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Magnesium in PDB 4g4s: Structure of Proteasome-PBA1-PBA2 Complex

Enzymatic activity of Structure of Proteasome-PBA1-PBA2 Complex

All present enzymatic activity of Structure of Proteasome-PBA1-PBA2 Complex:
3.4.25.1;

Protein crystallography data

The structure of Structure of Proteasome-PBA1-PBA2 Complex, PDB code: 4g4s was solved by E.Kish-Trier, H.Robinson, B.M.Stadtmueller, C.P.Hill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.78 / 2.49
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 132.409, 182.513, 388.782, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Proteasome-PBA1-PBA2 Complex (pdb code 4g4s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Proteasome-PBA1-PBA2 Complex, PDB code: 4g4s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4g4s

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Magnesium binding site 1 out of 8 in the Structure of Proteasome-PBA1-PBA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Proteasome-PBA1-PBA2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:21.8
occ:1.00
 O A:MET134 2.2 22.4 1.0
O A:ARG131 2.2 23.9 1.0
O A:HOH459 2.3 16.2 1.0
O A:TYR128 2.4 26.3 1.0
OG1 A:THR17 2.6 23.6 1.0
C A:ARG131 3.3 21.2 1.0
C A:MET134 3.4 19.7 1.0
CG2 A:THR17 3.4 16.8 1.0
C A:TYR128 3.5 19.3 1.0
CB A:THR17 3.6 20.6 1.0
O A:ALA132 3.7 17.4 1.0
C A:ALA132 3.9 25.6 1.0
CA A:ALA132 4.0 24.8 1.0
N A:ALA132 4.1 25.9 1.0
N A:MET134 4.1 26.9 1.0
CA A:MET134 4.2 32.4 1.0
CA A:TYR128 4.2 22.3 1.0
N A:ARG131 4.3 23.1 1.0
N A:THR17 4.3 12.9 1.0
N A:ARG135 4.4 19.2 1.0
CA A:ARG131 4.4 19.4 1.0
N A:THR129 4.5 14.6 1.0
CA A:ARG135 4.5 24.3 1.0
O A:HOH476 4.5 20.4 1.0
CA A:THR129 4.6 23.2 1.0
CA A:THR17 4.6 16.3 1.0
C A:THR129 4.6 21.4 1.0
CB A:MET134 4.6 30.2 1.0
N A:TYR133 4.7 29.1 1.0
N A:GLN130 4.7 16.0 1.0
CD A:PRO136 4.7 19.2 1.0
CB A:TYR128 4.7 16.7 1.0
C A:ARG135 4.9 25.0 1.0
C A:TYR133 5.0 33.9 1.0
O A:HOH429 5.0 26.3 1.0

Magnesium binding site 2 out of 8 in 4g4s

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Magnesium binding site 2 out of 8 in the Structure of Proteasome-PBA1-PBA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Proteasome-PBA1-PBA2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg201

b:20.2
occ:1.00
 O H:ILE163 2.2 8.4 1.0
O H:SER169 2.3 13.8 1.0
O H:HOH367 2.3 15.2 1.0
O H:ASP166 2.4 10.6 1.0
C H:ILE163 3.3 13.0 1.0
C H:SER169 3.3 17.9 1.0
C H:ASP166 3.6 15.2 1.0
CG2 H:ILE163 3.8 8.6 1.0
CA H:ILE163 3.9 10.8 1.0
NH1 H:ARG19 4.0 9.9 1.0
N H:GLY170 4.2 19.6 1.0
CA H:GLY170 4.2 11.1 1.0
CA H:SER169 4.2 13.0 1.0
N H:SER169 4.3 8.5 1.0
CA H:GLY167 4.3 11.3 1.0
N H:GLY167 4.3 14.5 1.0
CB H:ILE163 4.4 10.9 1.0
N H:ASP166 4.4 12.4 1.0
N H:LYS164 4.5 14.7 1.0
CZ H:ARG19 4.5 17.2 1.0
O H:HOH313 4.5 14.7 1.0
CB H:SER169 4.5 9.2 1.0
CA H:ASP166 4.5 12.2 1.0
C H:GLY167 4.5 12.9 1.0
O H:GLY167 4.6 12.3 1.0
C H:LYS164 4.8 18.2 1.0
NH2 H:ARG19 4.8 12.1 1.0
CA H:LYS164 4.9 15.7 1.0
O H:LYS164 4.9 16.8 1.0
O H:ALA162 5.0 11.4 1.0

