Magnesium in PDB 8bw1: Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL)

Enzymatic activity of Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL)

All present enzymatic activity of Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL):
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL), PDB code: 8bw1 was solved by K.A.J.Bozhueyuek, L.Praeve, C.Kegler, S.Kaiser, Y.Shi, W.Kuttenlochner, L.Schenk, M.Groll, G.K.A.Hochberg, H.B.Bode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.97, 300.87, 143.98, 90, 112.78, 90
R / Rfree (%) 17.5 / 21.2

Other elements in 8bw1:

The structure of Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL) (pdb code 8bw1). 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 in Complex with An Engineered Fellutamide Derivative (C14QAL), PDB code: 8bw1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8bw1

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL)


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 in Complex with An Engineered Fellutamide Derivative (C14QAL) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:77.7
occ:1.00
 O G:MET125 2.4 85.0 1.0
OG1 G:THR8 2.7 83.2 1.0
O G:ALA123 3.0 85.8 1.0
O G:ARG122 3.1 84.4 1.0
CG2 G:THR8 3.2 85.5 1.0
O G:TYR119 3.3 69.4 1.0
CB G:THR8 3.5 83.9 1.0
C G:MET125 3.5 86.8 1.0
C G:ALA123 3.5 87.8 1.0
CA G:ALA123 3.6 86.2 1.0
N G:THR8 3.7 86.0 1.0
C G:ARG122 4.0 86.0 1.0
CA G:ARG126 4.1 81.0 1.0
N G:ARG126 4.1 83.1 1.0
CA G:THR8 4.2 84.8 1.0
N G:ALA123 4.3 85.3 1.0
N G:MET125 4.4 92.3 1.0
CD G:PRO127 4.5 79.6 1.0
N G:TYR124 4.6 90.9 1.0
CA G:MET125 4.6 94.1 1.0
C G:TYR119 4.6 72.3 1.0
C G:ILE7 4.7 89.3 1.0
CA G:ILE7 4.8 90.7 1.0
C G:ARG126 4.9 79.6 1.0
CB G:ALA123 4.9 86.2 1.0
C G:TYR124 4.9 90.6 1.0

Magnesium binding site 2 out of 8 in 8bw1

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL)


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 in Complex with An Engineered Fellutamide Derivative (C14QAL) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:89.1
occ:1.00
 O I:ASP177 2.5 78.3 1.0
O I:ALA174 2.9 84.6 1.0
O I:SER180 2.9 83.9 1.0
OXT I:ASP204 3.6 108.9 1.0
C I:ASP177 3.7 82.4 1.0
C I:ALA174 3.9 85.9 1.0
C I:SER180 4.1 83.4 1.0
CA I:ASP175 4.1 90.8 1.0
NH2 Y:ARG19 4.2 98.3 1.0
O I:ASP204 4.3 105.5 1.0
C I:ASP204 4.4 104.5 1.0
C I:ASP175 4.4 87.9 1.0
O I:ALA178 4.4 86.5 1.0
CA I:ALA178 4.4 84.0 1.0
N I:ALA178 4.4 81.8 1.0
O I:ASP175 4.4 87.6 1.0
N I:ASP175 4.5 86.4 1.0
N I:ASP177 4.5 85.0 1.0
C I:ALA178 4.5 84.2 1.0
CA I:ASP177 4.7 84.7 1.0
NH1 Y:ARG19 4.8 98.8 1.0
CZ Y:ARG19 4.8 97.7 1.0
N I:SER180 4.8 80.0 1.0
CA I:GLY181 4.9 88.5 1.0
N I:GLY181 4.9 85.8 1.0
OD1 I:ASP175 4.9 104.7 1.0

Magnesium binding site 3 out of 8 in 8bw1

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL)


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 in Complex with An Engineered Fellutamide Derivative (C14QAL) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:44.6
occ:1.00
 OE1 J:GLN118 3.4 77.9 1.0
O J:THR124 3.7 72.2 1.0
OD2 J:ASP120 3.8 88.5 1.0
CB J:ASP120 3.9 80.5 1.0
CG J:ASP120 4.0 83.7 1.0
CG2 J:THR124 4.2 74.6 1.0
CB J:THR124 4.2 73.9 1.0
CD J:GLN118 4.3 76.1 1.0
N J:ASP120 4.3 75.4 1.0
CG J:GLN118 4.5 75.8 1.0
CE1 J:HIS133 4.6 78.6 1.0
CG1 I:VAL35 4.6 87.5 1.0
O J:GLN118 4.6 75.5 1.0
OD1 J:ASP120 4.7 87.5 1.0
C J:THR124 4.7 72.2 1.0
CA J:ASP120 4.7 76.8 1.0
CD2 I:LEU28 4.8 83.0 1.0
OG I:SER30 4.8 89.9 1.0
C J:ILE119 5.0 74.5 1.0

