Magnesium in PDB 6hva: Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 13

Enzymatic activity of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 13

All present enzymatic activity of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 13:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 13, PDB code: 6hva 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.870, 300.630, 144.810, 90.00, 112.79, 90.00
R / Rfree (%) 18.2 / 20.8

Other elements in 6hva:

The structure of Yeast 20S Proteasome with Human BETA2I (1-53) 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 with Human BETA2I (1-53) in Complex with 13 (pdb code 6hva). 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 with Human BETA2I (1-53) in Complex with 13, PDB code: 6hva:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6hva

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) 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 with Human BETA2I (1-53) in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:51.9
occ:1.00
 O G:MET125 2.1 50.4 1.0
O G:TYR119 2.6 42.3 1.0
OG1 G:THR8 2.6 50.3 1.0
O G:ARG122 2.7 49.0 1.0
CG2 G:THR8 3.2 50.0 1.0
C G:MET125 3.4 50.6 1.0
O G:ALA123 3.4 53.6 1.0
CB G:THR8 3.4 49.7 1.0
C G:TYR119 3.8 43.8 1.0
C G:ALA123 3.8 51.9 1.0
C G:ARG122 3.8 48.1 1.0
CA G:ALA123 3.9 50.9 1.0
CA G:ARG126 4.1 48.3 1.0
N G:ARG126 4.1 49.0 1.0
N G:THR8 4.2 51.9 1.0
CD G:PRO127 4.3 46.5 1.0
N G:ALA123 4.3 48.9 1.0
N G:MET125 4.3 52.1 1.0
CA G:MET125 4.4 53.4 1.0
CA G:THR8 4.4 51.0 1.0
CA G:TYR119 4.6 42.9 1.0
C G:ARG126 4.7 47.6 1.0
N G:TYR124 4.8 52.7 1.0
N G:THR120 4.8 44.4 1.0
N G:PRO127 4.8 46.2 1.0
CA G:THR120 4.9 44.5 1.0
CB G:MET125 5.0 56.9 1.0

Magnesium binding site 2 out of 8 in 6hva

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) 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 with Human BETA2I (1-53) in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:75.0
occ:1.00
 O I:ASP177 2.6 51.2 1.0
O I:SER180 2.6 56.2 1.0
O I:ALA174 3.1 50.6 1.0
OXT I:ASP204 3.4 74.3 1.0
C I:ASP177 3.7 51.7 1.0
C I:SER180 3.8 52.8 1.0
O I:ASP204 4.0 72.8 1.0
O I:ALA178 4.1 54.8 1.0
C I:ASP204 4.2 69.3 1.0
C I:ALA174 4.2 53.1 1.0
C I:ALA178 4.3 51.5 1.0
CA I:ALA178 4.3 52.6 1.0
NH1 Y:ARG19 4.3 57.7 1.0
N I:ALA178 4.5 51.1 1.0
CA I:ASP175 4.5 56.1 1.0
N I:SER180 4.6 50.1 1.0
N I:GLY181 4.7 51.5 1.0
CA I:GLY181 4.7 52.5 1.0
N I:ASP177 4.7 52.6 1.0
C I:ASP175 4.7 56.5 1.0
O I:ASP175 4.8 59.0 1.0
CA I:SER180 4.8 50.4 1.0
N I:ASP175 4.8 54.6 1.0
CA I:ASP177 4.8 52.1 1.0
NH2 Y:ARG19 4.9 58.2 1.0

Magnesium binding site 3 out of 8 in 6hva

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) 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 with Human BETA2I (1-53) in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:61.4
occ:1.00
 O Y:ASP168 2.4 47.4 1.0
O I:ASP204 2.5 72.8 1.0
O Y:ALA165 2.7 49.1 1.0
C I:ASP204 3.1 69.3 1.0
O Y:SER171 3.2 53.0 1.0
C Y:ASP168 3.3 47.6 1.0
O Y:HIS166 3.5 45.9 1.0
CA Y:ALA169 3.5 47.6 1.0
CA I:ASP204 3.5 67.0 1.0
O Y:ALA169 3.7 48.6 1.0
N Y:ALA169 3.7 48.5 1.0
C Y:ALA169 3.8 46.8 1.0
OXT I:ASP204 3.9 74.3 1.0
C Y:ALA165 3.9 49.2 1.0
CB I:ASP204 4.0 68.1 1.0
C Y:HIS166 4.1 48.5 1.0
NH1 Y:ARG19 4.2 57.7 1.0
N Y:ASP168 4.4 47.7 1.0
C Y:SER171 4.4 50.7 1.0
CA Y:ASP168 4.5 47.0 1.0
C Y:ARG167 4.6 49.5 1.0
CA Y:HIS166 4.7 50.0 1.0
N Y:HIS166 4.7 50.1 1.0
N Y:TYR170 4.8 46.2 1.0
N Y:SER171 4.8 46.9 1.0
CB Y:ALA169 4.8 47.3 1.0
O Y:ARG167 4.8 48.4 1.0
CZ Y:ARG19 4.8 56.1 1.0
CA Y:ALA165 4.9 48.1 1.0
N I:ASP204 4.9 64.6 1.0
N Y:ARG167 4.9 48.5 1.0
NH2 Y:ARG19 4.9 58.2 1.0

Magnesium binding site 4 out of 8 in 6hva

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) 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 with Human BETA2I (1-53) in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:59.3
occ:1.00
 O K:ASP168 2.3 47.3 1.0
O K:ALA165 2.3 51.7 1.0
O W:ASP204 2.6 70.5 1.0
O K:SER171 3.0 50.9 1.0
C K:ASP168 3.2 48.9 1.0
C W:ASP204 3.2 69.6 1.0
O K:HIS166 3.4 48.7 1.0
C K:ALA165 3.5 51.5 1.0
CA W:ASP204 3.5 65.8 1.0
CA K:ALA169 3.7 49.8 1.0
N K:ALA169 3.8 50.0 1.0
CB W:ASP204 3.9 65.3 1.0
O K:ALA169 3.9 49.0 1.0
C K:HIS166 3.9 50.6 1.0
C K:ALA169 4.0 49.8 1.0
OXT W:ASP204 4.1 75.8 1.0
C K:SER171 4.2 49.0 1.0
N K:ASP168 4.3 49.4 1.0
CA K:ASP168 4.3 49.0 1.0
N K:HIS166 4.4 49.9 1.0
CA K:HIS166 4.4 51.2 1.0
NH1 K:ARG19 4.4 57.5 1.0
CA K:ALA165 4.4 50.7 1.0
C K:ARG167 4.5 51.3 1.0
O K:ALA164 4.6 50.5 1.0
N K:SER171 4.7 48.2 1.0
N K:ARG167 4.7 50.2 1.0
O K:ARG167 4.8 51.4 1.0
N K:TYR170 4.9 50.5 1.0
CZ K:ARG19 4.9 56.0 1.0
N W:ASP204 4.9 64.7 1.0
CA K:SER171 5.0 46.8 1.0

Magnesium binding site 5 out of 8 in 6hva

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) 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 with Human BETA2I (1-53) in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:59.5
occ:1.00
 OXT L:ASP222 2.1 81.8 1.0
O V:ILE163 2.2 53.3 1.0
O V:ASP166 2.2 52.0 1.0
O V:SER169 2.8 52.2 1.0
C L:ASP222 3.0 73.5 1.0
C V:ASP166 3.1 52.0 1.0
C V:ILE163 3.3 55.7 1.0
CA L:ASP222 3.6 69.0 1.0
O V:TRP164 3.6 58.2 1.0
C V:TRP164 3.9 56.7 1.0
N V:LEU167 3.9 52.1 1.0
O L:ASP222 3.9 79.7 1.0
N V:ASP166 3.9 51.6 1.0
CA V:LEU167 3.9 51.3 1.0
C V:SER169 4.0 52.4 1.0
O V:GLY162 4.1 51.8 1.0
CA V:ASP166 4.1 51.3 1.0
N V:TRP164 4.2 56.5 1.0
CA V:TRP164 4.2 56.2 1.0
CB L:ASP222 4.2 66.9 1.0
CA V:ILE163 4.3 54.8 1.0
NH1 V:ARG19 4.3 60.3 1.0
C V:LEU167 4.5 50.1 1.0
N V:ASN165 4.5 54.9 1.0
O V:LEU167 4.6 49.9 1.0
C V:ASN165 4.6 52.9 1.0
O L:ARG221 4.7 64.2 1.0
N V:SER169 4.8 50.9 1.0
CA V:GLY170 4.8 54.1 1.0
N V:GLY170 4.8 53.0 1.0
N L:ASP222 4.9 66.2 1.0
CA V:SER169 4.9 51.5 1.0
CD2 V:LEU167 4.9 51.1 1.0
CB V:ASP166 5.0 51.2 1.0

Magnesium binding site 6 out of 8 in 6hva

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) 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 with Human BETA2I (1-53) in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:47.0
occ:1.00
 O N:SER169 2.7 42.2 1.0
O N:ILE163 2.7 43.4 1.0
O N:ASP166 3.1 48.5 1.0
NH1 N:ARG19 3.5 49.3 1.0
CD1 a:LEU34 3.6 53.9 1.0
C N:ILE163 3.8 46.6 1.0
C N:SER169 3.9 44.1 1.0
CG2 N:ILE163 4.0 48.7 1.0
CZ N:ARG19 4.1 47.8 1.0
C N:ASP166 4.1 46.4 1.0
NH2 N:ARG19 4.3 48.2 1.0
CA N:GLY167 4.3 45.1 1.0
CA N:GLY170 4.3 46.6 1.0
O N:GLY167 4.5 41.3 1.0
CA N:ILE163 4.5 47.1 1.0
N N:GLY170 4.5 44.6 1.0
N N:GLY167 4.6 45.9 1.0
C N:GLY167 4.7 43.1 1.0
N N:LYS164 4.8 48.1 1.0
CB N:ILE163 4.9 48.0 1.0
CG a:LEU34 4.9 52.9 1.0
O N:LYS164 4.9 50.5 1.0
CA N:SER169 5.0 43.6 1.0

Magnesium binding site 7 out of 8 in 6hva

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) 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 with Human BETA2I (1-53) in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:73.7
occ:1.00
 O W:ASP177 2.4 51.3 1.0
O W:SER180 3.0 53.9 1.0
O W:ALA174 3.1 50.1 1.0
C W:ASP177 3.5 52.5 1.0
OXT W:ASP204 3.6 75.8 1.0
O W:ASP204 4.0 70.5 1.0
NH1 K:ARG19 4.0 57.5 1.0
O W:ALA178 4.1 53.6 1.0
CA W:ALA178 4.1 53.4 1.0
C W:SER180 4.2 52.3 1.0
C W:ALA174 4.2 53.4 1.0
N W:ALA178 4.2 52.4 1.0
C W:ALA178 4.3 51.7 1.0
C W:ASP204 4.3 69.6 1.0
CA W:ASP175 4.3 57.8 1.0
N W:ASP177 4.5 53.9 1.0
O W:ASP175 4.5 56.6 1.0
C W:ASP175 4.5 56.6 1.0
NH2 K:ARG19 4.6 58.7 1.0
CA W:ASP177 4.6 53.4 1.0
CZ K:ARG19 4.7 56.0 1.0
N W:ASP175 4.7 55.4 1.0
N W:SER180 4.7 50.3 1.0

Magnesium binding site 8 out of 8 in 6hva

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) 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 with Human BETA2I (1-53) in Complex with 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:67.7
occ:1.00
 O Z:VAL198 2.6 50.1 1.0
O Z:THR192 2.9 54.9 1.0
O Z:HIS195 3.1 46.7 1.0
O Z:ASP222 3.3 76.3 1.0
NH2 Z:ARG28 3.5 59.8 1.0
O Z:ILE196 3.8 55.6 1.0
C Z:VAL198 3.8 52.3 1.0
CG2 Z:THR192 3.9 59.2 1.0
C Z:THR192 3.9 56.3 1.0
CA Z:ILE196 3.9 51.9 1.0
C Z:ILE196 4.0 52.0 1.0
C Z:HIS195 4.1 50.2 1.0
OD1 Z:ASP222 4.2 63.2 1.0
CA Z:THR192 4.3 57.3 1.0
C Z:ASP222 4.3 73.9 1.0
NH2 H:ARG19 4.4 61.2 1.0
N Z:ILE196 4.5 50.0 1.0
N Z:VAL198 4.5 50.6 1.0
CZ Z:ARG28 4.6 58.3 1.0
CA Z:GLY199 4.7 55.2 1.0
N Z:GLY199 4.7 52.9 1.0
CB Z:THR192 4.7 57.9 1.0
CA Z:VAL198 4.8 51.5 1.0
OXT Z:ASP222 4.8 76.5 1.0
NH1 Z:ARG28 4.8 60.5 1.0
NH1 H:ARG19 4.8 58.9 1.0
O Z:LYS220 4.9 61.7 1.0
N Z:GLN197 4.9 50.6 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 22:52:30 2020

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