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Magnesium in PDB 1jd2: Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor

Enzymatic activity of Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor

All present enzymatic activity of Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor:
3.4.99.46;

Protein crystallography data

The structure of Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor, PDB code: 1jd2 was solved by M.Groll, Y.Koguchi, R.Huber, J.Kohno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.200, 301.300, 144.800, 90.00, 112.60, 90.00
R / Rfree (%) 25.1 / 33.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor (pdb code 1jd2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor, PDB code: 1jd2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1jd2

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Magnesium binding site 1 out of 10 in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor


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 Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2

b:34.2
occ:1.00
 OE2 D:GLU105 1.9 28.9 1.0
O L:HOH211 1.9 43.0 1.0
O L:HOH206 2.3 51.9 1.0
OG L:SER75 2.5 32.1 1.0
O D:HOH253 2.5 30.9 1.0
CD D:GLU105 3.1 18.2 1.0
OG L:SER78 3.2 27.6 1.0
CB L:SER75 3.6 29.1 1.0
OE1 D:GLU105 3.7 23.5 1.0
OH L:TYR66 3.7 28.6 1.0
N L:SER75 3.9 24.9 1.0
NZ L:LYS72 4.0 25.7 1.0
CB L:SER78 4.1 24.5 1.0
CE L:LYS72 4.1 22.1 1.0
CB D:GLU105 4.2 23.9 1.0
CG D:GLU105 4.2 21.1 1.0
O L:LYS73 4.4 29.2 1.0
CA L:SER75 4.4 27.1 1.0
O L:HOH974 4.6 45.8 1.0
OD1 L:ASN77 4.9 25.4 1.0
CZ L:TYR66 4.9 20.8 1.0

Magnesium binding site 2 out of 10 in 1jd2

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Magnesium binding site 2 out of 10 in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor


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 Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg242

b:78.9
occ:1.00
 NZ F:LYS173 4.6 52.9 1.0

Magnesium binding site 3 out of 10 in 1jd2

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Magnesium binding site 3 out of 10 in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor


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 Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg243

b:55.1
occ:1.00
 O F:HOH244 1.7 40.6 1.0
OD1 F:ASN127 2.9 40.0 1.0
O G:HOH672 3.0 41.8 1.0
O B:HOH921 3.2 36.4 1.0
OH A:TYR8 3.2 33.6 1.0
OG F:SER13 3.3 27.1 1.0
O G:ALA127 3.4 30.4 1.0
O G:HOH538 3.7 34.4 1.0
CG F:ASN127 3.8 33.1 1.0
CZ A:TYR8 4.0 28.3 1.0
CB F:ASN127 4.1 32.0 1.0
CG2 G:ILE12 4.4 23.0 1.0
O G:TYR128 4.5 28.2 1.0
CE2 A:TYR8 4.6 29.6 1.0
N F:ASN127 4.6 24.5 1.0
C G:ALA127 4.6 27.1 1.0
CB F:SER13 4.7 23.8 1.0
CE1 A:TYR8 4.8 27.3 1.0
CA G:TYR128 4.9 30.6 1.0
C G:TYR128 4.9 25.8 1.0
O F:HOH245 4.9 33.2 1.0
CA F:ASN127 5.0 26.2 1.0

Magnesium binding site 4 out of 10 in 1jd2

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Magnesium binding site 4 out of 10 in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor


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 Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1

b:29.6
occ:1.00
 O G:TYR123 2.0 24.3 1.0
O G:HOH248 2.0 25.3 1.0
O G:MET129 2.1 27.2 1.0
O G:ARG126 2.4 24.3 1.0
OG1 G:THR13 2.9 29.8 1.0
CG2 G:THR13 3.1 23.4 1.0
C G:TYR123 3.1 23.9 1.0
C G:MET129 3.3 28.0 1.0
C G:ARG126 3.4 25.5 1.0
CB G:THR13 3.6 22.3 1.0
CA G:TYR123 3.9 24.0 1.0
N G:MET129 4.1 30.0 1.0
N G:ARG126 4.1 25.6 1.0
CA G:MET129 4.1 32.7 1.0
N G:THR124 4.2 22.4 1.0
CA G:ALA127 4.2 23.8 1.0
N G:ALA127 4.2 28.0 1.0
N G:ARG130 4.3 29.0 1.0
CA G:ARG126 4.4 24.3 1.0
C G:ALA127 4.4 27.1 1.0
C G:THR124 4.4 27.3 1.0
CA G:ARG130 4.4 26.6 1.0
CB G:MET129 4.5 38.2 1.0
CA G:THR124 4.5 24.9 1.0
CB G:TYR123 4.5 21.9 1.0
N G:GLN125 4.6 27.3 1.0
O G:THR124 4.7 27.8 1.0
N G:THR13 4.7 27.9 1.0
O G:HOH833 4.7 35.4 1.0
O G:ALA127 4.7 30.4 1.0
CA G:THR13 4.8 22.5 1.0
N G:TYR128 4.8 31.4 1.0
C G:ARG130 4.9 26.1 1.0
O G:ILE122 4.9 24.3 1.0
O G:HOH538 5.0 34.4 1.0
CD G:PRO131 5.0 17.6 1.0
C G:GLN125 5.0 24.0 1.0

Magnesium binding site 5 out of 10 in 1jd2

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Magnesium binding site 5 out of 10 in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor


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 Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg224

b:24.9
occ:1.00
 O H:HOH2265 1.9 30.1 1.0
O H:ASP166 2.1 26.7 1.0
OXT S:ASP194 2.1 34.7 1.0
O H:ILE163 2.3 31.6 1.0
O H:SER169 2.3 25.8 1.0
C H:ASP166 2.9 21.2 1.0
C S:ASP194 3.2 36.0 1.0
C H:ILE163 3.4 25.0 1.0
C H:SER169 3.4 20.8 1.0
N H:LEU167 3.6 21.4 1.0
CA H:LEU167 3.7 21.9 1.0
NH1 H:ARG19 3.7 27.7 1.0
CA S:ASP194 3.8 33.0 1.0
C H:LEU167 3.9 22.5 1.0
N H:ASP166 3.9 27.6 1.0
N H:SER169 4.0 23.9 1.0
CA H:ASP166 4.0 22.5 1.0
O H:GLY162 4.1 24.2 1.0
CA H:ILE163 4.1 21.3 1.0
O S:ASP194 4.1 43.1 1.0
O H:LEU167 4.1 24.5 1.0
CA H:SER169 4.2 17.1 1.0
CB S:ASP194 4.3 26.9 1.0
CZ H:ARG19 4.3 21.9 1.0
N H:GLY170 4.4 22.3 1.0
CA H:GLY170 4.4 23.7 1.0
N H:TRP164 4.5 25.9 1.0
N H:GLY168 4.6 24.7 1.0
CB H:SER169 4.6 15.5 1.0
CB H:ASP166 4.7 25.6 1.0
C H:TRP164 4.8 25.2 1.0
NH2 H:ARG19 4.8 27.2 1.0
CA H:TRP164 4.8 22.8 1.0
CG2 H:ILE163 4.9 20.3 1.0
O H:TRP164 4.9 31.4 1.0
C H:GLY162 4.9 19.9 1.0
O S:HOH973 5.0 56.9 1.0

Magnesium binding site 6 out of 10 in 1jd2

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Magnesium binding site 6 out of 10 in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor


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 Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg195

b:52.4
occ:1.00
 O I:HOH216 2.2 36.6 1.0
OG I:SER131 2.7 28.0 1.0
O I:HOH771 2.7 34.2 1.0
O H:HOH812 2.8 41.8 1.0
O I:GLY128 3.7 28.1 1.0
O I:HOH3153 3.8 56.3 1.0
CB I:SER131 3.8 21.2 1.0
O I:HOH720 4.1 43.3 1.0
O I:HOH219 4.2 38.8 1.0
C I:GLY128 4.8 21.7 1.0
O I:HOH214 5.0 36.5 1.0

Magnesium binding site 7 out of 10 in 1jd2

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Magnesium binding site 7 out of 10 in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor


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 Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg196

b:32.5
occ:1.00
 O I:ASP166 1.9 23.9 1.0
O I:ALA163 2.3 27.4 1.0
O I:HOH209 2.3 35.5 1.0
O I:HOH205 2.4 29.2 1.0
O I:SER169 2.8 30.8 1.0
C I:ASP166 2.9 20.4 1.0
C I:ALA163 3.2 22.0 1.0
N I:ASP166 3.5 24.0 1.0
CA I:ASP166 3.7 21.3 1.0
CA I:ASP164 3.8 22.1 1.0
C I:SER169 3.8 24.0 1.0
N I:ALA167 3.9 22.7 1.0
C I:ASP164 3.9 22.4 1.0
N I:ASP164 3.9 28.1 1.0
O I:ASP164 4.0 28.1 1.0
O I:ALA167 4.0 28.2 1.0
CA I:ALA167 4.1 24.3 1.0
CB I:ASP166 4.1 22.4 1.0
C I:ALA167 4.2 27.0 1.0
CA I:ALA163 4.2 20.2 1.0
N I:SER169 4.3 26.1 1.0
O R:HOH215 4.3 43.4 1.0
N I:ARG165 4.3 25.1 1.0
CA I:SER169 4.5 23.8 1.0
CB I:ALA163 4.6 23.6 1.0
C I:ARG165 4.6 21.4 1.0
O I:HOH587 4.7 25.0 1.0
N I:GLY170 4.7 23.7 1.0
CB I:SER169 4.8 24.4 1.0
OD2 I:ASP164 4.8 30.9 1.0
O I:HOH629 4.9 44.3 1.0
CA I:GLY170 4.9 24.4 1.0
OXT I:ASP194 4.9 31.3 1.0
N I:LEU168 5.0 26.2 1.0

Magnesium binding site 8 out of 10 in 1jd2

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Magnesium binding site 8 out of 10 in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor


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 Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg195

b:33.8
occ:1.00
 O L:HOH2847 1.5 54.0 1.0
O L:HOH254 2.1 30.9 1.0
O L:THR163 2.2 31.8 1.0
O L:VAL169 2.4 30.8 1.0
O L:HIS166 2.4 22.0 1.0
C L:THR163 3.1 28.3 1.0
O L:HOH2973 3.2 41.3 1.0
CG2 L:THR163 3.3 26.2 1.0
CA L:THR163 3.3 27.1 1.0
C L:HIS166 3.5 19.4 1.0
C L:VAL169 3.5 26.2 1.0
O L:HOH249 3.8 36.0 1.0
CB L:THR163 3.9 26.3 1.0
CA L:ILE167 4.2 21.4 1.0
N L:ILE167 4.2 22.9 1.0
NH2 L:ARG19 4.2 26.9 1.0
N L:VAL169 4.3 27.2 1.0
CA L:VAL169 4.3 23.6 1.0
N L:HIS166 4.3 23.9 1.0
N L:GLU164 4.3 30.4 1.0
N L:GLY170 4.4 22.8 1.0
CA L:HIS166 4.4 19.8 1.0
O L:ALA162 4.5 35.1 1.0
C L:ILE167 4.5 20.9 1.0
CA L:GLY170 4.5 17.4 1.0
CB L:VAL169 4.5 23.0 1.0
OD1 L:ASP194 4.5 39.6 1.0
N L:THR163 4.6 28.5 1.0
O L:ASP194 4.6 45.3 1.0
O L:ILE167 4.8 23.9 1.0
NH2 O:ARG19 4.8 21.5 1.0
CA L:GLU164 4.9 28.0 1.0
N L:GLN168 4.9 25.8 1.0
C L:GLU164 5.0 31.1 1.0
C L:ALA162 5.0 28.6 1.0
OG1 L:THR163 5.0 28.9 1.0

Magnesium binding site 9 out of 10 in 1jd2

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Magnesium binding site 9 out of 10 in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor


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 Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg188

b:27.1
occ:1.00
 O N:ILE163 2.2 22.1 1.0
O N:SER169 2.7 24.5 1.0
O N:HOH554 3.0 37.6 1.0
O N:ASP166 3.2 29.0 1.0
C N:ILE163 3.3 23.0 1.0
CG2 N:ILE163 3.6 17.5 1.0
CD1 T:LEU26 3.8 21.1 1.0
C N:SER169 3.9 22.2 1.0
NH1 N:ARG19 3.9 27.4 1.0
C N:ASP166 4.1 17.5 1.0
CA N:ILE163 4.1 17.1 1.0
O N:LYS164 4.2 27.8 1.0
CA N:GLY167 4.3 15.4 1.0
N N:LYS164 4.4 23.9 1.0
CA N:GLY170 4.4 17.1 1.0
C N:LYS164 4.5 23.5 1.0
CB N:ILE163 4.5 15.9 1.0
CZ N:ARG19 4.5 25.2 1.0
O N:HOH810 4.6 38.5 1.0
N N:GLY170 4.6 20.6 1.0
N N:GLY167 4.6 17.6 1.0
CA N:LYS164 4.6 23.0 1.0
NH2 N:ARG19 4.8 21.8 1.0
O T:HOH992 4.8 45.5 1.0
O N:HOH2492 4.8 35.9 1.0
CA N:SER169 4.9 20.2 1.0
C N:GLY167 4.9 18.7 1.0
N N:SER169 4.9 25.2 1.0
CG T:LEU26 5.0 19.8 1.0

Magnesium binding site 10 out of 10 in 1jd2

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Magnesium binding site 10 out of 10 in the Crystal Structure of the Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor


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 Yeast 20S Proteasome:Tmc-95A Complex: A Non- Covalent Proteasome Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg195

b:29.4
occ:1.00
 O P:ASP194 1.7 36.1 1.0
O K:ALA163 2.4 28.7 1.0
O K:ASP166 2.5 30.6 1.0
O K:HOH2446 2.6 27.8 1.0
C P:ASP194 2.7 34.8 1.0
O K:SER169 3.0 27.9 1.0
CA P:ASP194 3.2 30.2 1.0
C K:ASP166 3.4 23.5 1.0
C K:ALA163 3.5 24.8 1.0
CA K:ALA167 3.6 20.2 1.0
NH1 K:ARG19 3.7 30.8 1.0
CB P:ASP194 3.8 23.9 1.0
O K:ALA167 3.8 23.7 1.0
C K:ALA167 3.8 20.6 1.0
OXT P:ASP194 3.8 34.5 1.0
C K:SER169 3.9 25.5 1.0
N K:ALA167 3.9 22.2 1.0
CA K:ALA163 4.2 23.3 1.0
O K:HIS164 4.2 29.5 1.0
N K:SER169 4.2 25.6 1.0
C K:HIS164 4.5 23.0 1.0
O P:HOH2629 4.5 39.6 1.0
N K:HIS164 4.6 23.6 1.0
N P:ASP194 4.6 25.7 1.0
CA K:SER169 4.6 23.8 1.0
N K:TYR168 4.6 25.7 1.0
CA K:ASP166 4.6 20.9 1.0
N K:ASP166 4.7 24.6 1.0
CZ K:ARG19 4.7 29.8 1.0
N K:GLY170 4.7 27.2 1.0
CG P:ASP194 4.8 24.4 1.0
CA K:HIS164 4.8 22.0 1.0
CA K:GLY170 4.8 24.8 1.0
CB K:ALA163 4.8 24.3 1.0
C K:ARG165 4.8 25.3 1.0
CB K:ALA167 4.8 21.9 1.0
O K:ARG165 4.9 27.3 1.0
O K:ALA162 5.0 28.4 1.0

Reference:

M.Groll, Y.Koguchi, R.Huber, J.Kohno. Crystal Structure of the 20 S Proteasome:Tmc-95A Complex: A Non-Covalent Proteasome Inhibitor. J.Mol.Biol. V. 311 543 2001.
ISSN: ISSN 0022-2836
PubMed: 11493007
DOI: 10.1006/JMBI.2001.4869
Page generated: Tue Aug 13 06:32:58 2024

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