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Magnesium in PDB 4nnn: Ycp in Complex with MG132

Enzymatic activity of Ycp in Complex with MG132

All present enzymatic activity of Ycp in Complex with MG132:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with MG132, PDB code: 4nnn was solved by M.L.Stein, H.Cui, P.Beck, C.Dubiella, C.Voss, A.Krueger, B.Schmidt, 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 (°) 134.690, 299.690, 144.450, 90.00, 112.88, 90.00
R / Rfree (%) 23.8 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with MG132 (pdb code 4nnn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ycp in Complex with MG132, PDB code: 4nnn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4nnn

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Magnesium binding site 1 out of 8 in the Ycp in Complex with MG132


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ycp in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:47.0
occ:1.00
 O G:HOH446 1.9 48.0 1.0
O G:MET125 2.2 28.6 1.0
O G:ARG122 2.3 30.0 1.0
O G:TYR119 2.3 26.9 1.0
OG1 G:THR8 2.6 30.5 1.0
C G:MET125 3.4 28.8 1.0
CG2 G:THR8 3.4 27.6 1.0
C G:ARG122 3.4 29.7 1.0
C G:TYR119 3.5 26.5 1.0
CB G:THR8 3.5 29.5 1.0
O G:ALA123 3.8 31.1 1.0
CA G:ALA123 3.8 27.6 1.0
C G:ALA123 3.9 29.1 1.0
N G:ALA123 4.1 28.6 1.0
CA G:TYR119 4.2 26.3 1.0
N G:MET125 4.2 31.1 1.0
N G:ARG126 4.2 25.8 1.0
CA G:ARG126 4.3 25.3 1.0
CA G:MET125 4.3 30.5 1.0
CD G:PRO127 4.5 25.0 1.0
N G:THR8 4.5 28.9 1.0
N G:THR120 4.5 25.6 1.0
CA G:ARG122 4.6 28.9 1.0
CB G:TYR119 4.7 26.2 1.0
CA G:THR8 4.7 29.8 1.0
N G:ARG122 4.7 27.4 1.0
C G:ARG126 4.7 25.5 1.0
CA G:THR120 4.8 25.5 1.0
CB G:MET125 4.8 31.9 1.0
N G:TYR124 4.8 30.2 1.0
C G:THR120 4.9 25.8 1.0
N G:PRO127 4.9 25.2 1.0

Magnesium binding site 2 out of 8 in 4nnn

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Magnesium binding site 2 out of 8 in the Ycp in Complex with MG132


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycp in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:0.6
occ:1.00
 O H:HOH431 1.9 40.4 1.0
O H:HOH420 2.0 31.1 1.0
OE1 H:GLN91 2.2 32.5 1.0
CD H:GLN91 3.1 31.9 1.0
O N:ASN92 3.4 29.4 1.0
O N:HOH318 3.4 0.3 1.0
NE2 H:GLN91 3.6 30.7 1.0
C N:ASN92 4.0 28.4 1.0
OD1 N:ASP51 4.3 25.6 1.0
CA N:ASN92 4.4 28.4 1.0
CG H:GLN91 4.4 30.0 1.0
CB N:ASN92 4.5 28.5 1.0
OD2 N:ASP51 4.5 25.6 1.0
O H:HOH411 4.6 38.8 1.0
CG N:ASP51 4.8 25.1 1.0
N N:LEU93 4.9 28.0 1.0
CB H:GLN91 5.0 28.7 1.0

Magnesium binding site 3 out of 8 in 4nnn

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Magnesium binding site 3 out of 8 in the Ycp in Complex with MG132


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ycp in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:98.9
occ:1.00
 O I:HOH401 2.0 39.8 1.0
O I:ASP177 2.4 30.7 1.0
O I:SER180 3.1 31.7 1.0
O I:ALA178 3.3 29.4 1.0
C I:ASP177 3.4 30.1 1.0
CA I:ALA178 3.5 28.5 1.0
C I:ALA178 3.5 29.0 1.0
OXT I:ASP204 3.6 40.2 1.0
NH1 Y:ARG19 3.7 29.9 1.0
O I:ALA174 3.8 35.7 1.0
N I:ALA178 3.9 29.1 1.0
O I:ASP204 4.0 39.2 1.0
O I:HOH426 4.2 46.5 1.0
C I:ASP204 4.3 38.7 1.0
C I:SER180 4.3 30.8 1.0
N I:LEU179 4.4 29.2 1.0
NH2 Y:ARG19 4.4 32.0 1.0
CZ Y:ARG19 4.5 31.3 1.0
N I:SER180 4.6 29.5 1.0
CA I:ASP177 4.7 30.2 1.0
CG2 Y:VAL26 4.8 26.7 1.0
CB I:ALA178 4.8 26.7 1.0
O Y:ALA169 4.8 29.3 1.0
N I:ASP177 4.9 29.2 1.0
C I:ALA174 4.9 35.4 1.0

Magnesium binding site 4 out of 8 in 4nnn

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Magnesium binding site 4 out of 8 in the Ycp in Complex with MG132


