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Magnesium in PDB 1iru: Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution

Protein crystallography data

The structure of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution, PDB code: 1iru was solved by M.Unno, T.Mizushima, Y.Morimoto, Y.Tomisugi, K.Tanaka, N.Yasuoka, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.00 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 316.700, 205.900, 116.000, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 29.4

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution (pdb code 1iru). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 30 binding sites of Magnesium where determined in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution, PDB code: 1iru:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 30 in 1iru

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Magnesium binding site 1 out of 30 in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:83.1
occ:1.00
 O A:MET131 2.7 66.6 1.0
OG1 A:THR14 2.7 73.7 1.0
O A:ASN128 2.9 70.5 1.0
N A:THR14 3.3 75.1 1.0
CG2 A:THR14 3.3 73.0 1.0
CA A:ALA129 3.4 69.2 1.0
CB A:THR14 3.4 73.1 1.0
O A:ALA129 3.4 69.1 1.0
O A:TYR125 3.6 70.5 1.0
C A:MET131 3.7 66.2 1.0
C A:ALA129 3.7 69.8 1.0
C A:ASN128 3.9 70.2 1.0
CA A:THR14 3.9 74.8 1.0
N A:ALA129 4.1 68.8 1.0
C A:ILE13 4.2 75.0 1.0
CA A:ILE13 4.3 74.0 1.0
CA A:ARG132 4.3 64.7 1.0
N A:ARG132 4.4 64.9 1.0
CB A:ALA129 4.5 69.2 1.0
N A:MET131 4.5 68.0 1.0
CB A:ILE13 4.7 71.3 1.0
CA A:MET131 4.7 67.2 1.0
N A:GLU130 4.8 70.5 1.0
C A:TYR125 4.8 69.1 1.0
CD A:PRO133 4.8 67.1 1.0
O G:SER12 4.8 67.1 1.0

Magnesium binding site 2 out of 30 in 1iru

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Magnesium binding site 2 out of 30 in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg316

b:84.6
occ:1.00
 O B:ALA32 2.8 96.8 1.0
O B:TYR75 2.8 83.8 1.0
NZ B:LYS63 3.0 86.6 1.0
CB B:ALA32 3.4 95.3 1.0
OG1 B:THR47 3.4 0.0 1.0
CE B:LYS63 3.5 87.8 1.0
CA B:SER76 3.5 84.7 1.0
C B:ALA32 3.6 96.0 1.0
C B:TYR75 3.7 82.9 1.0
OG B:SER34 3.8 98.5 1.0
CA B:ALA32 3.8 95.4 1.0
N B:ALA32 4.0 95.1 1.0
N B:SER76 4.0 84.2 1.0
OG B:SER76 4.1 82.3 1.0
CE1 B:TYR75 4.2 70.1 1.0
N B:GLY77 4.3 86.5 1.0
CB B:SER76 4.3 84.2 1.0
CD1 B:TYR75 4.3 71.2 1.0
CZ B:TYR75 4.4 71.1 1.0
C B:SER76 4.5 85.5 1.0
CB B:THR47 4.6 0.7 1.0
O B:PRO33 4.6 96.1 1.0
CG B:TYR75 4.6 74.0 1.0
N B:PRO33 4.7 96.0 1.0
C B:GLY31 4.7 95.0 1.0
CE2 B:TYR75 4.7 71.3 1.0
CD2 B:TYR75 4.8 72.5 1.0
CG2 B:THR47 4.9 0.8 1.0
C B:PRO33 4.9 96.4 1.0
OH B:TYR75 4.9 69.2 1.0
CD B:LYS63 4.9 89.5 1.0
CA B:TYR75 5.0 81.3 1.0

Magnesium binding site 3 out of 30 in 1iru

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Magnesium binding site 3 out of 30 in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg314

b:76.8
occ:1.00
 CE2 C:TRP159 3.0 0.5 1.0
CZ2 C:TRP159 3.1 0.4 1.0
CD2 C:TRP159 3.1 0.3 1.0
O C:GLY158 3.1 0.1 1.0
CH2 C:TRP159 3.2 0.7 1.0
CE3 C:TRP159 3.2 0.5 1.0
CZ3 C:TRP159 3.2 1.0 1.0
CB D:GLN54 3.5 0.9 1.0
CA D:GLN54 3.6 0.0 1.0
NE1 C:TRP159 3.7 0.0 1.0
CG C:TRP159 3.9 0.3 1.0
C C:GLY158 3.9 0.1 1.0
N C:GLY158 4.0 98.6 1.0
CD1 C:TRP159 4.2 0.5 1.0
N D:ASP55 4.2 0.3 1.0
C D:GLN54 4.2 0.6 1.0
C C:GLY157 4.2 96.8 1.0
CA C:GLY157 4.2 96.0 1.0
N C:TRP159 4.6 0.5 1.0
CA C:TRP159 4.6 0.7 1.0
CA C:GLY158 4.7 0.1 1.0
OG1 D:THR58 4.8 96.4 1.0
N D:GLN54 4.8 0.3 1.0
CB C:TRP159 4.8 0.4 1.0
O C:GLY157 4.9 95.6 1.0

Magnesium binding site 4 out of 30 in 1iru

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Magnesium binding site 4 out of 30 in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg309

b:87.7
occ:1.00
 N D:ALA160 2.7 74.8 1.0
O D:ALA160 2.8 75.2 1.0
CB D:ASN159 2.8 74.5 1.0
CA D:ASN159 3.3 74.1 1.0
C D:ASN159 3.4 74.7 1.0
C D:ALA160 3.4 76.1 1.0
CA D:ALA160 3.6 75.8 1.0
CZ3 D:TRP156 3.7 80.9 1.0
CH2 D:TRP156 3.7 80.8 1.0
CE3 D:TRP156 4.1 79.7 1.0
CZ2 D:TRP156 4.1 80.5 1.0
CD2 D:TRP156 4.4 80.2 1.0
CE2 D:TRP156 4.4 80.3 1.0
CG2 D:ILE161 4.5 81.8 1.0
CB D:ALA160 4.5 77.5 1.0
O D:ASN159 4.6 75.2 1.0
N D:ILE161 4.6 77.7 1.0
N D:ASN159 4.7 74.6 1.0
O D:ALA158 5.0 75.0 1.0

Magnesium binding site 5 out of 30 in 1iru

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Magnesium binding site 5 out of 30 in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg311

b:97.0
occ:1.00
 O G:VAL45 2.2 68.5 1.0
N G:VAL216 2.6 81.2 1.0
CA G:TRP215 2.7 81.0 1.0
O G:SER214 2.8 77.5 1.0
C G:TRP215 2.9 81.2 1.0
CE3 G:TRP215 3.1 80.9 1.0
C G:VAL45 3.3 69.0 1.0
N G:TRP215 3.4 79.9 1.0
C G:SER214 3.4 78.7 1.0
CA G:VAL46 3.4 70.5 1.0
CA G:VAL216 3.7 81.1 1.0
CG2 G:VAL46 3.7 71.5 1.0
O G:VAL216 3.8 80.7 1.0
N G:VAL46 3.8 69.2 1.0
CZ3 G:TRP215 3.9 80.3 1.0
O G:TRP215 3.9 81.9 1.0
CG1 G:VAL216 4.0 80.5 1.0
CB G:TRP215 4.0 81.8 1.0
C G:VAL216 4.0 81.6 1.0
CD2 G:TRP215 4.1 81.0 1.0
CB G:VAL46 4.1 71.7 1.0
CB G:VAL216 4.3 80.1 1.0
CG G:TRP215 4.5 81.4 1.0
N G:VAL45 4.5 73.0 1.0
C G:VAL46 4.5 69.2 1.0
CA G:VAL45 4.5 69.8 1.0
CG1 G:VAL46 4.5 70.8 1.0
N G:PHE47 4.5 68.4 1.0
CA G:SER214 4.8 79.4 1.0

