP164 4.2 65.1 1.0
NH1 V:ARG19 4.3 78.3 1.0
CB L:ASP222 4.3 75.1 1.0
C V:LEU167 4.3 61.4 1.0
N V:ASN165 4.3 61.9 1.0
C V:ASN165 4.5 59.1 1.0
N V:SER169 4.5 57.4 1.0
O V:LEU167 4.6 60.5 1.0
CA V:SER169 4.7 58.6 1.0
C V:GLY162 4.7 63.1 1.0
N V:GLY170 4.7 58.5 1.0
CA V:GLY170 4.8 61.3 1.0
CB V:ASP166 4.8 57.6 1.0
CZ V:ARG19 4.8 73.5 1.0
NH2 V:ARG19 4.9 74.6 1.0
N V:ILE163 4.9 63.2 1.0
O L:ARG221 4.9 70.1 1.0
CA V:ASN165 4.9 61.3 1.0
CB V:SER169 5.0 59.2 1.0
CD2 V:LEU167 5.0 64.0 1.0

Magnesium binding site 6 out of 8 in 6hw3

Go back to Magnesium Binding Sites List in 6hw3
Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with 13


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast 20S Proteasome in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:45.7
occ:1.00
 O N:SER169 2.5 50.5 1.0
O N:ILE163 2.7 47.4 1.0
O N:ASP166 2.8 49.9 1.0
NH1 N:ARG19 3.5 55.3 1.0
CD1 a:LEU34 3.6 55.0 1.0
C N:SER169 3.7 48.6 1.0
C N:ILE163 3.8 50.2 1.0
C N:ASP166 3.9 48.7 1.0
CA N:GLY167 4.1 48.4 1.0
CG2 N:ILE163 4.1 51.0 1.0
CZ N:ARG19 4.2 54.0 1.0
O N:GLY167 4.2 47.8 1.0
C N:GLY167 4.4 47.9 1.0
N N:GLY167 4.4 48.0 1.0
CA N:GLY170 4.4 51.5 1.0
NH2 N:ARG19 4.5 52.6 1.0
CA N:ILE163 4.5 49.8 1.0
N N:GLY170 4.5 49.7 1.0
N N:SER169 4.7 46.2 1.0
CA N:SER169 4.8 45.8 1.0
O a:HOH306 4.8 56.1 1.0
CG a:LEU34 4.8 56.8 1.0
N N:LYS164 4.9 51.9 1.0
CB N:ILE163 4.9 50.8 1.0
O N:LYS164 5.0 55.6 1.0

Magnesium binding site 7 out of 8 in 6hw3

Go back to Magnesium Binding Sites List in 6hw3
Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with 13


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast 20S Proteasome in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg201

b:46.5
occ:1.00
 OE1 X:GLN118 3.6 51.0 1.0
O X:THR124 3.7 50.7 1.0
CB X:ASP120 3.8 46.2 1.0
N X:ASP120 4.1 41.4 1.0
CG X:ASP120 4.1 50.3 1.0
OD2 X:ASP120 4.2 53.4 1.0
CB X:THR124 4.2 48.1 1.0
CG X:GLN118 4.3 46.2 1.0
CD X:GLN118 4.3 47.6 1.0
CE1 X:HIS133 4.3 48.8 1.0
CG2 X:THR124 4.4 47.4 1.0
O X:GLN118 4.4 45.0 1.0
CA X:ASP120 4.6 43.6 1.0
C X:THR124 4.6 49.1 1.0
OD1 X:ASP120 4.7 55.4 1.0
C X:ILE119 4.8 42.0 1.0
CG1 W:VAL35 4.8 59.1 1.0
C X:GLN118 4.8 45.0 1.0
CD2 W:LEU28 5.0 57.4 1.0
CA X:ILE119 5.0 42.9 1.0

Magnesium binding site 8 out of 8 in 6hw3

Go back to Magnesium Binding Sites List in 6hw3
Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with 13


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast 20S Proteasome in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:54.7
occ:1.00
 O Z:HOH406 2.3 51.9 1.0
O Z:VAL198 2.6 58.8 1.0
O Z:HIS195 2.7 50.9 1.0
O Z:THR192 2.7 65.2 1.0
NH2 Z:ARG28 3.6 71.6 1.0
O Z:ILE196 3.6 57.5 1.0
O Z:ASP222 3.7 81.9 1.0
C Z:HIS195 3.7 53.2 1.0
CA Z:ILE196 3.7 53.3 1.0
C Z:VAL198 3.8 58.5 1.0
C Z:THR192 3.8 64.9 1.0
C Z:ILE196 3.8 53.5 1.0
CG2 Z:THR192 4.0 63.5 1.0
NH2 H:ARG19 4.1 74.1 1.0
N Z:ILE196 4.1 53.2 1.0
CA Z:THR192 4.2 63.9 1.0
N Z:VAL198 4.3 55.0 1.0
OD1 Z:ASP222 4.6 77.6 1.0
CA Z:VAL198 4.6 56.1 1.0
N Z:GLY199 4.7 60.5 1.0
CZ Z:ARG28 4.7 67.0 1.0
C Z:ASP222 4.7 79.5 1.0
CB Z:THR192 4.7 62.9 1.0
CA Z:GLY199 4.8 61.2 1.0
CZ H:ARG19 4.8 71.2 1.0
N Z:GLN197 4.8 52.4 1.0
NH1 H:ARG19 4.9 73.4 1.0
CA Z:HIS195 4.9 53.6 1.0
N Z:GLU193 5.0 64.4 1.0
N Z:HIS195 5.0 54.0 1.0
CB Z:ILE196 5.0 53.3 1.0

Reference:

B.T.Xin, E.M.Huber, G.De Bruin, W.Heinemeyer, E.Maurits, C.Espinal, Y.Du, M.Janssens, E.S.Weyburne, A.F.Kisselev, B.I.Florea, C.Driessen, G.A.Van Der Marel, M.Groll, H.S.Overkleeft. Structure-Based Design of Inhibitors Selective For Human Proteasome Beta 2C or Beta 2I Subunits. J.Med.Chem. V. 62 1626 2019.
ISSN: ISSN 0022-2623
PubMed: 30657666
DOI: 10.1021/ACS.JMEDCHEM.8B01884
Page generated: Wed Aug 13 07:34:52 2025

Last articles

Mg in 6WZK
Mg in 6WYI
Mg in 6WXN
Mg in 6WWV
Mg in 6WWU
Mg in 6WWT
Mg in 6WWQ
Mg in 6WWR
Mg in 6WWP
Mg in 6WWS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy