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Magnesium in PDB 6htp: Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7

Enzymatic activity of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7

All present enzymatic activity of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7, PDB code: 6htp 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 (°) 133.910, 300.420, 144.040, 90.00, 112.84, 90.00
R / Rfree (%) 17.7 / 20.6

Other elements in 6htp:

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

Magnesium binding site 1 out of 8 in 6htp

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7


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

b:65.8
occ:1.00
 O G:MET125 2.2 68.7 1.0
OG1 G:THR8 2.6 64.8 1.0
O G:ARG122 2.8 68.0 1.0
O G:TYR119 3.0 59.0 1.0
O G:ALA123 3.2 72.2 1.0
CG2 G:THR8 3.2 65.5 1.0
C G:MET125 3.4 67.1 1.0
CB G:THR8 3.5 64.8 1.0
C G:ALA123 3.6 70.7 1.0
CA G:ALA123 3.6 68.7 1.0
C G:ARG122 3.8 68.2 1.0
N G:THR8 3.9 68.8 1.0
CA G:ARG126 4.2 62.2 1.0
N G:ARG126 4.2 62.7 1.0
N G:ALA123 4.2 67.4 1.0
N G:MET125 4.2 69.7 1.0
C G:TYR119 4.3 60.3 1.0
CA G:THR8 4.3 67.6 1.0
CA G:MET125 4.4 71.6 1.0
N G:TYR124 4.5 72.2 1.0
CD G:PRO127 4.5 60.2 1.0
C G:ARG126 4.9 62.0 1.0
C G:TYR124 4.9 68.7 1.0
CB G:ALA123 4.9 69.2 1.0
C G:ILE7 4.9 72.2 1.0

Magnesium binding site 2 out of 8 in 6htp

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7


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

b:89.0
occ:1.00
 O I:ALA174 3.0 66.8 1.0
O I:SER180 3.0 73.1 1.0
O I:ASP177 3.2 63.5 1.0
OXT I:ASP204 3.3 97.3 1.0
CA I:ASP175 3.8 71.7 1.0
C I:ALA174 3.9 69.3 1.0
OD1 I:ASP175 4.0 72.6 1.0
C I:SER180 4.2 70.1 1.0
N I:ASP175 4.2 70.8 1.0
C I:ASP204 4.2 87.5 1.0
C I:ASP175 4.3 71.3 1.0
O I:ASP175 4.3 75.7 1.0
C I:ASP177 4.4 64.5 1.0
NH2 Y:ARG19 4.4 87.5 1.0
O I:ASP204 4.4 87.3 1.0
CA I:GLY181 4.7 72.3 1.0
OD1 I:ASP204 4.7 83.8 1.0
CB I:ASP175 4.8 72.6 1.0
O I:ALA178 4.8 69.3 1.0
CG I:ASP175 4.8 73.8 1.0
N I:GLY181 4.9 70.6 1.0
NH1 Y:ARG19 4.9 89.2 1.0
N I:ASP177 4.9 65.7 1.0

Magnesium binding site 3 out of 8 in 6htp

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7


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

b:0.1
occ:1.00
 O I:ASP204 2.8 87.3 1.0
O Y:HIS166 2.9 65.4 1.0
O Y:ASP168 2.9 66.3 1.0
C I:ASP204 3.4 87.5 1.0
CA Y:ALA169 3.4 71.6 1.0
C Y:ASP168 3.4 70.1 1.0
N Y:ALA169 3.6 72.5 1.0
O Y:ALA165 3.6 68.2 1.0
O Y:ARG167 3.8 68.6 1.0
C Y:HIS166 3.9 66.7 1.0
OXT I:ASP204 3.9 97.3 1.0
C Y:ARG167 4.0 71.0 1.0
CA I:ASP204 4.1 83.7 1.0
NE1 I:TRP182 4.1 78.8 1.0
C Y:ALA169 4.2 69.9 1.0
O Y:ALA169 4.3 71.2 1.0
N Y:ASP168 4.3 71.4 1.0
CB Y:ALA169 4.4 72.6 1.0
CA Y:ASP168 4.5 69.8 1.0
N Y:ARG167 4.6 66.8 1.0
O Y:SER171 4.7 66.2 1.0
CA Y:ARG167 4.7 69.6 1.0
C Y:ALA165 4.7 69.0 1.0
CD1 I:TRP182 4.7 78.0 1.0
CA Y:HIS166 4.7 69.6 1.0
O I:ALA178 4.7 69.3 1.0
CE2 I:TRP182 4.7 76.3 1.0
NE I:ARG27 4.9 65.6 1.0
NH1 Y:ARG19 4.9 89.2 1.0
CB I:ASP204 5.0 83.9 1.0

