Atomistry » Magnesium » PDB 5cr0-5d2h » 5cz6
Atomistry »
  Magnesium »
    PDB 5cr0-5d2h »
      5cz6 »

Magnesium in PDB 5cz6: Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans

Enzymatic activity of Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans

All present enzymatic activity of Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans, PDB code: 5cz6 was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.040, 301.440, 145.750, 90.00, 113.27, 90.00
R / Rfree (%) 19.4 / 22.6

Other elements in 5cz6:

The structure of Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans 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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans (pdb code 5cz6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans, PDB code: 5cz6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5cz6

Go back to Magnesium Binding Sites List in 5cz6
Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans


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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:56.7
occ:1.00
O G:MET125 2.1 55.5 1.0
O G:TYR119 2.4 50.5 1.0
O G:ARG122 2.4 54.8 1.0
OG1 G:THR8 2.7 43.5 1.0
CG2 G:THR8 3.3 50.2 1.0
C G:MET125 3.3 54.8 1.0
CB G:THR8 3.5 48.8 1.0
C G:TYR119 3.6 46.8 1.0
C G:ARG122 3.6 52.3 1.0
O G:ALA123 3.8 59.7 1.0
CA G:ALA123 3.9 52.4 1.0
C G:ALA123 3.9 55.3 1.0
N G:ARG126 4.2 49.7 1.0
CA G:ARG126 4.2 49.4 1.0
N G:MET125 4.2 56.4 1.0
N G:ALA123 4.2 50.7 1.0
CA G:MET125 4.3 58.3 1.0
CA G:TYR119 4.3 46.3 1.0
CD G:PRO127 4.4 46.7 1.0
N G:THR8 4.4 50.1 1.0
N G:THR120 4.6 45.0 1.0
CA G:THR8 4.6 50.6 1.0
CB G:MET125 4.7 64.0 1.0
C G:ARG126 4.7 48.6 1.0
N G:ARG122 4.7 49.7 1.0
CA G:THR120 4.7 45.6 1.0
CA G:ARG122 4.7 53.5 1.0
N G:TYR124 4.8 56.8 1.0
C G:THR120 4.8 46.0 1.0
CB G:TYR119 4.9 46.6 1.0
N G:PRO127 4.9 46.7 1.0

Magnesium binding site 2 out of 9 in 5cz6

Go back to Magnesium Binding Sites List in 5cz6
Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans


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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:64.1
occ:1.00
OE1 H:GLN91 2.5 63.6 1.0
OD1 N:ASP51 3.1 45.5 1.0
CD H:GLN91 3.4 60.4 1.0
NE2 H:GLN91 3.5 59.8 1.0
OD2 N:ASP51 3.6 43.4 1.0
O N:ASN92 3.7 46.7 1.0
CG N:ASP51 3.8 41.1 1.0
CG H:GLN91 4.8 56.6 1.0
C N:ASN92 4.8 49.1 1.0
ND1 H:HIS116 4.9 42.9 1.0

Magnesium binding site 3 out of 9 in 5cz6

Go back to Magnesium Binding Sites List in 5cz6
Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans


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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:70.3
occ:1.00
O I:SER180 2.6 51.0 1.0
O I:ASP177 2.7 51.3 1.0
O I:ALA174 2.8 45.2 1.0
C I:ALA174 3.7 49.8 1.0
OXT I:ASP204 3.8 58.6 1.0
C I:SER180 3.8 52.7 1.0
C I:ASP177 3.9 48.8 1.0
CA I:ASP175 4.0 52.5 1.0
N I:ASP175 4.3 51.7 1.0
C I:ASP175 4.4 53.4 1.0
OD1 I:ASP175 4.4 56.8 1.0
CA I:GLY181 4.6 50.9 1.0
O I:ALA178 4.6 49.5 1.0
O I:ASP204 4.6 55.7 1.0
NH1 Y:ARG19 4.6 57.9 1.0
N I:ASP177 4.6 50.2 1.0
C I:ASP204 4.6 56.2 1.0
N I:GLY181 4.6 51.4 1.0
O I:ASP175 4.6 60.0 1.0
NH2 Y:ARG19 4.6 57.9 1.0
CA I:ALA178 4.7 48.4 1.0
N I:SER180 4.7 47.1 1.0
C I:ALA178 4.7 48.8 1.0
N I:ALA178 4.7 47.2 1.0
CA I:SER180 4.8 50.2 1.0
CA I:ASP177 4.8 48.1 1.0
CA I:ALA174 4.9 47.7 1.0

