Magnesium in PDB 6htb: Yeast 20S Proteasome with Human BETA2C (S171G)

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA2C (S171G), PDB code: 6htb 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.680, 300.580, 145.050, 90.00, 113.06, 90.00
R / Rfree (%) 19.3 / 22

Other elements in 6htb:

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

Magnesium binding site 1 out of 8 in 6htb

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


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

b:58.3
occ:1.00
 O G:MET125 2.2 49.3 1.0
OG1 G:THR8 2.6 43.7 1.0
O G:ARG122 2.6 41.5 1.0
O G:TYR119 2.7 40.9 1.0
CG2 G:THR8 3.2 43.4 1.0
C G:MET125 3.4 47.7 1.0
O G:ALA123 3.4 53.3 1.0
CB G:THR8 3.5 43.1 1.0
C G:ARG122 3.7 44.5 1.0
C G:ALA123 3.7 48.7 1.0
CA G:ALA123 3.7 47.3 1.0
C G:TYR119 3.9 40.5 1.0
CA G:ARG126 4.1 41.8 1.0
N G:ALA123 4.2 45.2 1.0
N G:ARG126 4.2 43.1 1.0
N G:THR8 4.2 46.9 1.0
N G:MET125 4.2 48.0 1.0
CA G:MET125 4.4 50.4 1.0
CD G:PRO127 4.4 40.0 1.0
CA G:THR8 4.5 45.4 1.0
N G:TYR124 4.6 49.6 1.0
CA G:TYR119 4.7 39.5 1.0
C G:ARG126 4.7 40.6 1.0
N G:THR120 4.9 39.9 1.0
CA G:ARG122 4.9 47.9 1.0
N G:PRO127 4.9 39.5 1.0
CB G:MET125 4.9 55.8 1.0
N G:ARG122 5.0 46.0 1.0
C G:TYR124 5.0 46.8 1.0

Magnesium binding site 2 out of 8 in 6htb

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


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

b:69.8
occ:1.00
 O I:SER180 2.7 51.9 1.0
O I:ALA174 3.0 46.0 1.0
O I:ASP177 3.1 45.5 1.0
OXT I:ASP204 3.4 56.9 1.0
C I:ALA174 3.9 44.7 1.0
C I:SER180 3.9 45.6 1.0
CA I:ASP175 4.0 46.5 1.0
OD1 I:ASP175 4.2 44.8 1.0
C I:ASP177 4.3 44.5 1.0
N I:ASP175 4.3 45.5 1.0
C I:ASP204 4.4 51.6 1.0
CA I:GLY181 4.5 44.7 1.0
C I:ASP175 4.5 47.3 1.0
O I:ASP204 4.5 53.1 1.0
O I:ASP175 4.5 51.4 1.0
N I:GLY181 4.6 44.8 1.0
O I:ALA178 4.7 45.2 1.0
NH2 Y:ARG19 4.8 49.3 1.0
NH1 Y:ARG19 4.8 49.0 1.0
N I:SER180 4.9 44.2 1.0
N I:ASP177 4.9 44.6 1.0
CA I:SER180 5.0 45.3 1.0
C I:ALA178 5.0 44.1 1.0

Magnesium binding site 3 out of 8 in 6htb

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


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

b:59.3
occ:1.00
 O Y:ASP168 2.3 42.1 1.0
O I:ASP204 2.4 53.1 1.0
O Y:ALA165 2.4 43.0 1.0
O Y:SER171 2.9 48.3 1.0
C I:ASP204 3.2 51.6 1.0
C Y:ASP168 3.2 40.9 1.0
CA Y:ALA169 3.6 39.4 1.0
C Y:ALA165 3.6 41.4 1.0
CA I:ASP204 3.7 49.7 1.0
O Y:ALA169 3.7 44.0 1.0
N Y:ALA169 3.8 40.5 1.0
NH1 Y:ARG19 3.8 49.0 1.0
C Y:ALA169 3.8 41.9 1.0
O Y:HIS166 3.8 42.8 1.0
CB I:ASP204 4.1 50.5 1.0
OXT I:ASP204 4.1 56.9 1.0
C Y:SER171 4.1 43.2 1.0
C Y:HIS166 4.2 40.4 1.0
N Y:ASP168 4.4 40.3 1.0
CA Y:ASP168 4.4 40.5 1.0
CA Y:ALA165 4.4 41.2 1.0
N Y:SER171 4.5 41.9 1.0
N Y:HIS166 4.5 41.3 1.0
CA Y:HIS166 4.6 39.9 1.0
C Y:ARG167 4.7 41.3 1.0
CZ Y:ARG19 4.7 48.2 1.0
N Y:TYR170 4.7 40.8 1.0
O Y:ALA164 4.7 40.8 1.0
CA Y:SER171 4.8 42.6 1.0
N Y:ARG167 4.8 38.5 1.0
CB Y:ALA169 4.9 38.7 1.0
O Y:ARG167 4.9 44.5 1.0