Magnesium binding site 3 out of 8 in 4g4s

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Magnesium binding site 3 out of 8 in the Structure of Proteasome-PBA1-PBA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Proteasome-PBA1-PBA2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:18.1
occ:1.00
 O I:ASP166 2.3 15.2 1.0
O I:SER169 2.3 11.9 1.0
O I:ILE163 2.4 15.6 1.0
O I:HOH416 2.8 19.0 1.0
C I:ASP166 3.3 19.3 1.0
C I:SER169 3.3 15.4 1.0
C I:ILE163 3.4 16.2 1.0
O I:GLY162 3.7 16.0 1.0
NH1 I:ARG19 3.9 18.5 1.0
CA I:LEU167 4.0 16.4 1.0
N I:LEU167 4.0 17.2 1.0
CA I:ILE163 4.0 16.0 1.0
N I:ASP166 4.1 15.4 1.0
N I:SER169 4.1 15.5 1.0
N I:GLY170 4.2 14.8 1.0
CA I:SER169 4.2 15.1 1.0
CA I:GLY170 4.2 20.5 1.0
CA I:ASP166 4.3 19.6 1.0
C I:LEU167 4.3 19.2 1.0
N I:TRP164 4.4 16.3 1.0
CZ I:ARG19 4.4 20.6 1.0
C I:TRP164 4.4 15.5 1.0
O I:LEU167 4.5 17.0 1.0
O I:TRP164 4.6 14.1 1.0
CA I:TRP164 4.6 16.2 1.0
CB I:SER169 4.6 15.2 1.0
NH2 I:ARG19 4.6 11.7 1.0
C I:GLY162 4.7 19.7 1.0
N I:ASN165 4.7 15.6 1.0
N I:ILE163 4.9 15.6 1.0
C I:ASN165 4.9 19.4 1.0

Magnesium binding site 4 out of 8 in 4g4s

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Magnesium binding site 4 out of 8 in the Structure of Proteasome-PBA1-PBA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Proteasome-PBA1-PBA2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg301

b:26.1
occ:1.00
 O J:ASP178 2.1 14.6 1.0
O J:ALA175 2.2 14.9 1.0
O J:SER181 2.3 21.4 1.0
O J:HOH405 2.9 17.4 1.0
C J:ALA175 3.2 14.8 1.0
C J:ASP178 3.3 17.1 1.0
C J:SER181 3.3 16.5 1.0
O J:HOH467 3.9 24.9 1.0
N J:ASP178 3.9 10.5 1.0
CA J:ASP178 4.0 16.1 1.0
CA J:ASP176 4.0 15.6 1.0
N J:ASP176 4.1 15.0 1.0
N J:SER181 4.1 14.6 1.0
CA J:SER181 4.1 21.5 1.0
CA J:ALA175 4.1 11.6 1.0
N J:GLY182 4.2 12.9 1.0
CB J:ASP178 4.3 14.2 1.0
N J:ALA179 4.3 16.1 1.0
CA J:GLY182 4.4 16.3 1.0
C J:ASP176 4.4 14.8 1.0
O J:HOH406 4.4 18.0 1.0
CB J:ALA175 4.4 12.5 1.0
O J:HOH402 4.4 11.0 1.0
CB J:SER181 4.5 14.3 1.0
CA J:ALA179 4.5 15.9 1.0
C J:ALA179 4.6 16.6 1.0
OXT J:ASP205 4.7 15.0 1.0
N J:ARG177 4.7 16.0 1.0
OD1 J:ASP176 4.8 17.1 1.0
O J:ALA179 4.8 18.5 1.0
O J:ASP176 4.8 22.3 1.0
N J:LEU180 4.9 13.3 1.0

Magnesium binding site 5 out of 8 in 4g4s

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Magnesium binding site 5 out of 8 in the Structure of Proteasome-PBA1-PBA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Proteasome-PBA1-PBA2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg302

b:35.0
occ:1.00
 O J:HOH451 2.3 20.9 1.0
O J:HOH439 2.7 23.1 1.0
OG J:SER143 2.7 21.1 1.0
O J:GLY140 2.8 13.9 1.0
C J:GLY140 3.8 17.0 1.0
CB J:SER143 3.8 13.8 1.0
N J:GLY140 4.3 12.1 1.0
O J:HOH447 4.5 24.9 1.0
O J:HOH468 4.5 26.6 1.0
O J:HOH442 4.5 20.6 1.0
CA J:GLY140 4.5 10.3 1.0
N J:THR141 4.7 14.9 1.0
CA J:THR141 4.8 11.9 1.0
N J:SER143 4.8 9.1 1.0
CA J:SER143 4.9 15.9 1.0

Magnesium binding site 6 out of 8 in 4g4s

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Magnesium binding site 6 out of 8 in the Structure of Proteasome-PBA1-PBA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Proteasome-PBA1-PBA2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg302

b:22.4
occ:1.00
 O L:ASP168 2.2 13.8 1.0
O L:ALA165 2.4 13.4 1.0
O L:SER171 2.5 20.4 1.0
C L:ASP168 3.3 13.6 1.0
NH1 L:ARG19 3.5 15.5 1.0
C L:ALA165 3.5 13.0 1.0
O L:ALA169 3.5 15.5 1.0
C L:SER171 3.6 16.6 1.0
C L:ALA169 3.7 19.7 1.0
CA L:ALA169 3.8 12.6 1.0
N L:SER171 4.0 13.0 1.0
N L:ALA169 4.0 17.6 1.0
CA L:ALA165 4.2 10.6 1.0
CA L:SER171 4.3 11.2 1.0
O L:HIS166 4.3 15.3 1.0
CZ L:ARG19 4.4 16.1 1.0
CA L:ASP168 4.4 11.8 1.0
N L:ASP168 4.5 12.0 1.0
N L:TYR170 4.5 18.2 1.0
C L:HIS166 4.5 13.7 1.0
N L:GLY172 4.5 9.2 1.0
N L:HIS166 4.5 13.9 1.0
O L:ALA164 4.6 14.5 1.0
CA L:GLY172 4.7 11.3 1.0
CB L:SER171 4.7 13.1 1.0
CA L:HIS166 4.8 15.6 1.0
NH2 L:ARG19 4.9 16.6 1.0
C L:ARG167 4.9 14.1 1.0
C L:TYR170 5.0 14.7 1.0
N L:ARG167 5.0 9.8 1.0

Magnesium binding site 7 out of 8 in 4g4s

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Magnesium binding site 7 out of 8 in the Structure of Proteasome-PBA1-PBA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Proteasome-PBA1-PBA2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg301

b:24.3
occ:1.00
 O M:VAL188 2.6 21.8 1.0
O M:HIS185 2.7 14.5 1.0
O M:THR182 2.7 23.2 1.0
O M:HOH403 2.9 18.7 1.0
C M:HIS185 3.6 16.3 1.0
CA M:ILE186 3.7 21.1 1.0
C M:THR182 3.7 23.3 1.0
C M:VAL188 3.8 23.8 1.0
OXT M:ASP212 3.8 25.7 1.0
NH1 M:ARG18 3.9 16.9 1.0
C M:ILE186 3.9 18.6 1.0
O M:ILE186 4.0 25.4 1.0
O M:HOH404 4.0 17.3 1.0
CA M:THR182 4.1 21.8 1.0
CG2 M:THR182 4.1 18.8 1.0
N M:ILE186 4.1 16.0 1.0
N M:VAL188 4.2 14.2 1.0
CA M:VAL188 4.5 18.7 1.0
C M:ASP212 4.6 25.2 1.0
N M:GLN187 4.6 12.9 1.0
OD1 M:ASP212 4.7 20.2 1.0
CB M:THR182 4.7 21.4 1.0
N M:GLY189 4.8 22.1 1.0
O M:ASP212 4.8 22.6 1.0
N M:HIS185 4.8 20.2 1.0
CA M:HIS185 4.8 19.9 1.0
CA M:GLY189 4.9 16.6 1.0
N M:GLU183 4.9 20.7 1.0
CB M:ILE186 4.9 13.0 1.0
O M:ALA181 4.9 17.6 1.0
CB M:VAL188 4.9 21.4 1.0

Magnesium binding site 8 out of 8 in 4g4s

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Magnesium binding site 8 out of 8 in the Structure of Proteasome-PBA1-PBA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Proteasome-PBA1-PBA2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg302

b:17.2
occ:1.00
 OE1 E:GLU105 2.3 15.7 1.0
O M:HOH413 2.3 15.1 1.0
OG M:SER75 2.4 14.5 1.0
OG M:SER78 2.5 15.6 1.0
O M:HOH452 2.7 17.5 1.0
O M:HOH424 2.8 18.4 1.0
CB M:SER75 3.3 15.3 1.0
CD E:GLU105 3.4 22.5 1.0
CB M:SER78 3.5 13.0 1.0
N M:SER75 3.9 10.1 1.0
CB E:GLU105 3.9 11.5 1.0
CA M:SER75 4.2 20.3 1.0
OD1 M:ASN77 4.2 23.6 1.0
CG E:GLU105 4.2 17.8 1.0
OE2 E:GLU105 4.2 17.4 1.0
OH M:TYR65 4.4 17.3 1.0
NZ M:LYS72 4.5 29.3 1.0
CA M:SER78 4.7 16.2 1.0
N M:SER78 4.8 14.9 1.0
O E:TYR103 4.9 12.4 1.0
C M:SER75 4.9 17.3 1.0
ND2 M:ASN77 4.9 19.9 1.0
CG M:ASN77 5.0 21.7 1.0
O M:SER75 5.0 13.2 1.0
O M:LYS73 5.0 23.0 1.0

Reference:

B.M.Stadtmueller, E.Kish-Trier, K.Ferrell, C.N.Petersen, H.Robinson, D.G.Myszka, D.M.Eckert, T.Formosa, C.P.Hill. Structure of A Proteasome PBA1-PBA2 Complex: Implications For Proteasome Assembly, Activation, and Biological Function. J.Biol.Chem. V. 287 37371 2012.
ISSN: ISSN 0021-9258
PubMed: 22930756
DOI: 10.1074/JBC.M112.367003
Page generated: Mon Dec 14 15:59:50 2020

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