Magnesium binding site 4 out of 9 in 5cz6

Go back to Magnesium Binding Sites List in 5cz6
Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans


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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:55.6
occ:1.00
O Y:ASP168 2.3 47.0 1.0
O I:ASP204 2.4 55.7 1.0
O Y:ALA165 2.5 48.7 1.0
O Y:SER171 2.7 51.2 1.0
C I:ASP204 3.1 56.2 1.0
C Y:ASP168 3.2 49.2 1.0
CA Y:ALA169 3.5 49.0 1.0
O Y:ALA169 3.6 53.5 1.0
CA I:ASP204 3.7 55.6 1.0
C Y:ALA169 3.7 51.0 1.0
C Y:ALA165 3.7 47.5 1.0
NH1 Y:ARG19 3.7 57.9 1.0
N Y:ALA169 3.8 49.2 1.0
O Y:HIS166 3.9 53.3 1.0
C Y:SER171 3.9 50.0 1.0
CB I:ASP204 4.0 56.0 1.0
OXT I:ASP204 4.0 58.6 1.0
N Y:SER171 4.3 49.4 1.0
C Y:HIS166 4.4 48.8 1.0
CA Y:ASP168 4.4 49.0 1.0
N Y:ASP168 4.5 51.8 1.0
CA Y:ALA165 4.5 48.2 1.0
CZ Y:ARG19 4.5 56.3 1.0
N Y:TYR170 4.5 48.9 1.0
CA Y:SER171 4.7 48.6 1.0
N Y:HIS166 4.7 47.7 1.0
O Y:ALA164 4.8 46.1 1.0
CA Y:HIS166 4.8 47.0 1.0
C Y:ARG167 4.8 51.6 1.0
NH2 Y:ARG19 4.9 57.9 1.0
CB Y:ALA169 4.9 47.8 1.0
N Y:GLY172 5.0 49.4 1.0
CG I:ASP204 5.0 56.0 1.0

Magnesium binding site 5 out of 9 in 5cz6

Go back to Magnesium Binding Sites List in 5cz6
Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans


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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:53.2
occ:1.00
O K:ASP168 2.2 48.3 1.0
O K:ALA165 2.4 53.7 1.0
O W:ASP204 2.5 57.0 1.0
O K:SER171 2.6 53.4 1.0
C W:ASP204 3.2 58.7 1.0
C K:ASP168 3.2 50.1 1.0
C K:ALA165 3.5 51.7 1.0
CA W:ASP204 3.5 57.6 1.0
CA K:ALA169 3.7 52.2 1.0
O K:ALA169 3.8 55.8 1.0
C K:SER171 3.8 52.8 1.0
C K:ALA169 3.8 53.8 1.0
NH1 K:ARG19 3.8 61.3 1.0
N K:ALA169 3.8 51.1 1.0
CB W:ASP204 3.9 57.5 1.0
O K:HIS166 3.9 54.6 1.0
OXT W:ASP204 4.1 61.6 1.0
N K:SER171 4.2 54.6 1.0
CA K:ALA165 4.3 52.3 1.0
C K:HIS166 4.3 52.5 1.0
N K:ASP168 4.4 52.1 1.0
CA K:ASP168 4.4 50.1 1.0
CA K:SER171 4.5 51.6 1.0
N K:HIS166 4.5 51.0 1.0
CZ K:ARG19 4.5 58.6 1.0
N K:TYR170 4.6 52.8 1.0
O K:ALA164 4.6 52.2 1.0
CA K:HIS166 4.7 51.6 1.0
C K:ARG167 4.8 53.1 1.0
N K:GLY172 4.8 52.9 1.0
NH2 K:ARG19 4.9 61.9 1.0
N W:ASP204 4.9 57.3 1.0
CG W:ASP204 4.9 57.1 1.0
N K:ARG167 4.9 51.4 1.0
CB K:SER171 4.9 51.2 1.0
CA K:GLY172 5.0 55.0 1.0

