Magnesium in PDB 6hvy: Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring)

Enzymatic activity of Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring)

All present enzymatic activity of Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring):
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring), PDB code: 6hvy 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.630, 301.800, 145.570, 90.00, 113.06, 90.00
R / Rfree (%) 18.1 / 21.8

Other elements in 6hvy:

The structure of Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring) 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 5 (7- and 6-Membered Ring) (pdb code 6hvy). 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 5 (7- and 6-Membered Ring), PDB code: 6hvy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6hvy

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring)


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 5 (7- and 6-Membered Ring) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:49.3
occ:1.00
 O G:MET125 2.1 52.9 1.0
O G:TYR119 2.4 43.2 1.0
O G:ARG122 2.4 40.8 1.0
OG1 G:THR8 2.5 45.3 1.0
CG2 G:THR8 3.2 45.6 1.0
C G:MET125 3.4 50.9 1.0
CB G:THR8 3.5 45.7 1.0
C G:ARG122 3.6 45.5 1.0
O G:ALA123 3.6 51.6 1.0
C G:TYR119 3.6 41.7 1.0
CA G:ALA123 3.9 47.4 1.0
C G:ALA123 3.9 49.1 1.0
N G:ALA123 4.2 45.9 1.0
CA G:ARG126 4.2 45.9 1.0
N G:ARG126 4.2 45.4 1.0
N G:MET125 4.3 53.5 1.0
CA G:MET125 4.3 54.4 1.0
N G:THR8 4.3 49.0 1.0
CA G:TYR119 4.4 41.2 1.0
CD G:PRO127 4.5 44.0 1.0
CA G:THR8 4.5 47.5 1.0
N G:THR120 4.6 40.1 1.0
C G:ARG126 4.7 44.7 1.0
N G:ARG122 4.7 46.0 1.0
CA G:ARG122 4.8 48.6 1.0
N G:TYR124 4.8 48.4 1.0
CA G:THR120 4.8 41.0 1.0
O F:HOH314 4.8 46.6 1.0
CB G:MET125 4.8 58.9 1.0
C G:THR120 4.9 41.0 1.0
N G:PRO127 4.9 43.6 1.0
CB G:TYR119 4.9 40.9 1.0

Magnesium binding site 2 out of 8 in 6hvy

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring)


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 5 (7- and 6-Membered Ring) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:63.8
occ:1.00
 O I:ASP177 2.6 44.9 1.0
O I:SER180 2.7 47.0 1.0
O I:ALA174 3.1 45.8 1.0
O I:HOH418 3.2 54.1 1.0
O I:HOH417 3.5 63.2 1.0
OXT I:ASP204 3.6 54.5 1.0
C I:ASP177 3.7 45.4 1.0
C I:SER180 3.9 47.3 1.0
O I:ALA178 4.1 50.8 1.0
C I:ALA174 4.2 47.0 1.0
C I:ALA178 4.3 48.4 1.0
CA I:ALA178 4.3 45.9 1.0
O I:ASP204 4.4 50.7 1.0
NH1 Y:ARG19 4.4 54.7 1.0
CA I:ASP175 4.4 48.4 1.0
C I:ASP204 4.4 52.3 1.0
N I:ALA178 4.5 43.4 1.0
N I:SER180 4.6 45.7 1.0
NH2 Y:ARG19 4.6 54.2 1.0
N I:ASP177 4.7 46.8 1.0
CA I:GLY181 4.7 46.9 1.0
N I:ASP175 4.7 48.0 1.0
N I:GLY181 4.7 45.9 1.0
C I:ASP175 4.7 48.6 1.0
CA I:ASP177 4.8 46.2 1.0
CA I:SER180 4.8 46.9 1.0
O I:ASP175 4.9 55.5 1.0
OD1 I:ASP175 4.9 51.6 1.0
CZ Y:ARG19 4.9 53.4 1.0

Magnesium binding site 3 out of 8 in 6hvy

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring)