Magnesium binding site 4 out of 8 in 6htp

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7


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

b:80.1
occ:1.00
 O K:ASP168 2.1 57.2 1.0
O W:ASP204 2.3 92.8 1.0
O K:ALA165 2.4 66.8 1.0
O K:SER171 3.1 65.1 1.0
C K:ASP168 3.1 63.7 1.0
C W:ASP204 3.1 87.0 1.0
O K:HIS166 3.4 63.0 1.0
CA K:ALA169 3.6 69.3 1.0
CA W:ASP204 3.6 79.4 1.0
C K:ALA165 3.6 65.8 1.0
N K:ALA169 3.7 68.0 1.0
C K:ALA169 3.9 68.8 1.0
O K:ALA169 3.9 67.0 1.0
C K:HIS166 3.9 63.2 1.0
CB W:ASP204 4.0 78.6 1.0
NH1 K:ARG19 4.0 82.5 1.0
OXT W:ASP204 4.0 95.4 1.0
N K:ASP168 4.2 64.7 1.0
C K:SER171 4.2 66.8 1.0
CA K:ASP168 4.2 64.2 1.0
C K:ARG167 4.4 66.2 1.0
N K:HIS166 4.4 64.6 1.0
CA K:HIS166 4.4 65.5 1.0
CA K:ALA165 4.5 65.2 1.0
O K:ALA164 4.5 62.9 1.0
O K:ARG167 4.6 67.2 1.0
N K:SER171 4.6 66.2 1.0
N K:ARG167 4.7 61.6 1.0
N K:TYR170 4.7 68.1 1.0
CZ K:ARG19 4.9 81.3 1.0
CB K:ALA169 4.9 70.8 1.0
N W:ASP204 4.9 76.1 1.0
CA K:SER171 5.0 64.3 1.0

Magnesium binding site 5 out of 8 in 6htp

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7


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

b:91.5
occ:1.00
 OXT L:ASP222 2.4 88.7 1.0
O V:PHE164 2.7 78.7 1.0
O V:ASP166 2.7 63.9 1.0
O V:ILE163 2.9 60.0 1.0
C L:ASP222 2.9 90.3 1.0
C V:ASP166 3.2 68.8 1.0
C V:PHE164 3.4 75.3 1.0
O L:ASP222 3.6 91.4 1.0
CA L:ASP222 3.6 85.6 1.0
N V:LEU167 3.6 69.2 1.0
CA V:LEU167 3.7 68.7 1.0
CD2 V:LEU167 3.8 66.6 1.0
C V:ILE163 3.9 68.8 1.0
N V:ASP166 3.9 68.6 1.0
CA V:PHE164 3.9 73.9 1.0
O L:ARG221 4.0 77.2 1.0
CD1 L:ILE35 4.0 70.3 1.0
O V:SER169 4.1 63.5 1.0
N V:ASN165 4.2 72.0 1.0
CA V:ASP166 4.2 68.5 1.0
C V:ASN165 4.2 71.3 1.0
N V:PHE164 4.4 70.8 1.0
CB L:ASP222 4.6 86.3 1.0
CA V:ASN165 4.6 71.3 1.0
NH1 L:ARG28 4.6 76.7 1.0
C V:LEU167 4.6 69.2 1.0
O V:ASN165 4.6 73.6 1.0
N L:ASP222 4.7 82.4 1.0
CB V:LEU167 4.7 66.9 1.0
CG V:LEU167 4.7 66.3 1.0
O V:GLY162 4.7 70.6 1.0
C L:ARG221 4.8 81.5 1.0
O V:LEU167 4.9 68.9 1.0
NH1 V:ARG19 4.9 77.5 1.0
CG1 L:ILE35 5.0 68.6 1.0

