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Magnesium in PDB 6htd: Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 4

Enzymatic activity of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 4

All present enzymatic activity of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 4:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 4, PDB code: 6htd 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 (°) 134.270, 299.920, 144.210, 90.00, 112.68, 90.00
R / Rfree (%) 17.4 / 20.1

Other elements in 6htd:

The structure of Yeast 20S Proteasome with Human BETA2C (S171G) 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 BETA2C (S171G) in Complex with 4 (pdb code 6htd). 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 BETA2C (S171G) in Complex with 4, PDB code: 6htd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6htd

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) 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 BETA2C (S171G) in Complex with 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:51.1
occ:1.00
 O G:MET125 2.2 60.4 1.0
OG1 G:THR8 2.6 54.8 1.0
O G:ARG122 2.7 56.2 1.0
O G:TYR119 2.8 50.7 1.0
CG2 G:THR8 3.2 56.2 1.0
C G:MET125 3.4 58.2 1.0
O G:ALA123 3.4 64.2 1.0
CB G:THR8 3.4 55.6 1.0
C G:ALA123 3.7 61.9 1.0
C G:ARG122 3.7 58.8 1.0
CA G:ALA123 3.7 59.7 1.0
C G:TYR119 4.0 51.1 1.0
N G:THR8 4.1 61.1 1.0
N G:ALA123 4.2 58.9 1.0
N G:ARG126 4.2 53.7 1.0
CA G:ARG126 4.2 52.9 1.0
N G:MET125 4.2 59.6 1.0
CA G:MET125 4.4 62.2 1.0
CA G:THR8 4.4 58.7 1.0
CD G:PRO127 4.5 51.2 1.0
N G:TYR124 4.6 62.8 1.0
CA G:TYR119 4.7 49.4 1.0
C G:ARG126 4.8 52.6 1.0
CB G:MET125 4.9 67.1 1.0
C G:TYR124 4.9 59.0 1.0
CA G:ARG122 5.0 60.4 1.0
N G:THR120 5.0 51.1 1.0
N G:PRO127 5.0 51.5 1.0

Magnesium binding site 2 out of 8 in 6htd

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) 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 BETA2C (S171G) in Complex with 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:73.5
occ:1.00
 O I:ALA174 3.0 58.4 1.0
O I:ASP177 3.1 52.6 1.0
O I:SER180 3.1 64.0 1.0
OXT I:ASP204 3.3 85.8 1.0
CA I:ASP175 3.8 61.0 1.0
C I:ALA174 3.9 59.3 1.0
OD1 I:ASP175 4.2 68.2 1.0
C I:ASP204 4.2 76.0 1.0
O I:ASP175 4.2 62.5 1.0
C I:ASP175 4.2 60.4 1.0
C I:ASP177 4.3 54.7 1.0
N I:ASP175 4.3 60.3 1.0
NH2 Y:ARG19 4.3 75.7 1.0
C I:SER180 4.3 60.9 1.0
O I:ASP204 4.4 71.2 1.0
OD1 I:ASP204 4.7 71.2 1.0
NH1 Y:ARG19 4.7 74.7 1.0
O I:ALA178 4.8 58.6 1.0
CA I:GLY181 4.8 61.7 1.0
CB I:ASP175 4.8 62.2 1.0
N I:ASP177 4.8 56.9 1.0
CZ Y:ARG19 4.9 71.1 1.0
CG I:ASP175 5.0 64.3 1.0

Magnesium binding site 3 out of 8 in 6htd

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) 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 BETA2C (S171G) in Complex with 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:71.8
occ:1.00
 O K:ASP168 2.1 49.6 1.0
O W:ASP204 2.4 76.8 1.0
O K:ALA165 2.4 55.6 1.0
O K:SER171 2.9 52.5 1.0
C K:ASP168 3.1 53.1 1.0
C W:ASP204 3.2 73.7 1.0
C K:ALA165 3.5 54.8 1.0
O K:HIS166 3.5 50.4 1.0
CA W:ASP204 3.6 68.1 1.0
CA K:ALA169 3.6 57.0 1.0
N K:ALA169 3.7 56.4 1.0
O K:ALA169 3.9 54.6 1.0
C K:ALA169 3.9 55.8 1.0
CB W:ASP204 3.9 67.4 1.0
NH1 K:ARG19 3.9 70.3 1.0
C K:HIS166 4.0 52.6 1.0
C K:SER171 4.1 54.0 1.0
OXT W:ASP204 4.2 82.5 1.0
N K:ASP168 4.3 52.5 1.0
CA K:ASP168 4.3 52.8 1.0
N K:HIS166 4.4 53.8 1.0
CA K:ALA165 4.4 53.0 1.0
CA K:HIS166 4.5 54.3 1.0
O K:ALA164 4.5 50.3 1.0
N K:SER171 4.5 54.2 1.0
C K:ARG167 4.6 54.3 1.0
N K:TYR170 4.7 55.2 1.0
N K:ARG167 4.7 52.3 1.0
CZ K:ARG19 4.8 68.4 1.0
O K:ARG167 4.8 56.8 1.0
CA K:SER171 4.8 52.5 1.0
CB K:ALA169 5.0 57.5 1.0
N W:ASP204 5.0 65.4 1.0
CG W:ASP204 5.0 65.7 1.0