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 5 (7- and 6-Membered Ring) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:57.4
occ:1.00
 O I:ASP204 2.3 50.7 1.0
O Y:ASP168 2.3 43.6 1.0
O Y:ALA165 2.4 41.6 1.0
O Y:SER171 2.4 43.9 1.0
O Y:HOH413 2.5 43.5 1.0
C I:ASP204 3.2 52.3 1.0
C Y:ASP168 3.4 40.8 1.0
NH1 Y:ARG19 3.5 54.7 1.0
C Y:ALA165 3.6 41.3 1.0
C Y:SER171 3.7 43.4 1.0
O Y:ALA169 3.7 42.6 1.0
CA Y:ALA169 3.7 41.7 1.0
CA I:ASP204 3.7 52.3 1.0
C Y:ALA169 3.8 42.8 1.0
N Y:ALA169 3.9 42.2 1.0
CB I:ASP204 4.0 52.7 1.0
OXT I:ASP204 4.1 54.5 1.0
N Y:SER171 4.1 42.7 1.0
CA Y:ALA165 4.3 40.9 1.0
CZ Y:ARG19 4.3 53.4 1.0
O Y:HIS166 4.3 41.0 1.0
CA Y:SER171 4.5 42.8 1.0
CA Y:ASP168 4.6 40.7 1.0
N Y:TYR170 4.6 42.5 1.0
N Y:ASP168 4.6 41.1 1.0
C Y:HIS166 4.6 41.3 1.0
N Y:GLY172 4.6 44.5 1.0
N Y:HIS166 4.7 41.1 1.0
NH2 Y:ARG19 4.7 54.2 1.0
CA Y:GLY172 4.8 44.5 1.0
O Y:ALA164 4.8 40.5 1.0
CG I:ASP204 4.8 52.2 1.0
CA Y:HIS166 4.9 40.0 1.0
CB Y:SER171 5.0 42.0 1.0

Magnesium binding site 4 out of 8 in 6hvy

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring)


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 5 (7- and 6-Membered Ring) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:66.5
occ:1.00
 O K:ALA165 2.2 41.8 1.0
O K:ASP168 2.3 44.0 1.0
O W:ASP204 2.5 57.8 1.0
C W:ASP204 3.1 56.2 1.0
O K:SER171 3.1 47.5 1.0
C K:ASP168 3.2 43.1 1.0
C K:ALA165 3.4 43.8 1.0
CA W:ASP204 3.5 54.2 1.0
O K:HIS166 3.5 45.3 1.0
CA K:ALA169 3.7 44.4 1.0
N K:ALA169 3.8 42.7 1.0
OXT W:ASP204 3.9 58.6 1.0
C K:HIS166 3.9 44.0 1.0
CB W:ASP204 4.0 51.8 1.0
C K:ALA169 4.1 45.5 1.0
NH1 K:ARG19 4.1 52.9 1.0
O K:ALA169 4.2 46.8 1.0
N K:ASP168 4.2 36.9 1.0
N K:HIS166 4.3 43.1 1.0
CA K:ASP168 4.3 38.2 1.0
CA K:ALA165 4.3 44.1 1.0
C K:SER171 4.3 45.3 1.0
CA K:HIS166 4.4 44.4 1.0
C K:ARG167 4.5 42.8 1.0
N K:ARG167 4.6 43.0 1.0
O K:ALA164 4.7 43.4 1.0
N K:SER171 4.8 43.6 1.0
O K:ARG167 4.8 44.5 1.0
N W:ASP204 4.9 54.9 1.0
N K:TYR170 4.9 45.2 1.0
CZ K:ARG19 5.0 51.2 1.0

Magnesium binding site 5 out of 8 in 6hvy

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring)


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 5 (7- and 6-Membered Ring) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:76.3
occ:1.00
 O V:ILE163 2.2 44.8 1.0
OXT L:ASP222 2.3 59.6 1.0
O V:ASP166 2.4 46.0 1.0
C L:ASP222 3.0 64.1 1.0
O V:SER169 3.1 53.1 1.0
C V:ASP166 3.2 49.7 1.0
C V:ILE163 3.3 49.4 1.0
CA L:ASP222 3.6 64.3 1.0
O V:TRP164 3.6 51.3 1.0
C V:TRP164 3.7 51.8 1.0
N V:ASP166 3.8 44.7 1.0
O L:ASP222 3.8 67.2 1.0
N V:LEU167 3.9 51.5 1.0
O V:GLY162 3.9 45.0 1.0
CA V:LEU167 3.9 51.6 1.0
N V:TRP164 4.0 50.9 1.0
CA V:TRP164 4.1 51.0 1.0
N V:ASN165 4.1 52.0 1.0
CA V:ASP166 4.1 48.6 1.0
C V:SER169 4.2 50.3 1.0
CA V:ILE163 4.3 49.1 1.0
C V:ASN165 4.3 50.1 1.0
O L:ARG221 4.4 64.0 1.0
CB L:ASP222 4.4 65.8 1.0
NH1 V:ARG19 4.5 60.2 1.0
C V:LEU167 4.6 51.0 1.0
CD2 V:LEU167 4.7 49.0 1.0
CA V:ASN165 4.7 51.5 1.0
N L:ASP222 4.8 62.9 1.0
O V:LEU167 4.9 49.3 1.0
C V:GLY162 4.9 47.4 1.0
N V:SER169 4.9 49.2 1.0
O V:ASN165 5.0 49.3 1.0

Magnesium binding site 6 out of 8 in 6hvy

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring)


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 5 (7- and 6-Membered Ring) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:52.0
occ:1.00
 O N:ILE163 2.7 44.9 1.0
O N:SER169 2.8 52.2 1.0
O N:ASP166 3.2 46.8 1.0
CD1 a:LEU34 3.6 50.1 1.0
NH1 N:ARG19 3.6 47.9 1.0
C N:ILE163 3.9 45.0 1.0
C N:SER169 4.0 46.4 1.0
CG2 N:ILE163 4.0 45.2 1.0
C N:ASP166 4.1 43.4 1.0
CZ N:ARG19 4.1 48.5 1.0
CA N:GLY167 4.2 43.9 1.0
NH2 N:ARG19 4.3 51.0 1.0
CA N:GLY170 4.5 47.4 1.0
O N:GLY167 4.5 41.1 1.0
CA N:ILE163 4.6 44.8 1.0
N N:GLY167 4.6 42.5 1.0
C N:GLY167 4.6 43.5 1.0
N N:GLY170 4.7 47.3 1.0
CG a:LEU34 4.9 50.1 1.0
N N:LYS164 4.9 45.9 1.0
CB N:ILE163 4.9 44.2 1.0

Magnesium binding site 7 out of 8 in 6hvy

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring)


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 5 (7- and 6-Membered Ring) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:60.5
occ:1.00
 O W:ASP177 2.4 45.5 1.0
O W:SER180 2.6 49.8 1.0
O W:ALA174 2.9 47.2 1.0
C W:ASP177 3.5 46.8 1.0
C W:SER180 3.8 49.8 1.0
OXT W:ASP204 3.9 58.6 1.0
C W:ALA174 4.0 47.8 1.0
O W:ALA178 4.1 49.6 1.0
CA W:ALA178 4.2 47.5 1.0
C W:ALA178 4.3 47.6 1.0
N W:ALA178 4.3 46.7 1.0
CA W:ASP175 4.3 49.3 1.0
O W:HOH406 4.3 43.0 1.0
N W:ASP177 4.4 49.1 1.0
NH1 K:ARG19 4.5 52.9 1.0
N W:SER180 4.5 49.6 1.0
CA W:ASP177 4.5 47.7 1.0
N W:ASP175 4.6 49.9 1.0
C W:ASP175 4.6 49.0 1.0
O W:ASP204 4.6 57.8 1.0
C W:ASP204 4.7 56.2 1.0
N W:GLY181 4.7 49.7 1.0
CA W:SER180 4.7 49.5 1.0
NH2 K:ARG19 4.7 52.7 1.0
CA W:GLY181 4.8 49.7 1.0
O W:ASP175 4.8 48.8 1.0
OD1 W:ASP175 4.9 50.8 1.0
CZ K:ARG19 4.9 51.2 1.0

Magnesium binding site 8 out of 8 in 6hvy

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with 5 (7- and 6-Membered Ring)


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 5 (7- and 6-Membered Ring) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:57.1
occ:1.00
 O Z:VAL198 2.6 48.8 1.0
O Z:THR192 2.7 54.7 1.0
O Z:HIS195 3.1 46.8 1.0
O Z:ASP222 3.5 68.0 1.0
C Z:THR192 3.7 56.0 1.0
CG2 Z:THR192 3.7 56.5 1.0
C Z:VAL198 3.8 49.2 1.0
NH2 Z:ARG28 3.8 54.7 1.0
O Z:ILE196 4.0 50.4 1.0
CA Z:THR192 4.1 55.8 1.0
C Z:HIS195 4.1 47.2 1.0
OD1 Z:ASP222 4.2 68.3 1.0
CA Z:ILE196 4.2 46.7 1.0
C Z:ILE196 4.2 46.5 1.0
NH2 H:ARG19 4.3 58.8 1.0
C Z:ASP222 4.5 65.2 1.0
CB Z:THR192 4.5 55.7 1.0
N Z:VAL198 4.6 45.6 1.0
N Z:ILE196 4.6 46.2 1.0
CA Z:GLY199 4.7 51.8 1.0
N Z:GLY199 4.7 50.1 1.0
CA Z:VAL198 4.7 47.7 1.0
CZ Z:ARG28 4.8 54.4 1.0
O Z:LYS220 4.8 59.8 1.0
NH1 Z:ARG28 4.9 55.5 1.0
N Z:GLU193 4.9 55.3 1.0
OXT Z:ASP222 5.0 60.3 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: Mon Dec 14 22:53:09 2020

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