Magnesium binding site 6 out of 8 in 6htp

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7


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

b:55.7
occ:1.00
 O N:ILE163 2.7 57.2 1.0
O N:SER169 2.8 63.7 1.0
O N:ASP166 3.1 59.2 1.0
NH1 N:ARG19 3.5 66.7 1.0
CD1 a:LEU34 3.5 74.3 1.0
C N:ILE163 3.8 59.5 1.0
CG2 N:ILE163 3.9 61.1 1.0
C N:SER169 4.0 61.9 1.0
CZ N:ARG19 4.1 65.1 1.0
C N:ASP166 4.2 58.7 1.0
NH2 N:ARG19 4.3 67.8 1.0
CA N:GLY167 4.3 58.8 1.0
CA N:GLY170 4.3 65.8 1.0
CA N:ILE163 4.5 59.6 1.0
O N:GLY167 4.5 57.0 1.0
N N:GLY170 4.6 63.6 1.0
N N:GLY167 4.7 58.6 1.0
C N:GLY167 4.7 57.8 1.0
CG a:LEU34 4.8 73.5 1.0
N N:LYS164 4.8 62.2 1.0
CB N:ILE163 4.9 59.4 1.0
O N:LYS164 4.9 69.2 1.0
C N:LYS164 5.0 65.5 1.0

Magnesium binding site 7 out of 8 in 6htp

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7


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

b:83.9
occ:1.00
 O W:SER180 2.9 75.2 1.0
O W:ALA174 2.9 57.8 1.0
O W:ASP177 2.9 62.8 1.0
OXT W:ASP204 3.4 95.4 1.0
CA W:ASP175 3.8 71.1 1.0
C W:ALA174 3.8 64.0 1.0
C W:SER180 4.1 70.9 1.0
C W:ASP177 4.1 64.4 1.0
OD1 W:ASP175 4.2 75.6 1.0
N W:ASP175 4.2 67.4 1.0
C W:ASP175 4.3 71.0 1.0
C W:ASP204 4.3 87.0 1.0
O W:ASP175 4.3 73.2 1.0
NH2 K:ARG19 4.4 84.1 1.0
O W:ASP204 4.4 92.8 1.0
O W:ALA178 4.6 69.3 1.0
CA W:GLY181 4.7 70.2 1.0
NH1 K:ARG19 4.7 82.5 1.0
N W:ASP177 4.7 66.0 1.0
N W:GLY181 4.8 70.1 1.0
CA W:ALA178 4.9 64.8 1.0
C W:ALA178 4.9 66.5 1.0
N W:ALA178 4.9 63.4 1.0
CB W:ASP175 4.9 75.0 1.0
OD1 W:ASP204 4.9 77.8 1.0
CZ K:ARG19 5.0 81.3 1.0

Magnesium binding site 8 out of 8 in 6htp

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 7


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

b:74.7
occ:1.00
 O Z:VAL198 2.7 68.5 1.0
O Z:THR192 3.1 72.2 1.0
O Z:ASP222 3.1 83.7 1.0
O Z:HIS195 3.3 61.2 1.0
NH2 Z:ARG28 3.6 75.1 1.0
O Z:ILE196 3.7 70.8 1.0
C Z:VAL198 3.9 69.6 1.0
CG2 Z:THR192 4.0 77.5 1.0
NH2 H:ARG19 4.1 84.2 1.0
C Z:THR192 4.1 75.0 1.0
CA Z:ILE196 4.1 64.8 1.0
C Z:ILE196 4.1 66.5 1.0
OD1 Z:ASP222 4.2 90.8 1.0
C Z:ASP222 4.2 88.8 1.0
C Z:HIS195 4.3 63.5 1.0
O Z:LYS220 4.4 79.8 1.0
CE Z:LYS220 4.4 86.5 1.0
CZ Z:ARG28 4.5 72.7 1.0
CA Z:THR192 4.5 75.3 1.0
NH1 Z:ARG28 4.6 74.3 1.0
CA Z:GLY199 4.6 73.2 1.0
NH1 H:ARG19 4.7 87.1 1.0
N Z:VAL198 4.7 66.8 1.0
N Z:GLY199 4.7 70.9 1.0
N Z:ILE196 4.7 62.8 1.0
OXT Z:ASP222 4.8 86.7 1.0
CZ H:ARG19 4.8 82.2 1.0
NZ Z:LYS220 4.8 86.9 1.0
CA Z:VAL198 4.9 67.7 1.0
CB Z:THR192 4.9 75.6 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: Tue Oct 1 02:14:06 2024

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