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Magnesium in PDB 5cgf: Yeast 20S Proteasome BETA5-G48C Mutant

Enzymatic activity of Yeast 20S Proteasome BETA5-G48C Mutant

All present enzymatic activity of Yeast 20S Proteasome BETA5-G48C Mutant:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-G48C Mutant, PDB code: 5cgf 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.460, 300.960, 143.860, 90.00, 112.88, 90.00
R / Rfree (%) 18.6 / 20.1

Other elements in 5cgf:

The structure of Yeast 20S Proteasome BETA5-G48C Mutant also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA5-G48C Mutant (pdb code 5cgf). 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 BETA5-G48C Mutant, PDB code: 5cgf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5cgf

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:47.2
occ:1.00
 O G:MET125 2.1 47.0 1.0
O G:ARG122 2.3 43.4 1.0
O G:TYR119 2.4 40.3 1.0
OG1 G:THR8 2.6 42.2 1.0
O G:HOH406 2.6 38.1 1.0
CG2 G:THR8 3.3 44.5 1.0
C G:MET125 3.3 47.7 1.0
C G:ARG122 3.5 44.8 1.0
CB G:THR8 3.5 44.4 1.0
C G:TYR119 3.6 39.8 1.0
O G:ALA123 3.6 48.5 1.0
CA G:ALA123 3.8 45.8 1.0
C G:ALA123 3.8 47.2 1.0
N G:ALA123 4.1 44.9 1.0
N G:MET125 4.2 50.4 1.0
N G:ARG126 4.2 43.8 1.0
CA G:ARG126 4.2 42.3 1.0
CA G:MET125 4.3 51.0 1.0
N G:THR8 4.4 47.0 1.0
CA G:TYR119 4.4 39.6 1.0
CD G:PRO127 4.5 39.6 1.0
CA G:THR8 4.5 45.8 1.0
N G:THR120 4.6 39.8 1.0
N G:ARG122 4.6 43.6 1.0
CA G:ARG122 4.6 46.3 1.0
N G:TYR124 4.7 48.5 1.0
CA G:THR120 4.7 39.6 1.0
CB G:MET125 4.8 55.5 1.0
C G:ARG126 4.8 40.6 1.0
C G:THR120 4.8 40.4 1.0
CB G:TYR119 4.9 39.9 1.0
N G:PRO127 4.9 39.6 1.0

Magnesium binding site 2 out of 8 in 5cgf

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:63.5
occ:1.00
 O I:ASP177 2.3 44.4 1.0
O I:ALA174 2.4 45.4 1.0
O I:SER180 2.6 47.9 1.0
O Y:HOH404 2.6 42.5 1.0
O I:HOH408 3.3 54.8 1.0
C I:ALA174 3.5 44.5 1.0
C I:ASP177 3.5 44.2 1.0
C I:SER180 3.7 46.5 1.0
O Y:HOH403 3.8 48.2 1.0
CA I:ASP175 3.9 47.2 1.0
OXT I:ASP204 4.1 54.5 1.0
N I:ASP175 4.1 45.7 1.0
N I:ASP177 4.2 44.2 1.0
C I:ASP175 4.2 47.2 1.0
N I:ALA178 4.4 43.3 1.0
CA I:ASP177 4.4 43.9 1.0
CA I:ALA178 4.5 44.1 1.0
O I:ASP175 4.5 49.6 1.0
N I:SER180 4.5 45.0 1.0
O I:ALA178 4.5 46.4 1.0
C I:ALA178 4.5 45.2 1.0
OD1 I:ASP175 4.6 49.7 1.0
N I:GLY181 4.6 45.8 1.0
CA I:GLY181 4.6 45.6 1.0
CA I:ALA174 4.6 42.6 1.0
CA I:SER180 4.6 46.2 1.0
N I:ARG176 4.8 46.1 1.0
NH1 Y:ARG19 4.8 47.9 1.0
CB I:ASP177 4.9 44.5 1.0
CB I:ALA174 4.9 41.5 1.0
NH2 Y:ARG19 5.0 49.2 1.0
C I:ASP204 5.0 52.5 1.0

Magnesium binding site 3 out of 8 in 5cgf

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:53.3
occ:1.00
 O Y:ASP168 2.2 40.7 1.0
O Y:SER171 2.3 43.9 1.0
O I:ASP204 2.4 53.4 1.0
O Y:ALA165 2.5 41.5 1.0
C I:ASP204 3.2 52.5 1.0
C Y:ASP168 3.3 40.3 1.0
NH1 Y:ARG19 3.5 47.9 1.0
C Y:SER171 3.5 42.5 1.0
C Y:ALA165 3.6 40.4 1.0
O Y:ALA169 3.6 39.6 1.0
CA Y:ALA169 3.6 39.3 1.0
C Y:ALA169 3.7 40.0 1.0
CA I:ASP204 3.8 51.2 1.0
N Y:ALA169 3.9 39.9 1.0
N Y:SER171 4.0 41.0 1.0
CB I:ASP204 4.0 52.1 1.0
OXT I:ASP204 4.1 54.5 1.0
CA Y:ALA165 4.2 40.3 1.0
CZ Y:ARG19 4.3 48.1 1.0
CA Y:SER171 4.3 40.9 1.0
O Y:HIS166 4.3 40.8 1.0
O Y:HOH404 4.4 42.5 1.0
N Y:TYR170 4.4 40.5 1.0
CA Y:ASP168 4.5 40.1 1.0
N Y:GLY172 4.5 42.8 1.0
N Y:ASP168 4.5 39.9 1.0
C Y:HIS166 4.6 39.6 1.0
N Y:HIS166 4.6 40.4 1.0
NH2 Y:ARG19 4.7 49.2 1.0
CA Y:GLY172 4.7 42.2 1.0
O Y:ALA164 4.7 40.7 1.0
CB Y:SER171 4.8 40.8 1.0
CG I:ASP204 4.9 53.1 1.0
CA Y:HIS166 4.9 39.7 1.0

Magnesium binding site 4 out of 8 in 5cgf

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:45.0
occ:1.00
 O K:ASP168 2.2 40.6 1.0
O K:ALA165 2.3 41.8 1.0
O W:ASP204 2.3 48.6 1.0
O K:SER171 2.4 43.2 1.0
C W:ASP204 3.1 49.2 1.0
C K:ASP168 3.3 38.7 1.0
C K:ALA165 3.4 41.1 1.0
CA W:ASP204 3.6 48.0 1.0
C K:SER171 3.7 42.5 1.0
NH1 K:ARG19 3.7 48.3 1.0
CA K:ALA169 3.7 39.0 1.0
O K:ALA169 3.8 41.6 1.0
C K:ALA169 3.9 40.5 1.0
CB W:ASP204 3.9 47.3 1.0
N K:ALA169 3.9 38.1 1.0
OXT W:ASP204 4.0 51.1 1.0
O K:HIS166 4.1 42.3 1.0
CA K:ALA165 4.1 41.1 1.0
N K:SER171 4.2 40.8 1.0
C K:HIS166 4.4 40.1 1.0
CA K:ASP168 4.4 38.1 1.0
CA K:SER171 4.4 40.8 1.0
N K:ASP168 4.4 38.4 1.0
N K:HIS166 4.5 40.3 1.0
CZ K:ARG19 4.5 47.6 1.0
N K:TYR170 4.6 41.1 1.0
O K:ALA164 4.6 40.9 1.0
N K:GLY172 4.6 43.2 1.0
CA K:HIS166 4.7 40.2 1.0
CA K:GLY172 4.8 43.7 1.0
NH2 K:ARG19 4.8 50.2 1.0
CG W:ASP204 4.8 47.1 1.0
CB K:SER171 4.9 40.2 1.0
C K:ARG167 4.9 39.0 1.0
CB K:ALA165 4.9 41.4 1.0
N W:ASP204 5.0 47.7 1.0

Magnesium binding site 5 out of 8 in 5cgf

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:63.1
occ:1.00
 O V:ASP166 2.1 43.8 1.0
OXT L:ASP222 2.1 62.1 1.0
O V:ILE163 2.2 43.2 1.0
O V:SER169 2.4 44.5 1.0
C L:ASP222 3.1 60.4 1.0
C V:ASP166 3.2 43.9 1.0
C V:ILE163 3.3 44.8 1.0
C V:SER169 3.6 45.5 1.0
CA L:ASP222 3.7 60.4 1.0
CA V:LEU167 3.8 43.8 1.0
O V:GLY162 3.9 43.0 1.0
N V:LEU167 3.9 44.0 1.0
NH1 V:ARG19 3.9 52.7 1.0
O L:ASP222 4.0 60.1 1.0
N V:ASP166 4.1 43.2 1.0
CA V:ILE163 4.1 44.8 1.0
C V:LEU167 4.2 43.2 1.0
CA V:ASP166 4.2 43.1 1.0
C V:TRP164 4.3 46.7 1.0
N V:TRP164 4.3 45.9 1.0
CB L:ASP222 4.3 60.8 1.0
O V:TRP164 4.3 47.9 1.0
N V:SER169 4.3 44.8 1.0
O V:LEU167 4.4 41.9 1.0
CA V:SER169 4.4 45.3 1.0
N V:GLY170 4.5 46.7 1.0
CA V:GLY170 4.5 50.2 1.0
CA V:TRP164 4.5 46.8 1.0
CZ V:ARG19 4.6 51.5 1.0
N V:ASN165 4.6 45.8 1.0
NH2 V:ARG19 4.8 54.1 1.0
C V:ASN165 4.8 43.5 1.0
CB V:SER169 4.8 45.2 1.0
C V:GLY162 4.8 43.9 1.0
O L:ARG221 4.9 62.1 1.0
N V:GLY168 4.9 44.0 1.0
CD2 V:LEU167 5.0 44.0 1.0
N V:ILE163 5.0 44.7 1.0
CB V:ASP166 5.0 43.0 1.0