Magnesium binding site 6 out of 30 in 1iru

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Magnesium binding site 6 out of 30 in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg317

b:85.9
occ:1.00
 O G:SER154 2.6 67.3 1.0
OG1 G:THR123 3.2 67.3 1.0
CD2 G:HIS120 3.4 58.1 1.0
CB A:ALA85 3.4 76.9 1.0
C G:SER154 3.5 67.0 1.0
CB G:SER154 3.7 64.9 1.0
CA G:SER154 3.7 66.4 1.0
OD1 A:ASP86 4.0 80.0 1.0
CB G:THR123 4.1 63.7 1.0
NE2 G:HIS120 4.1 58.1 1.0
NH2 A:ARG132 4.3 54.8 1.0
CG2 G:THR123 4.4 63.5 1.0
CE A:MET83 4.4 75.4 1.0
N A:ASP86 4.5 74.7 1.0
OG G:SER154 4.5 65.7 1.0
CG G:HIS120 4.6 58.1 1.0
CA A:ALA85 4.6 77.6 1.0
N G:GLY155 4.7 67.3 1.0
CG A:ASP86 4.8 79.0 1.0
C A:ALA85 4.9 76.4 1.0
NH1 A:ARG132 5.0 57.0 1.0
N A:ALA85 5.0 79.6 1.0

Magnesium binding site 7 out of 30 in 1iru

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Magnesium binding site 7 out of 30 in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg319

b:66.9
occ:1.00
 OE1 G:GLU192 2.7 84.3 1.0
CG1 G:ILE196 3.3 78.2 1.0
CD G:LYS195 3.6 91.3 1.0
CD2 G:LEU179 3.6 91.2 1.0
O G:GLU192 3.7 80.3 1.0
CD1 G:ILE196 3.8 79.2 1.0
CD G:GLU192 3.8 83.1 1.0
CG G:LYS195 3.9 88.6 1.0
CB G:GLU192 4.1 81.2 1.0
CG G:LEU179 4.1 91.4 1.0
CB G:LYS195 4.1 86.6 1.0
CD1 G:LEU179 4.2 90.3 1.0
O G:GLU175 4.2 93.3 1.0
CE G:LYS195 4.2 91.0 1.0
CA G:GLU192 4.3 80.2 1.0
CG G:GLU192 4.4 82.6 1.0
N G:ILE196 4.4 82.4 1.0
C G:GLU192 4.4 80.5 1.0
CB G:ILE196 4.7 79.1 1.0
OE2 G:GLU192 4.7 81.9 1.0
NZ G:LYS195 4.8 91.2 1.0
CA G:ILE196 4.9 80.8 1.0

Magnesium binding site 8 out of 30 in 1iru

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Magnesium binding site 8 out of 30 in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg306

b:87.3
occ:1.00
 O I:ILE163 2.5 67.0 1.0
OXT 1:ASP213 2.5 86.9 1.0
O I:SER169 2.7 75.2 1.0
O I:ASP166 2.7 63.2 1.0
C 1:ASP213 3.4 86.2 1.0
C I:ASP166 3.4 63.2 1.0
C I:ILE163 3.6 66.5 1.0
O I:PHE164 3.7 64.5 1.0
CA 1:ASP213 3.7 85.1 1.0
CA I:LEU167 3.7 66.1 1.0
N I:LEU167 3.8 64.3 1.0
C I:SER169 3.9 75.1 1.0
C I:PHE164 3.9 64.7 1.0
N I:ASP166 4.1 62.5 1.0
CA I:PHE164 4.1 65.3 1.0
CB 1:ASP213 4.2 84.2 1.0
C I:LEU167 4.3 66.9 1.0
N I:PHE164 4.3 65.5 1.0
CA I:ASP166 4.4 62.8 1.0
CD2 I:LEU167 4.4 67.7 1.0
O 1:ASP213 4.4 87.3 1.0
NH1 I:ARG19 4.5 76.2 1.0
NH2 I:ARG19 4.5 73.9 1.0
N I:SER169 4.6 74.1 1.0
O I:LEU167 4.6 66.5 1.0
O I:GLY162 4.6 65.9 1.0
CZ I:ARG19 4.7 72.2 1.0
CA I:ILE163 4.7 66.0 1.0
N I:ASN165 4.7 63.5 1.0
CA I:SER169 4.8 73.7 1.0
N I:GLY170 4.8 75.4 1.0
O 1:LYS212 4.8 84.0 1.0
CA I:GLY170 4.9 73.0 1.0
C I:ASN165 4.9 63.1 1.0
N I:GLY168 4.9 68.9 1.0
CB I:LEU167 5.0 66.5 1.0
N 1:ASP213 5.0 84.0 1.0