Magnesium binding site 4 out of 8 in 6htd

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) 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 BETA2C (S171G) in Complex with 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:53.7
occ:1.00
 O N:ILE163 2.8 47.7 1.0
O N:SER169 2.9 51.3 1.0
O N:ASP166 3.1 47.8 1.0
CD1 a:LEU34 3.4 64.0 1.0
NH1 N:ARG19 3.5 55.0 1.0
C N:ILE163 3.9 49.2 1.0
CG2 N:ILE163 4.0 50.1 1.0
C N:SER169 4.0 50.6 1.0
C N:ASP166 4.1 47.5 1.0
CZ N:ARG19 4.2 53.8 1.0
CA N:GLY167 4.2 47.9 1.0
NH2 N:ARG19 4.3 56.2 1.0
CA N:GLY170 4.4 54.7 1.0
O N:GLY167 4.5 47.2 1.0
CA N:ILE163 4.6 49.1 1.0
N N:GLY167 4.6 47.9 1.0
C N:GLY167 4.7 47.1 1.0
N N:GLY170 4.7 52.9 1.0
CG a:LEU34 4.7 63.2 1.0
N N:LYS164 4.8 50.7 1.0
O N:LYS164 4.9 56.3 1.0
CB N:ILE163 4.9 48.9 1.0
C N:LYS164 5.0 53.7 1.0

Magnesium binding site 5 out of 8 in 6htd

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) 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 BETA2C (S171G) in Complex with 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:71.9
occ:1.00
 OXT L:ASP222 2.2 79.1 1.0
O V:ILE163 2.4 54.5 1.0
O V:ASP166 2.5 55.8 1.0
C L:ASP222 2.9 79.2 1.0
O V:PHE164 2.9 65.1 1.0
C V:ASP166 3.2 59.2 1.0
C V:PHE164 3.4 65.1 1.0
CA L:ASP222 3.4 75.2 1.0
C V:ILE163 3.5 59.9 1.0
O V:SER169 3.6 58.4 1.0
O L:ASP222 3.7 82.0 1.0
N V:LEU167 3.8 58.7 1.0
CA V:LEU167 3.8 58.6 1.0
CA V:PHE164 3.8 64.9 1.0
N V:ASP166 3.9 59.5 1.0
N V:PHE164 4.1 61.3 1.0
CA V:ASP166 4.2 59.0 1.0
CB L:ASP222 4.2 75.3 1.0
N V:ASN165 4.2 63.6 1.0
O L:ARG221 4.2 70.0 1.0
CD2 V:LEU167 4.3 57.8 1.0
C V:ASN165 4.3 62.1 1.0
O V:GLY162 4.4 60.1 1.0
C V:LEU167 4.5 58.3 1.0
NH1 V:ARG19 4.6 68.9 1.0
N L:ASP222 4.6 73.2 1.0
CD1 L:ILE35 4.6 59.2 1.0
CA V:ASN165 4.7 62.5 1.0
CA V:ILE163 4.7 60.4 1.0
C V:SER169 4.7 58.5 1.0
O V:LEU167 4.8 58.5 1.0
C L:ARG221 4.9 72.3 1.0
O V:ASN165 4.9 63.0 1.0
CB V:LEU167 4.9 56.7 1.0

Magnesium binding site 6 out of 8 in 6htd

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) 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 BETA2C (S171G) in Complex with 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:80.5
occ:1.00
 O W:ASP177 2.8 54.8 1.0
O W:ALA174 3.0 49.3 1.0
O W:SER180 3.1 58.1 1.0
OXT W:ASP204 3.5 82.5 1.0
C W:ASP177 3.9 54.1 1.0
CA W:ASP175 3.9 60.2 1.0
C W:ALA174 4.0 53.9 1.0
O W:ASP175 4.2 63.7 1.0
NH2 K:ARG19 4.2 72.8 1.0
C W:ASP175 4.2 60.4 1.0
C W:SER180 4.3 58.5 1.0
C W:ASP204 4.3 73.7 1.0
O W:ASP204 4.3 76.8 1.0
N W:ASP175 4.4 57.1 1.0
O W:ALA178 4.4 57.5 1.0
NH1 K:ARG19 4.5 70.3 1.0
OD1 W:ASP175 4.6 64.6 1.0
CA W:ALA178 4.6 54.0 1.0
N W:ASP177 4.6 55.9 1.0
N W:ALA178 4.7 53.3 1.0
C W:ALA178 4.7 55.0 1.0
CZ K:ARG19 4.7 68.4 1.0
CA W:ASP177 4.9 54.3 1.0
OD1 W:ASP204 4.9 64.9 1.0

Magnesium binding site 7 out of 8 in 6htd

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) 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 BETA2C (S171G) in Complex with 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:83.2
occ:1.00
 O I:ASP204 2.7 71.2 1.0
O Y:ASP168 2.9 53.4 1.0
O Y:HIS166 2.9 51.7 1.0
C I:ASP204 3.2 76.0 1.0
C Y:ASP168 3.4 56.5 1.0
CA Y:ALA169 3.4 58.4 1.0
O Y:ALA165 3.5 55.9 1.0
N Y:ALA169 3.6 58.9 1.0
OXT I:ASP204 3.8 85.8 1.0
C Y:HIS166 3.8 54.3 1.0
CA I:ASP204 3.9 73.7 1.0
O Y:ARG167 4.1 59.3 1.0
C Y:ARG167 4.2 60.2 1.0
NE1 I:TRP182 4.2 68.2 1.0
C Y:ALA169 4.2 56.9 1.0
O Y:ALA169 4.3 59.8 1.0
N Y:ASP168 4.4 59.3 1.0
CB Y:ALA169 4.4 59.2 1.0
O Y:SER171 4.5 59.4 1.0
CA Y:ASP168 4.5 56.4 1.0
C Y:ALA165 4.5 56.1 1.0
N Y:ARG167 4.6 54.2 1.0
CA Y:HIS166 4.6 56.7 1.0
NH1 Y:ARG19 4.7 74.7 1.0
CB I:ASP204 4.7 73.4 1.0
CA Y:ARG167 4.8 57.2 1.0
CD1 I:TRP182 4.8 66.2 1.0
O I:ALA178 4.8 58.6 1.0
CE2 I:TRP182 4.9 66.8 1.0

Magnesium binding site 8 out of 8 in 6htd

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) 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 BETA2C (S171G) in Complex with 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:65.9
occ:1.00
 O Z:VAL198 2.5 58.1 1.0
O Z:THR192 3.0 62.5 1.0
O Z:ASP222 3.1 75.8 1.0
O Z:HIS195 3.2 54.3 1.0
NH2 Z:ARG28 3.5 65.3 1.0
O Z:ILE196 3.7 60.6 1.0
C Z:VAL198 3.7 59.9 1.0
CG2 Z:THR192 4.0 67.8 1.0
C Z:THR192 4.1 65.6 1.0
C Z:ILE196 4.1 56.2 1.0
CA Z:ILE196 4.1 54.8 1.0
OD1 Z:ASP222 4.2 79.0 1.0
NH2 H:ARG19 4.2 74.1 1.0
C Z:ASP222 4.2 77.9 1.0
C Z:HIS195 4.3 54.5 1.0
O Z:LYS220 4.4 69.3 1.0
CA Z:THR192 4.5 65.5 1.0
CZ Z:ARG28 4.5 62.4 1.0
CE Z:LYS220 4.5 76.8 1.0
CA Z:GLY199 4.5 63.5 1.0
NH1 Z:ARG28 4.6 63.4 1.0
N Z:VAL198 4.6 56.3 1.0
N Z:GLY199 4.6 61.5 1.0
NH1 H:ARG19 4.6 76.2 1.0
N Z:ILE196 4.7 53.7 1.0
CA Z:VAL198 4.7 57.9 1.0
OXT Z:ASP222 4.7 74.5 1.0
CZ H:ARG19 4.8 72.1 1.0
CB Z:THR192 4.9 65.5 1.0
NZ Z:LYS220 4.9 77.8 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 02:13:45 2024

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