Magnesium binding site 6 out of 9 in 5cz6

Go back to Magnesium Binding Sites List in 5cz6
Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans


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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:59.9
occ:1.00
O V:ASP166 2.2 41.5 1.0
O V:ILE163 2.3 47.4 1.0
OXT L:ASP222 2.4 55.4 1.0
O V:SER169 2.6 57.4 1.0
C L:ASP222 3.1 60.0 1.0
C V:ASP166 3.1 45.6 1.0
C V:ILE163 3.4 49.2 1.0
C V:SER169 3.7 50.9 1.0
CA L:ASP222 3.7 60.5 1.0
CA V:LEU167 3.8 47.6 1.0
N V:LEU167 3.8 46.4 1.0
O L:ASP222 3.9 62.4 1.0
O V:GLY162 3.9 44.4 1.0
N V:ASP166 4.0 46.5 1.0
NH1 V:ARG19 4.0 60.7 1.0
C V:TRP164 4.1 51.4 1.0
O V:TRP164 4.1 56.6 1.0
CA V:ASP166 4.2 46.1 1.0
CA V:ILE163 4.2 47.7 1.0
N V:TRP164 4.2 52.1 1.0
C V:LEU167 4.3 47.9 1.0
CB L:ASP222 4.4 63.0 1.0
CA V:TRP164 4.4 51.1 1.0
N V:SER169 4.4 46.5 1.0
O V:LEU167 4.4 47.4 1.0
N V:ASN165 4.5 49.3 1.0
CA V:SER169 4.5 48.0 1.0
N V:GLY170 4.6 50.5 1.0
CA V:GLY170 4.6 53.2 1.0
C V:ASN165 4.7 45.7 1.0
CZ V:ARG19 4.7 56.5 1.0
O L:ARG221 4.8 60.4 1.0
C V:GLY162 4.9 47.4 1.0
CB V:SER169 4.9 48.7 1.0
CD2 V:LEU167 4.9 45.7 1.0
NH2 V:ARG19 4.9 59.8 1.0
N V:GLY168 5.0 47.3 1.0

Magnesium binding site 7 out of 9 in 5cz6

Go back to Magnesium Binding Sites List in 5cz6
Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans


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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:47.9
occ:1.00
O N:ILE163 2.6 45.1 1.0
O N:SER169 2.6 42.8 1.0
O N:ASP166 2.8 44.3 1.0
CD1 a:LEU34 3.5 48.0 1.0
C N:ILE163 3.7 43.7 1.0
NH1 N:ARG19 3.7 43.4 1.0
C N:SER169 3.8 42.9 1.0
C N:ASP166 3.8 41.7 1.0
CG2 N:ILE163 4.0 42.5 1.0
CA N:GLY167 4.1 41.0 1.0
CZ N:ARG19 4.3 44.4 1.0
CA N:ILE163 4.3 42.9 1.0
N N:GLY167 4.4 41.2 1.0
O N:GLY167 4.4 37.8 1.0
CA N:GLY170 4.5 44.5 1.0
C N:GLY167 4.5 39.3 1.0
N N:GLY170 4.6 43.0 1.0
NH2 N:ARG19 4.6 46.5 1.0
N N:SER169 4.7 42.1 1.0
CG a:LEU34 4.7 47.0 1.0
N N:LYS164 4.7 45.2 1.0
CA N:SER169 4.8 41.0 1.0
CB N:ILE163 4.8 42.1 1.0
O N:LYS164 4.8 48.2 1.0
C N:LYS164 4.9 47.0 1.0
N N:ASP166 4.9 40.4 1.0
CA N:ASP166 5.0 41.1 1.0
CA N:LYS164 5.0 45.9 1.0

