Atomistry » Magnesium » PDB 6hvv-6i0u » 6hvy
Atomistry »
  Magnesium »
    PDB 6hvv-6i0u »
      6hvy »

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

Go back to Magnesium Binding Sites List in 6hvy
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

Go back to Magnesium Binding Sites List in 6hvy
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

Go back to Magnesium Binding Sites List in 6hvy
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

Go back to Magnesium Binding Sites List in 6hvy
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

Go back to Magnesium Binding Sites List in 6hvy
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

Go back to Magnesium Binding Sites List in 6hvy
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

Go back to Magnesium Binding Sites List in 6hvy
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

Go back to Magnesium Binding Sites List in 6hvy
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: Tue Oct 1 02:35:32 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy