Magnesium in PDB 6hvs: Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18

Enzymatic activity of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18

All present enzymatic activity of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18, PDB code: 6hvs 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 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.080, 300.650, 143.500, 90.00, 112.75, 90.00
R / Rfree (%) 17.6 / 20.5

Other elements in 6hvs:

The structure of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18 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 18 (pdb code 6hvs). 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 18, PDB code: 6hvs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6hvs

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18


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 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:57.5
occ:1.00
 O G:MET125 2.1 60.3 1.0
OG1 G:THR8 2.6 59.1 1.0
O G:ARG122 2.8 58.4 1.0
O G:TYR119 2.9 54.2 1.0
O G:ALA123 3.1 64.7 1.0
CG2 G:THR8 3.2 60.3 1.0
C G:MET125 3.3 60.4 1.0
CB G:THR8 3.5 59.6 1.0
C G:ALA123 3.6 63.3 1.0
CA G:ALA123 3.7 61.8 1.0
C G:ARG122 3.9 58.0 1.0
CA G:ARG126 4.0 58.2 1.0
N G:ARG126 4.1 58.5 1.0
N G:THR8 4.1 63.3 1.0
C G:TYR119 4.1 54.0 1.0
N G:MET125 4.2 62.0 1.0
N G:ALA123 4.3 59.0 1.0
CD G:PRO127 4.4 56.5 1.0
CA G:MET125 4.4 63.2 1.0
CA G:THR8 4.4 61.8 1.0
N G:TYR124 4.6 64.2 1.0
C G:ARG126 4.7 57.5 1.0
CA G:TYR119 4.9 52.6 1.0
N G:PRO127 4.9 56.0 1.0
C G:TYR124 4.9 61.5 1.0
CB G:ALA123 5.0 63.1 1.0

Magnesium binding site 2 out of 8 in 6hvs

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18


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 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:74.3
occ:1.00
 O I:SER180 2.9 61.1 1.0
O I:ASP177 2.9 53.0 1.0
O I:ALA174 3.0 60.6 1.0
OXT I:ASP204 3.1 78.5 1.0
O I:ASP204 3.8 82.8 1.0
C I:ASP204 3.9 75.3 1.0
C I:ALA174 4.0 60.9 1.0
C I:ASP177 4.0 57.0 1.0
C I:SER180 4.1 58.2 1.0
CA I:ASP175 4.1 62.1 1.0
NH2 Y:ARG19 4.4 64.6 1.0
O I:ALA178 4.4 59.4 1.0
C I:ASP175 4.5 61.2 1.0
O I:ASP175 4.5 63.0 1.0
N I:ASP175 4.5 61.0 1.0
NH1 Y:ARG19 4.5 64.3 1.0
OD1 I:ASP175 4.6 64.1 1.0
CA I:ALA178 4.7 58.0 1.0
C I:ALA178 4.7 58.3 1.0
CA I:GLY181 4.7 59.4 1.0
N I:ALA178 4.8 57.0 1.0
N I:ASP177 4.8 57.8 1.0
N I:GLY181 4.8 57.5 1.0
CZ Y:ARG19 4.9 63.0 1.0
OD1 I:ASP204 4.9 76.6 1.0
N I:SER180 5.0 56.2 1.0

Magnesium binding site 3 out of 8 in 6hvs

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18


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 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:58.1
occ:1.00
 O K:ASP168 2.5 49.8 1.0
O K:ALA165 2.5 56.4 1.0
O W:ASP204 2.5 86.2 1.0
C W:ASP204 3.1 78.9 1.0
O K:SER171 3.1 60.5 1.0
C K:ASP168 3.3 53.1 1.0
O K:HIS166 3.4 56.2 1.0
CA W:ASP204 3.4 73.2 1.0
CA K:ALA169 3.6 55.3 1.0
C K:ALA165 3.7 56.2 1.0
N K:ALA169 3.8 55.3 1.0
CB W:ASP204 3.8 71.9 1.0
O K:ALA169 3.8 53.9 1.0
C K:ALA169 3.9 55.9 1.0
C K:HIS166 4.0 57.0 1.0
NH1 K:ARG19 4.1 63.7 1.0
OXT W:ASP204 4.1 82.5 1.0
C K:SER171 4.4 55.4 1.0
N K:ASP168 4.4 53.2 1.0
CA K:ASP168 4.5 53.8 1.0
CA K:HIS166 4.5 57.5 1.0
N K:HIS166 4.5 54.9 1.0
C K:ARG167 4.6 55.0 1.0
CA K:ALA165 4.7 56.6 1.0
O K:ARG167 4.7 52.4 1.0
N K:SER171 4.8 52.9 1.0
N W:ASP204 4.8 70.7 1.0
N K:ARG167 4.8 56.5 1.0
CG W:ASP204 4.9 70.8 1.0
N K:TYR170 4.9 56.8 1.0
O K:ALA164 4.9 55.5 1.0
CZ K:ARG19 4.9 62.6 1.0
CB K:ALA169 4.9 54.2 1.0

Magnesium binding site 4 out of 8 in 6hvs

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18


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 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:50.7
occ:1.00
 O N:ILE163 2.5 51.7 1.0
O N:SER169 2.7 51.1 1.0
O N:ASP166 3.1 50.4 1.0
CD1 a:LEU34 3.5 59.1 1.0
NH1 N:ARG19 3.6 53.2 1.0
C N:ILE163 3.6 52.1 1.0
CG2 N:ILE163 3.8 53.2 1.0
C N:SER169 3.9 49.9 1.0
C N:ASP166 4.1 50.1 1.0
CZ N:ARG19 4.1 51.7 1.0
NH2 N:ARG19 4.3 53.8 1.0
CA N:GLY170 4.3 52.7 1.0
CA N:ILE163 4.3 51.5 1.0
CA N:GLY167 4.4 49.2 1.0
N N:GLY170 4.5 50.9 1.0
O N:GLY167 4.6 46.8 1.0
N N:LYS164 4.7 54.0 1.0
CB N:ILE163 4.7 52.5 1.0
N N:GLY167 4.7 49.6 1.0
C N:GLY167 4.8 48.0 1.0
O N:LYS164 4.8 56.8 1.0
CG a:LEU34 4.8 58.9 1.0
CA N:LYS164 4.9 55.0 1.0
C N:LYS164 4.9 55.4 1.0

Magnesium binding site 5 out of 8 in 6hvs

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18


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 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:77.4
occ:1.00
 OXT L:ASP222 2.0 78.5 1.0
O V:ASP166 2.3 57.1 1.0
O V:ILE163 2.3 58.5 1.0
C L:ASP222 2.8 75.1 1.0
O V:SER169 3.1 54.0 1.0
C V:ASP166 3.1 57.5 1.0
O V:TRP164 3.2 61.8 1.0
C V:ILE163 3.5 60.4 1.0
CA L:ASP222 3.5 72.6 1.0
O L:ASP222 3.6 79.5 1.0
C V:TRP164 3.7 62.4 1.0
N V:LEU167 3.8 57.5 1.0
CA V:LEU167 3.8 56.9 1.0
N V:ASP166 3.9 57.8 1.0
NH1 V:ARG19 4.1 64.6 1.0
CA V:ASP166 4.1 57.1 1.0
CA V:TRP164 4.1 61.8 1.0
N V:TRP164 4.2 61.3 1.0
O V:GLY162 4.2 57.4 1.0
CB L:ASP222 4.3 69.3 1.0
C V:SER169 4.3 56.8 1.0
O L:ARG221 4.3 63.7 1.0
N V:ASN165 4.4 61.0 1.0
C V:ASN165 4.5 59.5 1.0
C V:LEU167 4.5 55.3 1.0
CA V:ILE163 4.5 60.3 1.0
CD2 V:LEU167 4.6 56.4 1.0
N L:ASP222 4.7 70.6 1.0
O V:LEU167 4.7 52.9 1.0
CD1 L:ILE35 4.9 65.8 1.0
CA V:ASN165 4.9 60.1 1.0
C L:ARG221 4.9 68.0 1.0