Magnesium binding site 6 out of 8 in 5cgf

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:52.0
occ:1.00
 O N:SER169 2.7 40.4 1.0
O N:ILE163 2.7 39.2 1.0
O N:ASP166 3.0 40.1 1.0
CD1 a:LEU34 3.5 45.3 1.0
NH1 N:ARG19 3.6 40.4 1.0
C N:ILE163 3.8 39.9 1.0
C N:SER169 3.9 40.1 1.0
CG2 N:ILE163 3.9 38.0 1.0
C N:ASP166 4.0 38.2 1.0
CA N:GLY167 4.1 37.1 1.0
CZ N:ARG19 4.2 40.9 1.0
NH2 N:ARG19 4.4 42.3 1.0
O N:GLY167 4.4 37.8 1.0
CA N:ILE163 4.5 38.7 1.0
CA N:GLY170 4.5 41.6 1.0
C N:GLY167 4.5 37.4 1.0
N N:GLY167 4.5 37.4 1.0
N N:GLY170 4.6 41.0 1.0
CG a:LEU34 4.8 44.5 1.0
CB N:ILE163 4.8 38.1 1.0
N N:SER169 4.9 38.7 1.0
N N:LYS164 4.9 41.3 1.0
CA N:SER169 4.9 38.4 1.0
O N:LYS164 5.0 44.4 1.0

Magnesium binding site 7 out of 8 in 5cgf

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:50.6
occ:1.00
 O W:ASP177 2.1 44.5 1.0
O W:SER180 2.4 43.9 1.0
O W:ALA174 2.5 41.4 1.0
C W:ASP177 3.3 42.6 1.0
C W:SER180 3.6 43.8 1.0
C W:ALA174 3.7 41.6 1.0
OXT W:ASP204 4.1 51.1 1.0
N W:ALA178 4.2 42.1 1.0
N W:ASP177 4.2 42.8 1.0
CA W:ASP175 4.2 44.6 1.0
CA W:ALA178 4.2 42.0 1.0
N W:SER180 4.2 43.9 1.0
O W:ALA178 4.2 43.8 1.0
C W:ALA178 4.2 42.6 1.0
CA W:ASP177 4.3 42.5 1.0
N W:ASP175 4.4 43.4 1.0
CA W:SER180 4.4 44.3 1.0
C W:ASP175 4.5 43.8 1.0
N W:GLY181 4.5 43.1 1.0
CA W:GLY181 4.6 43.2 1.0
O W:ASP175 4.7 45.5 1.0
CA W:ALA174 4.7 39.5 1.0
NH1 K:ARG19 4.7 48.3 1.0
CB W:ASP177 4.8 43.4 1.0
N W:LEU179 4.9 42.1 1.0
CB W:SER180 4.9 44.6 1.0
OD1 W:ASP175 4.9 49.5 1.0
N W:ARG176 5.0 43.0 1.0

Magnesium binding site 8 out of 8 in 5cgf

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-G48C Mutant


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 BETA5-G48C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:60.6
occ:1.00
 O Z:VAL198 2.5 45.2 1.0
O Z:THR192 2.7 54.1 1.0
O Z:HIS195 2.9 43.9 1.0
O Z:ASP222 3.6 60.9 1.0
C Z:THR192 3.7 53.5 1.0
C Z:VAL198 3.7 47.1 1.0
NH2 Z:ARG28 3.8 51.4 1.0
C Z:HIS195 3.9 45.3 1.0
CG2 Z:THR192 3.9 54.4 1.0
CA Z:ILE196 3.9 44.3 1.0
O Z:ILE196 3.9 46.6 1.0
CA Z:THR192 4.0 52.9 1.0
C Z:ILE196 4.1 44.8 1.0
NH2 H:ARG19 4.2 56.0 1.0
N Z:ILE196 4.4 44.5 1.0
N Z:VAL198 4.4 45.7 1.0
OD1 Z:ASP222 4.5 61.8 1.0
C Z:ASP222 4.6 62.5 1.0
CB Z:THR192 4.6 53.5 1.0
CA Z:VAL198 4.6 46.6 1.0
N Z:GLY199 4.7 48.4 1.0
CA Z:GLY199 4.7 50.0 1.0
CZ Z:ARG28 4.8 51.3 1.0
N Z:GLU193 4.9 53.7 1.0
N Z:GLN197 4.9 44.5 1.0
CZ H:ARG19 4.9 56.2 1.0
NH1 H:ARG19 4.9 57.4 1.0
OXT Z:ASP222 5.0 64.6 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: Sun Sep 29 02:05:46 2024

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