Magnesium binding site 4 out of 8 in 8bw1

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL)


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 in Complex with An Engineered Fellutamide Derivative (C14QAL) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:95.2
occ:1.00
 O K:ALA165 2.2 81.5 1.0
O K:ASP168 2.3 79.3 1.0
O W:ASP204 2.5 108.7 1.0
O K:SER171 2.7 83.9 1.0
C W:ASP204 3.2 106.0 1.0
C K:ASP168 3.3 80.5 1.0
C K:ALA165 3.4 82.2 1.0
CA W:ASP204 3.5 100.9 1.0
O K:HIS166 3.6 84.0 1.0
NH1 K:ARG19 3.6 106.1 1.0
CA K:ALA169 3.7 83.9 1.0
N K:ALA169 3.8 81.9 1.0
CB W:ASP204 3.9 99.6 1.0
C K:ALA169 4.0 84.9 1.0
C K:SER171 4.0 82.5 1.0
O K:ALA169 4.0 86.5 1.0
C K:HIS166 4.0 82.6 1.0
OXT W:ASP204 4.2 114.4 1.0
CA K:ALA165 4.3 82.7 1.0
N K:HIS166 4.3 82.1 1.0
N K:ASP168 4.4 79.7 1.0
CA K:ASP168 4.5 80.7 1.0
N K:SER171 4.5 81.5 1.0
O K:ALA164 4.5 86.8 1.0
CA K:HIS166 4.5 84.6 1.0
C K:ARG167 4.5 78.7 1.0
N K:ARG167 4.7 81.0 1.0
O K:ARG167 4.7 73.7 1.0
CZ K:ARG19 4.7 103.5 1.0
N K:TYR170 4.7 82.7 1.0
CA K:SER171 4.8 80.8 1.0
N K:GLY172 4.9 81.8 1.0
N W:ASP204 4.9 97.4 1.0
CB K:ALA169 5.0 85.1 1.0

Magnesium binding site 5 out of 8 in 8bw1

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL)


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 in Complex with An Engineered Fellutamide Derivative (C14QAL) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:78.7
occ:1.00
 O N:ILE163 2.6 72.8 1.0
O N:SER169 2.7 77.7 1.0
O N:ASP166 3.2 68.8 1.0
NH1 N:ARG19 3.4 81.5 1.0
CD1 a:LEU34 3.7 87.8 1.0
C N:ILE163 3.8 74.4 1.0
C N:SER169 3.8 75.2 1.0
CG2 N:ILE163 4.0 76.5 1.0
CZ N:ARG19 4.1 80.3 1.0
CA N:GLY170 4.2 77.1 1.0
NH2 N:ARG19 4.3 83.6 1.0
C N:ASP166 4.3 71.2 1.0
N N:GLY170 4.5 75.9 1.0
CA N:ILE163 4.5 74.8 1.0
O N:GLY167 4.6 74.3 1.0
CA N:GLY167 4.7 73.0 1.0
N N:LYS164 4.7 75.0 1.0
O N:LYS164 4.8 76.4 1.0
C N:GLY167 4.9 73.3 1.0
CB N:ILE163 4.9 75.5 1.0
C N:LYS164 4.9 76.5 1.0
N N:GLY167 4.9 71.3 1.0
CA N:LYS164 4.9 76.1 1.0
CA N:SER169 5.0 73.5 1.0

Magnesium binding site 6 out of 8 in 8bw1

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL)


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 in Complex with An Engineered Fellutamide Derivative (C14QAL) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:111.7
occ:1.00
 OXT L:ASP222 2.2 115.6 1.0
O V:ASP166 2.3 79.6 1.0
O V:ILE163 2.3 81.8 1.0
C L:ASP222 3.0 111.3 1.0
C V:ASP166 3.1 80.9 1.0
O V:TRP164 3.1 84.1 1.0
O V:SER169 3.4 83.6 1.0
C V:ILE163 3.4 83.9 1.0
C V:TRP164 3.5 84.8 1.0
CA L:ASP222 3.6 109.8 1.0
O L:ASP222 3.7 115.2 1.0
N V:LEU167 3.8 80.5 1.0
N V:ASP166 3.8 81.0 1.0
CA V:LEU167 3.9 81.7 1.0
CA V:TRP164 4.0 84.7 1.0
N V:TRP164 4.0 84.6 1.0
CA V:ASP166 4.1 81.2 1.0
O V:GLY162 4.2 81.6 1.0
N V:ASN165 4.2 82.7 1.0
NH1 V:ARG19 4.5 99.0 1.0
C V:LEU167 4.5 83.1 1.0
O L:ARG221 4.5 100.8 1.0
C V:ASN165 4.5 82.6 1.0
CB L:ASP222 4.5 108.5 1.0
CA V:ILE163 4.5 85.0 1.0
C V:SER169 4.5 86.4 1.0
O V:LEU167 4.5 84.7 1.0
CD2 V:LEU167 4.6 78.7 1.0
N L:ASP222 4.8 106.5 1.0
CD1 L:ILE35 4.8 86.3 1.0
CA V:ASN165 4.8 82.2 1.0