Magnesium binding site 6 out of 8 in 6hvs

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18


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 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:69.9
occ:1.00
 O W:ASP177 2.7 57.1 1.0
O W:SER180 2.9 61.0 1.0
O W:ALA174 3.0 53.3 1.0
OXT W:ASP204 3.2 82.5 1.0
O W:ASP204 3.8 86.2 1.0
C W:ASP177 3.9 59.6 1.0
C W:ASP204 3.9 78.9 1.0
C W:ALA174 4.1 58.9 1.0
CA W:ASP175 4.1 64.3 1.0
C W:SER180 4.1 59.9 1.0
NH2 K:ARG19 4.3 64.9 1.0
O W:ALA178 4.3 58.2 1.0
NH1 K:ARG19 4.3 63.7 1.0
O W:ASP175 4.4 62.4 1.0
C W:ASP175 4.4 62.0 1.0
CA W:ALA178 4.5 59.3 1.0
N W:ASP175 4.5 61.7 1.0
C W:ALA178 4.6 58.1 1.0
N W:ALA178 4.6 59.0 1.0
OD1 W:ASP175 4.7 75.2 1.0
CZ K:ARG19 4.7 62.6 1.0
N W:ASP177 4.7 61.3 1.0
CA W:GLY181 4.9 59.0 1.0
CA W:ASP177 4.9 60.1 1.0
N W:GLY181 4.9 58.3 1.0
N W:SER180 4.9 57.9 1.0
OD1 W:ASP204 5.0 70.6 1.0

Magnesium binding site 7 out of 8 in 6hvs

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18


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 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:65.7
occ:1.00
 O I:ASP204 2.5 82.8 1.0
O Y:ASP168 2.7 51.2 1.0
O Y:ALA165 2.9 53.2 1.0
C I:ASP204 3.0 75.3 1.0
O Y:HIS166 3.2 49.0 1.0
C Y:ASP168 3.4 52.9 1.0
CA I:ASP204 3.4 72.6 1.0
CA Y:ALA169 3.5 52.7 1.0
O Y:SER171 3.6 56.0 1.0
N Y:ALA169 3.7 54.2 1.0
O Y:ALA169 3.8 55.4 1.0
OXT I:ASP204 3.9 78.5 1.0
C Y:ALA169 4.0 51.9 1.0
C Y:HIS166 4.0 53.6 1.0
CB I:ASP204 4.0 73.4 1.0
C Y:ALA165 4.1 54.0 1.0
NH1 Y:ARG19 4.2 64.3 1.0
N Y:ASP168 4.5 53.5 1.0
C Y:ARG167 4.5 54.6 1.0
O Y:ARG167 4.5 51.6 1.0
CA Y:ASP168 4.5 52.5 1.0
CA Y:HIS166 4.6 55.2 1.0
CB Y:ALA169 4.7 52.5 1.0
NE1 I:TRP182 4.7 67.7 1.0
N I:ASP204 4.7 69.2 1.0
N Y:HIS166 4.8 54.4 1.0
N Y:ARG167 4.8 54.4 1.0
C Y:SER171 4.8 55.1 1.0
N Y:TYR170 5.0 51.0 1.0

Magnesium binding site 8 out of 8 in 6hvs

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 18


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 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:59.9
occ:1.00
 O Z:VAL198 2.7 53.7 1.0
O Z:HIS195 2.8 53.0 1.0
O Z:THR192 2.9 60.4 1.0
O Z:ASP222 3.4 74.7 1.0
NH2 Z:ARG28 3.5 64.5 1.0
O Z:ILE196 3.6 57.2 1.0
CA Z:ILE196 3.6 56.4 1.0
NH2 H:ARG19 3.7 67.2 1.0
C Z:HIS195 3.8 55.8 1.0
C Z:ILE196 3.8 56.1 1.0
C Z:VAL198 3.9 57.0 1.0
C Z:THR192 4.0 60.8 1.0
CG2 Z:THR192 4.1 63.8 1.0
N Z:ILE196 4.1 55.6 1.0
OD1 Z:ASP222 4.3 71.6 1.0
CA Z:THR192 4.4 62.2 1.0
C Z:ASP222 4.4 74.2 1.0
N Z:VAL198 4.5 54.6 1.0
CZ H:ARG19 4.6 65.7 1.0
CZ Z:ARG28 4.6 61.5 1.0
N Z:GLN197 4.7 55.1 1.0
NH1 H:ARG19 4.8 65.6 1.0
CA Z:VAL198 4.8 55.9 1.0
CB Z:ILE196 4.8 56.2 1.0
N Z:GLY199 4.9 59.3 1.0
CB Z:THR192 4.9 63.0 1.0
OXT Z:ASP222 4.9 72.3 1.0
NH1 Z:ARG28 4.9 62.6 1.0
CA Z:GLY199 4.9 61.1 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 22:52:32 2020

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