Magnesium binding site 8 out of 9 in 5cz6

Go back to Magnesium Binding Sites List in 5cz6
Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans


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-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:76.8
occ:1.00
O W:ASP177 2.7 51.5 1.0
O W:SER180 2.8 47.6 1.0
O W:ALA174 2.9 48.0 1.0
OXT W:ASP204 3.8 61.6 1.0
C W:ASP177 3.8 48.5 1.0
C W:ALA174 3.9 51.2 1.0
C W:SER180 4.0 52.0 1.0
CA W:ASP175 4.0 54.2 1.0
NH1 K:ARG19 4.3 61.3 1.0
N W:ASP175 4.3 54.1 1.0
C W:ASP175 4.4 53.3 1.0
NH2 K:ARG19 4.4 61.9 1.0
O W:ALA178 4.5 52.0 1.0
O W:ASP204 4.5 57.0 1.0
N W:ASP177 4.5 50.0 1.0
CA W:ALA178 4.5 49.0 1.0
O W:ASP175 4.5 55.2 1.0
C W:ASP204 4.6 58.7 1.0
N W:ALA178 4.6 46.7 1.0
OD1 W:ASP175 4.6 60.4 1.0
C W:ALA178 4.6 51.1 1.0
CZ K:ARG19 4.7 58.6 1.0
CA W:ASP177 4.7 50.0 1.0
N W:SER180 4.8 52.1 1.0
CA W:GLY181 4.8 52.5 1.0
N W:GLY181 4.8 52.1 1.0
CA W:SER180 4.9 52.7 1.0

Magnesium binding site 9 out of 9 in 5cz6

Go back to Magnesium Binding Sites List in 5cz6
Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Yeast 20S Proteasome BETA5-T1A Mutant in Complex with Syringolin A, Propeptide Expressed in Trans within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:69.4
occ:1.00
O Z:VAL198 2.4 45.5 1.0
O Z:THR192 2.7 54.1 1.0
O Z:HIS195 3.0 46.3 1.0
C Z:VAL198 3.6 48.0 1.0
CG2 Z:THR192 3.6 56.2 1.0
C Z:THR192 3.6 54.4 1.0
NH2 Z:ARG28 3.8 53.0 1.0
O Z:ASP222 3.9 58.6 1.0
CA Z:THR192 4.0 55.0 1.0
O Z:ILE196 4.0 52.8 1.0
C Z:HIS195 4.0 47.6 1.0
CA Z:ILE196 4.2 46.7 1.0
C Z:ILE196 4.2 48.0 1.0
NH2 H:ARG19 4.2 59.7 1.0
CB Z:THR192 4.4 55.5 1.0
N Z:VAL198 4.4 46.3 1.0
OD1 Z:ASP222 4.4 57.9 1.0
N Z:GLY199 4.5 48.6 1.0
CA Z:GLY199 4.5 51.0 1.0
CA Z:VAL198 4.5 47.5 1.0
N Z:ILE196 4.6 46.1 1.0
CZ Z:ARG28 4.7 54.2 1.0
C Z:ASP222 4.7 61.1 1.0
NH1 Z:ARG28 4.9 56.1 1.0
N Z:GLU193 4.9 54.7 1.0
O Z:LYS220 4.9 56.2 1.0
OXT Z:ASP222 5.0 63.8 1.0
CB Z:VAL198 5.0 48.0 1.0

Reference:

E.M.Huber, W.Heinemeyer, X.Li, C.S.Arendt, M.Hochstrasser, M.Groll. A Unified Mechanism For Proteolysis and Autocatalytic Activation in the 20S Proteasome. Nat Commun V. 7 10900 2016.
ISSN: ESSN 2041-1723
PubMed: 26964885
DOI: 10.1038/NCOMMS10900
Page generated: Mon Dec 14 20:08:40 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy