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Magnesium in PDB 6hv5: Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 4

Enzymatic activity of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 4

All present enzymatic activity of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 4:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 4, PDB code: 6hv5 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 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.690, 300.440, 144.130, 90.00, 112.59, 90.00
R / Rfree (%) 17.3 / 20.4

Other elements in 6hv5:

The structure of Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 4 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 4 (pdb code 6hv5). 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 4, PDB code: 6hv5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6hv5

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


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

b:66.6
occ:1.00
 O G:MET125 2.2 60.9 1.0
OG1 G:THR8 2.8 65.3 1.0
O G:TYR119 2.9 57.2 1.0
O G:ARG122 3.0 60.8 1.0
O G:ALA123 3.2 66.1 1.0
CG2 G:THR8 3.2 64.2 1.0
C G:MET125 3.3 62.1 1.0
CB G:THR8 3.5 63.4 1.0
C G:ALA123 3.7 63.4 1.0
CA G:ALA123 3.8 63.2 1.0
CA G:ARG126 3.9 61.2 1.0
C G:ARG122 4.0 60.1 1.0
N G:ARG126 4.0 60.5 1.0
N G:THR8 4.1 65.5 1.0
C G:TYR119 4.1 57.0 1.0
N G:MET125 4.3 64.7 1.0
CD G:PRO127 4.3 60.6 1.0
CA G:MET125 4.4 65.5 1.0
N G:ALA123 4.4 60.6 1.0
CA G:THR8 4.4 64.8 1.0
N G:TYR124 4.6 64.8 1.0
C G:ARG126 4.6 61.7 1.0
N G:PRO127 4.8 60.6 1.0
C G:TYR124 4.9 63.7 1.0
CA G:TYR119 4.9 55.4 1.0

Magnesium binding site 2 out of 8 in 6hv5

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 4


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

b:85.7
occ:1.00
 O I:ASP177 2.7 57.8 1.0
O I:ALA174 2.7 66.5 1.0
O I:SER180 2.7 67.0 1.0
OXT I:ASP204 3.5 95.1 1.0
C I:ALA174 3.8 66.3 1.0
C I:ASP177 3.9 61.0 1.0
C I:SER180 3.9 63.7 1.0
CA I:ASP175 4.0 67.6 1.0
N I:ASP175 4.3 66.7 1.0
O I:ASP204 4.3 86.1 1.0
C I:ASP175 4.3 65.3 1.0
C I:ASP204 4.3 83.6 1.0
O I:ASP175 4.4 63.4 1.0
O I:ALA178 4.5 70.1 1.0
N I:ASP177 4.6 63.4 1.0
CA I:GLY181 4.6 64.4 1.0
OD1 I:ASP175 4.6 74.3 1.0
CA I:ALA178 4.7 62.4 1.0
NH2 Y:ARG19 4.7 73.8 1.0
N I:GLY181 4.7 63.7 1.0
N I:ALA178 4.7 60.4 1.0
C I:ALA178 4.7 63.3 1.0
NH1 Y:ARG19 4.7 71.2 1.0
N I:SER180 4.8 59.8 1.0
CA I:ASP177 4.8 62.7 1.0
CA I:SER180 4.9 60.4 1.0
CA I:ALA174 4.9 63.2 1.0

Magnesium binding site 3 out of 8 in 6hv5

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 4


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:77.8
occ:1.00
 O I:ASP204 2.3 86.1 1.0
O Y:ASP168 2.5 57.0 1.0
O Y:ALA165 2.6 55.9 1.0
C I:ASP204 3.0 83.6 1.0
O Y:SER171 3.1 62.4 1.0
C Y:ASP168 3.4 58.5 1.0
CA I:ASP204 3.4 79.0 1.0
O Y:HIS166 3.5 56.5 1.0
CA Y:ALA169 3.6 58.5 1.0
C Y:ALA165 3.8 59.9 1.0
O Y:ALA169 3.8 63.9 1.0
N Y:ALA169 3.8 59.2 1.0
CB I:ASP204 3.9 80.2 1.0
C Y:ALA169 3.9 57.8 1.0
OXT I:ASP204 3.9 95.1 1.0
NH1 Y:ARG19 4.0 71.2 1.0
C Y:HIS166 4.1 59.8 1.0
C Y:SER171 4.3 61.4 1.0
N Y:ASP168 4.5 59.9 1.0
CA Y:ASP168 4.5 57.8 1.0
CA Y:HIS166 4.6 61.6 1.0
N Y:HIS166 4.6 61.4 1.0
C Y:ARG167 4.7 60.5 1.0
CA Y:ALA165 4.7 59.4 1.0
N Y:SER171 4.8 58.2 1.0
CZ Y:ARG19 4.8 70.5 1.0
N I:ASP204 4.8 76.5 1.0
N Y:TYR170 4.8 56.9 1.0
O Y:ARG167 4.9 58.5 1.0
CB Y:ALA169 4.9 58.3 1.0
CG I:ASP204 4.9 81.4 1.0
N Y:ARG167 4.9 59.5 1.0
O Y:ALA164 5.0 58.7 1.0

Magnesium binding site 4 out of 8 in 6hv5

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


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

b:75.8
occ:1.00
 O K:ASP168 2.3 52.6 1.0
O K:ALA165 2.4 60.6 1.0
O W:ASP204 2.5 88.0 1.0
O K:SER171 3.0 63.8 1.0
C W:ASP204 3.2 84.9 1.0
C K:ASP168 3.2 57.8 1.0
O K:HIS166 3.4 58.3 1.0
CA W:ASP204 3.5 77.3 1.0
CA K:ALA169 3.6 60.7 1.0
C K:ALA165 3.6 61.9 1.0
N K:ALA169 3.7 60.3 1.0
O K:ALA169 3.8 58.6 1.0
C K:ALA169 3.9 59.7 1.0
CB W:ASP204 3.9 76.2 1.0
C K:HIS166 4.0 61.5 1.0
NH1 K:ARG19 4.1 69.0 1.0
OXT W:ASP204 4.1 91.0 1.0
C K:SER171 4.2 60.6 1.0
N K:ASP168 4.3 59.1 1.0
CA K:ASP168 4.4 58.5 1.0
N K:HIS166 4.5 60.3 1.0
CA K:HIS166 4.5 62.4 1.0
CA K:ALA165 4.5 61.9 1.0
C K:ARG167 4.6 61.7 1.0
N K:SER171 4.6 57.9 1.0
O K:ALA164 4.7 61.3 1.0
N K:ARG167 4.8 61.7 1.0
N K:TYR170 4.8 59.6 1.0
O K:ARG167 4.8 59.9 1.0
CZ K:ARG19 4.9 67.8 1.0
N W:ASP204 4.9 75.0 1.0
CB K:ALA169 5.0 60.1 1.0
CA K:SER171 5.0 57.2 1.0
CG W:ASP204 5.0 74.6 1.0

Magnesium binding site 5 out of 8 in 6hv5

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 4


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:79.3
occ:1.00
 OXT L:ASP222 2.0 94.3 1.0
O V:ASP166 2.2 60.7 1.0
O V:ILE163 2.3 63.5 1.0
O V:SER169 2.8 63.3 1.0
C L:ASP222 3.0 87.1 1.0
C V:ASP166 3.1 63.1 1.0
C V:ILE163 3.4 67.7 1.0
CA L:ASP222 3.6 83.8 1.0
O V:TRP164 3.6 69.1 1.0
N V:LEU167 3.8 63.1 1.0
CA V:LEU167 3.8 63.6 1.0
O L:ASP222 3.8 92.2 1.0
C V:TRP164 3.9 70.0 1.0
N V:ASP166 4.0 63.6 1.0
C V:SER169 4.0 64.3 1.0
NH1 V:ARG19 4.1 73.8 1.0
CA V:ASP166 4.1 63.4 1.0
O V:GLY162 4.2 62.7 1.0
N V:TRP164 4.3 68.7 1.0
CB L:ASP222 4.3 80.8 1.0
CA V:TRP164 4.3 69.3 1.0
CA V:ILE163 4.4 67.7 1.0
C V:LEU167 4.4 61.8 1.0
O V:LEU167 4.5 59.1 1.0
N V:ASN165 4.6 67.8 1.0
C V:ASN165 4.6 65.3 1.0
O L:ARG221 4.7 79.3 1.0
N V:SER169 4.7 62.3 1.0
CA V:GLY170 4.8 66.8 1.0
CD2 V:LEU167 4.8 63.2 1.0
N V:GLY170 4.8 64.9 1.0
CA V:SER169 4.9 63.7 1.0
N L:ASP222 4.9 82.1 1.0
CB V:ASP166 5.0 64.1 1.0

Magnesium binding site 6 out of 8 in 6hv5

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 4


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

b:59.1
occ:1.00
 O N:ILE163 2.6 58.6 1.0
O N:SER169 2.9 60.7 1.0
O N:ASP166 3.3 62.4 1.0
CD1 a:LEU34 3.5 65.0 1.0
NH1 N:ARG19 3.6 62.8 1.0
C N:ILE163 3.7 60.6 1.0
CG2 N:ILE163 3.9 62.6 1.0
C N:SER169 4.1 59.0 1.0
CZ N:ARG19 4.3 61.0 1.0
C N:ASP166 4.3 59.4 1.0
NH2 N:ARG19 4.4 62.8 1.0
CA N:GLY170 4.4 61.1 1.0
CA N:ILE163 4.5 60.8 1.0
CA N:GLY167 4.5 57.2 1.0
N N:GLY170 4.7 59.9 1.0
N N:LYS164 4.7 62.6 1.0
CB N:ILE163 4.8 62.1 1.0
O N:GLY167 4.8 54.9 1.0
O N:LYS164 4.8 64.7 1.0
CG a:LEU34 4.8 64.6 1.0
N N:GLY167 4.8 58.0 1.0
CA N:LYS164 4.9 63.6 1.0
C N:LYS164 4.9 63.4 1.0
C N:GLY167 4.9 55.5 1.0

Magnesium binding site 7 out of 8 in 6hv5

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Human BETA2I (1-53) in Complex with 4


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

b:81.1
occ:1.00
 O W:ASP177 2.5 59.5 1.0
O W:SER180 3.1 64.8 1.0
O W:ALA174 3.4 54.4 1.0
OXT W:ASP204 3.4 91.0 1.0
C W:ASP177 3.6 62.3 1.0
O W:ASP204 3.7 88.0 1.0
NH1 K:ARG19 3.8 69.0 1.0
O W:ALA178 3.9 65.6 1.0
CA W:ALA178 3.9 62.9 1.0
C W:ASP204 4.0 84.9 1.0
NH2 K:ARG19 4.1 71.3 1.0
C W:ALA178 4.1 62.2 1.0
N W:ALA178 4.2 61.5 1.0
C W:SER180 4.4 63.3 1.0
CZ K:ARG19 4.4 67.8 1.0
C W:ALA174 4.5 62.4 1.0
CA W:ASP175 4.6 68.7 1.0
O W:ASP175 4.6 65.5 1.0
N W:ASP177 4.6 64.4 1.0
C W:ASP175 4.7 66.0 1.0
CA W:ASP177 4.7 63.5 1.0
N W:SER180 4.9 60.7 1.0
CG2 K:VAL26 4.9 64.6 1.0

Magnesium binding site 8 out of 8 in 6hv5

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


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

b:83.5
occ:1.00
 O Z:VAL198 2.7 62.7 1.0
O Z:THR192 3.0 67.4 1.0
O Z:HIS195 3.0 61.3 1.0
O Z:ASP222 3.2 92.0 1.0
NH2 Z:ARG28 3.5 71.7 1.0
O Z:ILE196 3.6 67.9 1.0
CA Z:ILE196 3.8 63.2 1.0
C Z:ILE196 3.9 64.0 1.0
C Z:VAL198 3.9 65.3 1.0
C Z:HIS195 4.0 63.1 1.0
CG2 Z:THR192 4.0 72.2 1.0
C Z:THR192 4.0 68.6 1.0
NH2 H:ARG19 4.1 73.1 1.0
OD1 Z:ASP222 4.2 79.0 1.0
C Z:ASP222 4.2 87.7 1.0
N Z:ILE196 4.4 61.9 1.0
CA Z:THR192 4.5 70.4 1.0
CZ Z:ARG28 4.6 70.1 1.0
N Z:VAL198 4.6 62.1 1.0
OXT Z:ASP222 4.7 90.2 1.0
NH1 H:ARG19 4.7 74.6 1.0
NH1 Z:ARG28 4.8 73.0 1.0
CA Z:GLY199 4.8 69.4 1.0
N Z:GLY199 4.8 66.9 1.0
CZ H:ARG19 4.8 73.1 1.0
CA Z:VAL198 4.9 63.4 1.0
CB Z:THR192 4.9 71.0 1.0
N Z:GLN197 4.9 61.3 1.0
O Z:LYS220 5.0 74.1 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: Tue Oct 1 02:22:22 2024

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