Magnesium binding site 9 out of 30 in 1iru

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Magnesium binding site 9 out of 30 in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg304

b:56.5
occ:1.00
 O J:ASP178 2.6 72.6 1.0
O J:SER181 2.7 71.9 1.0
O J:VAL175 3.4 71.2 1.0
OXT J:ASP205 3.5 81.2 1.0
C J:ASP178 3.7 70.9 1.0
O J:ALA179 3.7 70.8 1.0
C J:ALA179 3.8 70.6 1.0
C J:SER181 3.9 72.3 1.0
CA J:ALA179 3.9 69.9 1.0
O J:ASP205 4.1 82.1 1.0
C J:ASP205 4.2 81.6 1.0
N J:ALA179 4.2 69.9 1.0
N J:SER181 4.3 73.2 1.0
NH2 Z:ARG19 4.3 70.5 1.0
NH1 Z:ARG19 4.3 68.3 1.0
N J:VAL180 4.5 71.8 1.0
C J:VAL175 4.6 72.6 1.0
CZ Z:ARG19 4.7 67.6 1.0
CA J:SER181 4.7 72.1 1.0
CA J:GLY182 4.7 71.2 1.0
N J:GLY182 4.8 72.8 1.0
N J:ASP178 4.8 72.0 1.0
CA J:ASP178 4.9 71.6 1.0
CA J:ASP176 4.9 74.5 1.0

Magnesium binding site 10 out of 30 in 1iru

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Magnesium binding site 10 out of 30 in the Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Mammalian 20S Proteasome at 2.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg315

b:69.3
occ:1.00
 OE1 J:GLN65 2.6 69.1 1.0
OD1 K:ASN82 2.8 68.0 1.0
CD K:ARG85 3.2 50.1 1.0
CD J:GLN65 3.3 67.6 1.0
NE2 J:GLN65 3.4 68.5 1.0
NH1 K:ARG85 3.6 50.4 1.0
CG K:ASN82 3.6 67.4 1.0
CB K:ASN82 3.7 65.8 1.0
O K:ASN82 3.8 62.0 1.0
CA K:ASN82 3.8 64.5 1.0
CG C:GLN102 3.9 68.5 1.0
CB K:ARG85 4.2 56.6 1.0
NE K:ARG85 4.2 49.1 1.0
C K:ASN82 4.3 63.9 1.0
CG K:ARG85 4.3 52.2 1.0
CZ K:ARG85 4.4 49.8 1.0
CD2 K:LEU124 4.6 57.6 1.0
NH2 K:ARG86 4.7 73.8 1.0
CD C:GLN102 4.8 70.4 1.0
CG J:GLN65 4.8 66.2 1.0
O K:HOH316 4.8 55.8 1.0
ND2 K:ASN82 4.9 68.0 1.0
N K:ARG86 4.9 60.6 1.0
O C:LEU99 5.0 69.4 1.0

Reference:

M.Unno, T.Mizushima, Y.Morimoto, Y.Tomisugi, K.Tanaka, N.Yasuoka, T.Tsukihara. The Structure of the Mammalian 20S Proteasome at 2.75 A Resolution. Structure V. 10 609 2002.
ISSN: ISSN 0969-2126
PubMed: 12015144
DOI: 10.1016/S0969-2126(02)00748-7
Page generated: Tue Aug 13 05:11:10 2024

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