Magnesium binding site 4 out of 8 in 6htb

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


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

b:57.8
occ:1.00
 O K:ASP168 2.3 40.5 1.0
O K:ALA165 2.3 44.4 1.0
O W:ASP204 2.4 51.1 1.0
O K:SER171 2.7 45.1 1.0
C W:ASP204 3.2 49.8 1.0
C K:ASP168 3.3 40.2 1.0
C K:ALA165 3.5 43.1 1.0
CA W:ASP204 3.7 48.0 1.0
CA K:ALA169 3.7 40.8 1.0
NH1 K:ARG19 3.7 48.8 1.0
O K:ALA169 3.7 38.4 1.0
C K:ALA169 3.8 42.5 1.0
N K:ALA169 3.9 40.3 1.0
C K:SER171 3.9 42.6 1.0
O K:HIS166 3.9 43.4 1.0
CB W:ASP204 3.9 48.4 1.0
OXT W:ASP204 4.1 50.2 1.0
C K:HIS166 4.3 42.5 1.0
CA K:ALA165 4.3 41.8 1.0
N K:SER171 4.4 42.9 1.0
N K:ASP168 4.5 39.4 1.0
CA K:ASP168 4.5 39.3 1.0
N K:HIS166 4.5 41.9 1.0
CZ K:ARG19 4.5 47.9 1.0
CA K:HIS166 4.7 41.0 1.0
O K:ALA164 4.7 40.5 1.0
CA K:SER171 4.7 41.8 1.0
N K:TYR170 4.7 42.4 1.0
C K:ARG167 4.8 41.1 1.0
N K:GLY172 4.9 44.3 1.0
NH2 K:ARG19 4.9 50.3 1.0
N K:ARG167 4.9 40.8 1.0
CA K:GLY172 4.9 45.7 1.0
CG W:ASP204 5.0 47.0 1.0

Magnesium binding site 5 out of 8 in 6htb

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


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

b:72.4
occ:1.00
 O V:ILE163 2.0 45.4 1.0
O V:ASP166 2.1 47.8 1.0
OXT L:ASP222 2.2 60.0 1.0
O V:SER169 2.9 50.5 1.0
C L:ASP222 3.0 59.0 1.0
C V:ASP166 3.1 51.1 1.0
C V:ILE163 3.2 51.5 1.0
O V:PHE164 3.5 58.0 1.0
CA L:ASP222 3.5 60.2 1.0
C V:PHE164 3.7 55.6 1.0
N V:LEU167 3.8 51.7 1.0
CA V:LEU167 3.8 51.2 1.0
O L:ASP222 3.9 52.5 1.0
N V:ASP166 3.9 49.7 1.0
CA V:PHE164 4.0 55.4 1.0
N V:PHE164 4.0 53.2 1.0
C V:SER169 4.0 48.3 1.0
CB L:ASP222 4.1 61.0 1.0
CA V:ASP166 4.1 50.2 1.0
NH1 V:ARG19 4.2 56.6 1.0
O V:GLY162 4.2 47.4 1.0
CA V:ILE163 4.3 50.6 1.0
C V:LEU167 4.3 52.2 1.0
N V:ASN165 4.4 54.6 1.0
O V:LEU167 4.5 51.1 1.0
C V:ASN165 4.6 51.4 1.0
O L:ARG221 4.6 52.4 1.0
CD2 V:LEU167 4.7 50.4 1.0
N V:SER169 4.7 47.9 1.0
N L:ASP222 4.8 58.4 1.0
CA V:SER169 4.9 48.2 1.0
CZ V:ARG19 4.9 55.1 1.0
CB V:ASP166 4.9 49.2 1.0
N V:GLY170 4.9 50.5 1.0
NH2 V:ARG19 5.0 53.6 1.0
CA V:GLY170 5.0 51.9 1.0
CA V:ASN165 5.0 54.7 1.0

Magnesium binding site 6 out of 8 in 6htb

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


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

b:64.7
occ:1.00
 O N:SER169 2.8 45.7 1.0
O N:ILE163 3.0 43.9 1.0
O N:ASP166 3.3 41.2 1.0
NH1 N:ARG19 3.3 45.7 1.0
CD1 a:LEU34 3.5 55.1 1.0
CZ N:ARG19 3.9 45.1 1.0
C N:SER169 4.0 43.6 1.0
C N:ILE163 4.1 43.1 1.0
CG2 N:ILE163 4.1 43.0 1.0
NH2 N:ARG19 4.1 47.0 1.0
CA N:GLY167 4.2 40.6 1.0
C N:ASP166 4.2 40.4 1.0
O N:GLY167 4.3 40.1 1.0
CA N:GLY170 4.4 45.7 1.0
C N:GLY167 4.5 40.1 1.0
N N:GLY167 4.6 40.2 1.0
N N:GLY170 4.7 44.7 1.0
CA N:ILE163 4.7 42.3 1.0
CG a:LEU34 4.8 53.8 1.0
O a:HOH329 4.8 46.6 1.0
NE N:ARG19 4.9 45.5 1.0

Magnesium binding site 7 out of 8 in 6htb

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


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

b:64.3
occ:1.00
 O W:ASP177 2.4 46.6 1.0
O W:SER180 2.7 51.9 1.0
O W:HOH409 2.7 53.0 1.0
O W:ALA174 3.2 41.6 1.0
C W:ASP177 3.5 43.9 1.0
OXT W:ASP204 3.6 50.2 1.0
O W:ALA178 3.7 44.8 1.0
C W:SER180 3.9 46.8 1.0
C W:ALA178 4.0 43.9 1.0
CA W:ALA178 4.0 42.7 1.0
N W:ALA178 4.2 42.9 1.0
NH1 K:ARG19 4.2 48.8 1.0
O W:ASP204 4.3 51.1 1.0
C W:ALA174 4.3 44.5 1.0
N W:SER180 4.4 45.6 1.0
C W:ASP204 4.4 49.8 1.0
CA W:ASP175 4.6 46.2 1.0
N W:ASP177 4.6 43.9 1.0
CA W:ASP177 4.7 43.9 1.0
NH2 K:ARG19 4.7 50.3 1.0
CA W:SER180 4.7 46.4 1.0
O W:ASP175 4.8 48.7 1.0
C W:ASP175 4.8 46.4 1.0
N W:LEU179 4.8 43.8 1.0
CZ K:ARG19 4.8 47.9 1.0
N W:GLY181 4.8 46.7 1.0
N W:ASP175 4.9 46.4 1.0
CA W:GLY181 4.9 46.5 1.0

Magnesium binding site 8 out of 8 in 6htb

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


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

b:70.5
occ:1.00
 O Z:VAL198 2.7 50.0 1.0
O Z:THR192 2.9 50.7 1.0
O Z:HIS195 3.0 42.7 1.0
O Z:ASP222 3.4 55.5 1.0
O Z:ILE196 3.7 51.7 1.0
NH2 Z:ARG28 3.8 53.7 1.0
C Z:VAL198 3.9 49.3 1.0
C Z:THR192 3.9 53.4 1.0
CA Z:ILE196 3.9 43.8 1.0
C Z:HIS195 4.0 44.5 1.0
C Z:ILE196 4.0 45.4 1.0
CG2 Z:THR192 4.1 56.9 1.0
NH2 H:ARG19 4.2 59.6 1.0
OD1 Z:ASP222 4.3 62.5 1.0
CA Z:THR192 4.4 53.2 1.0
C Z:ASP222 4.4 60.9 1.0
N Z:ILE196 4.4 42.9 1.0
N Z:VAL198 4.6 46.2 1.0
CE Z:LYS220 4.6 62.4 1.0
CZ Z:ARG28 4.8 52.2 1.0
OXT Z:ASP222 4.8 53.4 1.0
NH1 H:ARG19 4.8 62.4 1.0
NZ Z:LYS220 4.8 64.2 1.0
CA Z:VAL198 4.8 48.1 1.0
N Z:GLY199 4.8 51.4 1.0
CZ H:ARG19 4.8 59.0 1.0
CA Z:GLY199 4.8 51.2 1.0
NH1 Z:ARG28 4.9 54.7 1.0
CB Z:THR192 4.9 54.3 1.0
O Z:LYS220 5.0 58.5 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 22:51:11 2020

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