Magnesium in PDB 5cgh: Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5

Enzymatic activity of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5

All present enzymatic activity of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5, PDB code: 5cgh was solved by C.Dubiella, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.910, 300.210, 145.870, 90.00, 112.90, 90.00
R / Rfree (%) 20.7 / 22.7

Other elements in 5cgh:

The structure of Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5 (pdb code 5cgh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5, PDB code: 5cgh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5cgh

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5


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 BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:43.2
occ:1.00
 O G:MET125 2.1 45.0 1.0
O G:ARG122 2.3 43.8 1.0
O G:TYR119 2.3 33.0 1.0
OG1 G:THR8 2.7 37.4 1.0
CG2 G:THR8 3.3 37.4 1.0
C G:MET125 3.4 42.5 1.0
C G:ARG122 3.4 43.4 1.0
C G:TYR119 3.5 33.1 1.0
CB G:THR8 3.6 37.5 1.0
O G:ALA123 3.6 38.8 1.0
CA G:ALA123 3.8 39.4 1.0
C G:ALA123 3.8 40.1 1.0
N G:ALA123 4.1 40.8 1.0
N G:MET125 4.2 43.6 1.0
CA G:TYR119 4.2 32.3 1.0
N G:ARG126 4.3 38.0 1.0
CA G:MET125 4.3 45.5 1.0
CA G:ARG126 4.3 35.7 1.0
N G:THR8 4.5 39.9 1.0
N G:THR120 4.5 32.8 1.0
N G:ARG122 4.6 42.8 1.0
CA G:ARG122 4.6 45.5 1.0
CD G:PRO127 4.6 32.6 1.0
CA G:THR8 4.6 39.3 1.0
CA G:THR120 4.7 32.3 1.0
N G:TYR124 4.7 40.7 1.0
CB G:MET125 4.8 50.5 1.0
C G:THR120 4.8 33.9 1.0
CB G:TYR119 4.8 32.1 1.0
C G:ARG126 4.8 34.2 1.0
N G:PRO127 5.0 32.9 1.0
N G:GLN121 5.0 35.0 1.0

Magnesium binding site 2 out of 7 in 5cgh

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5


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 BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:63.6
occ:1.00
 O I:HOH417 2.4 41.4 1.0
O I:ASP177 2.4 42.3 1.0
O I:ALA174 2.4 46.3 1.0
O I:SER180 2.5 45.8 1.0
C I:ALA174 3.5 45.0 1.0
C I:ASP177 3.5 42.0 1.0
C I:SER180 3.7 43.6 1.0
O I:HOH407 3.8 40.6 1.0
CA I:ASP175 3.8 45.4 1.0
OXT I:ASP204 4.0 45.8 1.0
N I:ASP175 4.1 44.8 1.0
C I:ASP175 4.2 45.1 1.0
N I:ASP177 4.2 41.8 1.0
O I:ASP175 4.4 49.1 1.0
CA I:ASP177 4.4 42.4 1.0
N I:ALA178 4.4 41.4 1.0
O I:ALA178 4.5 45.8 1.0
CA I:ALA178 4.5 41.4 1.0
N I:SER180 4.5 43.2 1.0
N I:GLY181 4.6 42.6 1.0
CA I:GLY181 4.6 43.6 1.0
C I:ALA178 4.6 42.8 1.0
CA I:ALA174 4.6 43.6 1.0
CA I:SER180 4.6 43.7 1.0
OD1 I:ASP175 4.7 46.8 1.0
N I:ARG176 4.8 42.9 1.0
NH1 Y:ARG19 4.8 57.3 1.0
NH2 Y:ARG19 4.9 54.2 1.0
C I:ASP204 4.9 49.8 1.0
CB I:ALA174 4.9 43.3 1.0
O I:ASP204 4.9 47.5 1.0
CB I:ASP177 5.0 43.4 1.0

Magnesium binding site 3 out of 7 in 5cgh

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5


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 BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:47.7
occ:1.00
 O Y:ASP168 2.2 43.6 1.0
O Y:ALA165 2.3 39.8 1.0
O I:ASP204 2.3 47.5 1.0
O Y:SER171 2.5 45.2 1.0
C I:ASP204 3.2 49.8 1.0
C Y:ASP168 3.3 41.3 1.0
C Y:ALA165 3.4 40.6 1.0
C Y:SER171 3.7 42.4 1.0
CA I:ASP204 3.7 54.0 1.0
CA Y:ALA169 3.7 40.4 1.0
O Y:ALA169 3.9 44.1 1.0
C Y:ALA169 3.9 40.9 1.0
NH1 Y:ARG19 3.9 57.3 1.0
N Y:ALA169 3.9 40.7 1.0
CB I:ASP204 4.0 55.9 1.0
O Y:HIS166 4.0 44.9 1.0
OXT I:ASP204 4.2 45.8 1.0
CA Y:ALA165 4.2 40.8 1.0
N Y:SER171 4.2 39.5 1.0
C Y:HIS166 4.3 43.3 1.0
CZ Y:ARG19 4.3 55.0 1.0
N Y:HIS166 4.4 40.9 1.0
CA Y:ASP168 4.5 40.3 1.0
N Y:ASP168 4.5 41.4 1.0
CA Y:SER171 4.5 40.4 1.0
NH2 Y:ARG19 4.5 54.2 1.0
O Y:ALA164 4.6 39.4 1.0
CA Y:HIS166 4.6 41.8 1.0
N Y:GLY172 4.7 43.5 1.0
N Y:TYR170 4.7 40.2 1.0
O I:HOH417 4.7 41.4 1.0
CA Y:GLY172 4.7 44.3 1.0
C Y:ARG167 4.9 42.5 1.0
CG I:ASP204 5.0 56.5 1.0
N Y:ARG167 5.0 42.8 1.0
CB Y:SER171 5.0 39.6 1.0

Magnesium binding site 4 out of 7 in 5cgh

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5


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 BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:53.0
occ:1.00
 O K:ASP168 2.2 46.3 1.0
O K:ALA165 2.2 42.1 1.0
O K:SER171 2.3 45.8 1.0
O W:ASP204 2.4 51.2 1.0
C W:ASP204 3.2 52.3 1.0
C K:ASP168 3.3 43.0 1.0
C K:ALA165 3.4 42.1 1.0
C K:SER171 3.5 43.8 1.0
CA W:ASP204 3.7 53.8 1.0
CA K:ALA169 3.8 41.9 1.0
O K:ALA169 3.9 44.6 1.0
C K:ALA169 3.9 43.6 1.0
CB W:ASP204 3.9 54.9 1.0
NH1 K:ARG19 3.9 51.1 1.0
N K:ALA169 4.0 41.4 1.0
O K:HIS166 4.1 45.5 1.0
CA K:ALA165 4.1 42.1 1.0
N K:SER171 4.1 42.7 1.0
OXT W:ASP204 4.2 51.9 1.0
CZ K:ARG19 4.3 50.3 1.0
CA K:SER171 4.4 42.0 1.0
C K:HIS166 4.4 43.0 1.0
N K:HIS166 4.4 41.1 1.0
CA K:ASP168 4.5 42.0 1.0
N K:ASP168 4.5 43.0 1.0
NH2 K:ARG19 4.5 51.2 1.0
N K:GLY172 4.5 44.2 1.0
O K:ALA164 4.5 42.2 1.0
CA K:GLY172 4.6 44.8 1.0
N K:TYR170 4.6 44.1 1.0
CA K:HIS166 4.6 41.7 1.0
CB K:SER171 4.8 41.6 1.0
CG W:ASP204 4.9 55.1 1.0
C K:ARG167 4.9 44.3 1.0
CB K:ALA165 5.0 42.5 1.0

Magnesium binding site 5 out of 7 in 5cgh

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5


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 BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:58.8
occ:1.00
 OXT L:ASP222 2.7 59.9 1.0
O V:ASP166 2.8 43.8 1.0
O V:TRP164 2.9 50.3 1.0
O V:ILE163 3.0 47.1 1.0
C L:ASP222 3.2 63.8 1.0
C V:ASP166 3.3 43.5 1.0
C V:TRP164 3.4 50.6 1.0
N V:ASP166 3.7 44.0 1.0
O L:ASP222 3.7 62.2 1.0
N V:LEU167 3.7 43.1 1.0
CD1 L:ILE35 3.8 52.4 1.0
CA L:ASP222 3.8 63.9 1.0
CA V:LEU167 3.9 43.6 1.0
C V:ASN165 3.9 45.2 1.0
N V:ASN165 3.9 48.5 1.0
CD2 V:LEU167 4.0 43.7 1.0
C V:ILE163 4.0 49.3 1.0
O L:ARG221 4.0 57.8 1.0
CA V:TRP164 4.1 51.0 1.0
CA V:ASP166 4.1 43.3 1.0
O V:SER169 4.2 46.0 1.0
CA V:ASN165 4.3 46.5 1.0
N V:TRP164 4.4 49.8 1.0
O V:ASN165 4.5 43.4 1.0
O V:GLY162 4.5 43.7 1.0
NH1 L:ARG28 4.7 53.9 1.0
CG1 L:ILE35 4.8 50.9 1.0
N L:ASP222 4.8 62.5 1.0
C L:ARG221 4.8 60.1 1.0
CG V:LEU167 4.9 43.8 1.0
C V:LEU167 4.9 43.5 1.0
CB V:LEU167 4.9 43.8 1.0
CB L:ASP222 4.9 64.6 1.0