Magnesium binding site 7 out of 8 in 8bw1

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL)


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 in Complex with An Engineered Fellutamide Derivative (C14QAL) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:82.6
occ:1.00
 O Y:ASP168 2.4 82.8 1.0
O I:ASP204 2.4 105.5 1.0
O Y:ALA165 2.4 81.7 1.0
O Y:SER171 2.8 88.3 1.0
C I:ASP204 3.1 104.5 1.0
C Y:ASP168 3.3 82.7 1.0
NH1 Y:ARG19 3.5 98.8 1.0
CA I:ASP204 3.5 103.4 1.0
CA Y:ALA169 3.5 80.2 1.0
C Y:ALA165 3.6 80.3 1.0
O Y:HIS166 3.7 79.1 1.0
N Y:ALA169 3.8 81.7 1.0
C Y:ALA169 3.8 78.9 1.0
O Y:ALA169 3.9 75.8 1.0
CB I:ASP204 3.9 106.0 1.0
C Y:SER171 4.0 87.0 1.0
OXT I:ASP204 4.1 108.9 1.0
C Y:HIS166 4.2 81.0 1.0
CA Y:ALA165 4.5 81.2 1.0
N Y:SER171 4.5 81.7 1.0
N Y:ASP168 4.5 86.3 1.0
CA Y:ASP168 4.5 84.2 1.0
N Y:HIS166 4.6 81.0 1.0
CZ Y:ARG19 4.6 97.7 1.0
C Y:ARG167 4.6 85.1 1.0
N Y:TYR170 4.7 78.8 1.0
CA Y:HIS166 4.7 81.8 1.0
O Y:ALA164 4.7 81.0 1.0
O Y:ARG167 4.7 81.2 1.0
CB Y:ALA169 4.8 80.3 1.0
CA Y:SER171 4.8 83.9 1.0
N Y:ARG167 4.8 83.4 1.0
N I:ASP204 4.9 99.8 1.0

Magnesium binding site 8 out of 8 in 8bw1

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with An Engineered Fellutamide Derivative (C14QAL)


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 in Complex with An Engineered Fellutamide Derivative (C14QAL) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:83.8
occ:1.00
 O Z:VAL198 2.7 83.9 1.0
O Z:THR192 2.9 90.8 1.0
O Z:ASP222 3.3 119.6 1.0
O Z:HIS195 3.3 83.0 1.0
NH2 Z:ARG28 3.5 100.1 1.0
CG2 Z:THR192 3.8 90.2 1.0
O Z:ILE196 3.9 88.8 1.0
OD1 Z:ASP222 4.0 111.3 1.0
C Z:VAL198 4.0 86.1 1.0
C Z:THR192 4.0 90.6 1.0
NH2 H:ARG19 4.1 106.0 1.0
CA Z:ILE196 4.1 88.6 1.0
C Z:ASP222 4.2 119.5 1.0
C Z:ILE196 4.2 88.5 1.0
C Z:HIS195 4.3 85.7 1.0
CA Z:THR192 4.4 90.0 1.0
CZ Z:ARG28 4.4 97.1 1.0
NH1 Z:ARG28 4.5 99.4 1.0
OXT Z:ASP222 4.6 121.0 1.0
N Z:ILE196 4.7 86.8 1.0
CA Z:GLY199 4.7 86.7 1.0
CB Z:THR192 4.7 89.7 1.0
O Z:LYS220 4.7 108.0 1.0
CG Z:ASP222 4.8 116.3 1.0
N Z:GLY199 4.8 84.6 1.0
N Z:VAL198 4.8 86.7 1.0
NH1 H:ARG19 4.9 106.8 1.0
CZ H:ARG19 4.9 104.8 1.0
CA Z:VAL198 5.0 85.0 1.0

Reference:

K.A.J.Bozhueyuek, L.Praeve, C.Kegler, S.Kaiser, Y.Shi, W.Kuttenlochner, L.Schenk, M.Groll, G.K.A.Hochberg, H.B.Bode. Evolutionary Inspired Engineering of Megasynthetases To Be Published.
Page generated: Thu Oct 3 19:53:15 2024

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