Magnesium binding site 6 out of 7 in 5cgh

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5


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 BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:43.0
occ:1.00
 O N:ILE163 2.5 40.5 1.0
O N:SER169 2.5 40.4 1.0
O N:ASP166 2.8 41.1 1.0
C N:ILE163 3.6 41.6 1.0
C N:SER169 3.7 39.4 1.0
NH1 N:ARG19 3.7 39.9 1.0
CD1 a:LEU34 3.7 42.3 1.0
C N:ASP166 3.8 40.5 1.0
CG2 N:ILE163 3.9 40.2 1.0
CA N:GLY167 4.2 41.0 1.0
CA N:ILE163 4.2 41.1 1.0
CZ N:ARG19 4.3 39.0 1.0
CA N:GLY170 4.4 41.4 1.0
O N:GLY167 4.4 41.3 1.0
N N:GLY167 4.4 41.0 1.0
N N:GLY170 4.5 40.0 1.0
C N:GLY167 4.5 40.5 1.0
NH2 N:ARG19 4.5 38.4 1.0
N N:LYS164 4.6 42.8 1.0
CB N:ILE163 4.7 40.2 1.0
N N:SER169 4.7 38.7 1.0
CA N:SER169 4.7 37.7 1.0
N N:ASP166 4.9 39.9 1.0
CG a:LEU34 4.9 43.2 1.0
C N:LYS164 4.9 45.0 1.0
CA N:LYS164 4.9 45.0 1.0
CA N:ASP166 4.9 39.9 1.0
O N:LYS164 5.0 46.8 1.0

Magnesium binding site 7 out of 7 in 5cgh

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5


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 BETA5-G48C Mutant in Complex with Alpha- Chloroacetamide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:60.0
occ:1.00
 O Z:VAL198 2.6 48.6 1.0
O Z:THR192 2.7 53.5 1.0
O Z:HIS195 3.3 45.2 1.0
O Z:ASP222 3.4 68.0 1.0
CG2 Z:THR192 3.5 55.9 1.0
NH2 Z:ARG28 3.6 56.7 1.0
C Z:THR192 3.7 54.5 1.0
C Z:VAL198 3.8 49.0 1.0
CA Z:THR192 4.0 54.4 1.0
OD1 Z:ASP222 4.1 63.6 1.0
O Z:ILE196 4.1 49.0 1.0
NH2 H:ARG19 4.3 56.9 1.0
C Z:HIS195 4.3 46.5 1.0
C Z:ASP222 4.4 68.5 1.0
CA Z:ILE196 4.4 47.0 1.0
CB Z:THR192 4.4 54.8 1.0
CZ Z:ARG28 4.5 55.7 1.0
C Z:ILE196 4.5 46.8 1.0
CA Z:GLY199 4.5 50.5 1.0
N Z:GLY199 4.6 49.8 1.0
NH1 Z:ARG28 4.6 57.3 1.0
O Z:LYS220 4.7 54.4 1.0
N Z:VAL198 4.7 46.5 1.0
CA Z:VAL198 4.8 47.3 1.0
N Z:ILE196 4.8 46.7 1.0
OXT Z:ASP222 4.9 66.3 1.0
N Z:GLU193 4.9 53.9 1.0

Reference:

C.Dubiella, R.Baur, H.Cui, E.M.Huber, M.Groll. Selective Inhibition of the Immunoproteasome By Structure-Based Targeting of A Non-Catalytic Cysteine. Angew.Chem.Int.Ed.Engl. V. 54 15888 2015.
ISSN: ESSN 1521-3773
PubMed: 26563572
DOI: 10.1002/ANIE.201506631
Page generated: Mon Dec 14 20:07:01 2020

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