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ycp in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:67.8
occ:1.00
 O K:ASP168 2.1 27.4 1.0
O K:ALA165 2.2 28.1 1.0
O K:HOH406 2.2 53.8 1.0
O W:ASP204 2.5 28.9 1.0
O K:SER171 3.0 26.0 1.0
C W:ASP204 3.0 28.3 1.0
C K:ASP168 3.1 26.6 1.0
C K:ALA165 3.4 27.3 1.0
CA K:ALA169 3.5 25.6 1.0
CA W:ASP204 3.6 27.6 1.0
N K:ALA169 3.7 25.9 1.0
OXT W:ASP204 3.7 28.7 1.0
O K:HIS166 3.8 28.3 1.0
C K:ALA169 3.8 25.7 1.0
C K:SER171 4.0 25.8 1.0
O K:ALA169 4.0 25.8 1.0
C K:HIS166 4.1 27.5 1.0
CB W:ASP204 4.1 27.4 1.0
N K:ASP168 4.2 26.5 1.0
CA K:ASP168 4.3 26.4 1.0
CA K:ALA165 4.3 26.9 1.0
N K:HIS166 4.3 27.5 1.0
NH1 K:ARG19 4.4 25.0 1.0
N K:SER171 4.4 24.9 1.0
CA K:HIS166 4.4 27.5 1.0
O K:ALA164 4.5 29.1 1.0
N K:TYR170 4.6 25.7 1.0
C K:ARG167 4.6 26.4 1.0
CA K:SER171 4.6 25.0 1.0
N K:ARG167 4.7 26.4 1.0
CZ K:ARG19 4.8 25.5 1.0
N K:GLY172 4.8 25.8 1.0
CB K:SER171 4.9 24.8 1.0
CB K:ALA169 4.9 24.7 1.0
N W:ASP204 5.0 28.1 1.0
CA K:GLY172 5.0 26.3 1.0
NH2 K:ARG19 5.0 25.4 1.0

Magnesium binding site 5 out of 8 in 4nnn

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Magnesium binding site 5 out of 8 in the Ycp in Complex with MG132


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ycp in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:60.6
occ:1.00
 O N:HOH307 1.8 75.1 1.0
O N:SER169 2.3 25.0 1.0
O N:ILE163 2.3 27.7 1.0
O N:ASP166 2.3 26.2 1.0
O N:HOH332 3.2 76.4 1.0
C N:SER169 3.3 24.8 1.0
C N:ILE163 3.4 26.6 1.0
C N:ASP166 3.5 26.1 1.0
CD1 a:LEU34 3.8 25.8 1.0
CG2 N:ILE163 3.8 24.8 1.0
NH1 N:ARG19 3.9 24.4 1.0
CA N:ILE163 4.0 26.1 1.0
CA N:GLY167 4.1 25.3 1.0
CA N:SER169 4.2 24.4 1.0
N N:SER169 4.2 24.3 1.0
N N:GLY170 4.2 24.6 1.0
N N:GLY167 4.2 25.5 1.0
O N:GLY167 4.3 25.4 1.0
C N:GLY167 4.3 25.2 1.0
CA N:GLY170 4.3 24.9 1.0
CB N:SER169 4.4 24.4 1.0
CB N:ILE163 4.5 24.9 1.0
N N:LYS164 4.5 27.1 1.0
CZ N:ARG19 4.5 24.8 1.0
CA N:ASP166 4.6 26.4 1.0
N N:ASP166 4.6 26.6 1.0
C N:LYS164 4.7 27.4 1.0
O N:LYS164 4.8 28.3 1.0
CA N:LYS164 4.8 27.2 1.0
NH2 N:ARG19 4.9 24.6 1.0
CG a:LEU34 5.0 25.8 1.0

Magnesium binding site 6 out of 8 in 4nnn

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Magnesium binding site 6 out of 8 in the Ycp in Complex with MG132


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ycp in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:1.0
occ:1.00
 O V:ASP166 1.9 31.9 1.0
O V:SER169 2.2 30.6 1.0
O V:ILE163 2.3 35.6 1.0
O V:HOH404 2.4 61.4 1.0
OXT L:ASP222 2.6 41.4 1.0
C V:ASP166 2.9 31.7 1.0
C V:ILE163 3.3 34.9 1.0
C L:ASP222 3.4 39.8 1.0
C V:SER169 3.4 30.4 1.0
O V:GLY162 3.4 37.3 1.0
N V:LEU167 3.7 30.1 1.0
N V:ASP166 3.7 31.7 1.0
CA V:LEU167 3.8 29.5 1.0
CA V:ASP166 3.9 31.6 1.0
CA V:ILE163 4.0 34.1 1.0
CA L:ASP222 4.0 37.2 1.0
O L:ASP222 4.1 38.8 1.0
NH1 V:ARG19 4.2 26.8 1.0
N V:SER169 4.2 30.2 1.0
N V:TRP164 4.2 35.6 1.0
C V:TRP164 4.2 35.5 1.0
CA V:SER169 4.2 29.7 1.0
C V:LEU167 4.3 29.6 1.0
N V:GLY170 4.4 29.5 1.0
N V:ASN165 4.4 33.0 1.0
O V:TRP164 4.4 36.9 1.0
C V:GLY162 4.4 35.1 1.0
CA V:TRP164 4.5 35.7 1.0
C V:ASN165 4.5 32.6 1.0
CA V:GLY170 4.5 30.5 1.0
CB V:SER169 4.6 29.0 1.0
CB L:ASP222 4.6 38.4 1.0
O V:LEU167 4.6 30.1 1.0
CZ V:ARG19 4.6 27.3 1.0
CB V:ASP166 4.7 31.5 1.0
N V:ILE163 4.7 34.2 1.0
N V:GLY168 4.8 29.4 1.0
NH2 V:ARG19 4.9 27.0 1.0
CA V:ASN165 5.0 32.5 1.0

Magnesium binding site 7 out of 8 in 4nnn

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Magnesium binding site 7 out of 8 in the Ycp in Complex with MG132


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ycp in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:42.2
occ:1.00
 O Y:ASP168 2.2 27.9 1.0
O I:ASP204 2.3 39.2 1.0
O Y:ALA165 2.5 30.2 1.0
O Y:HOH404 2.8 38.6 1.0
O Y:SER171 2.9 32.9 1.0
C I:ASP204 2.9 38.7 1.0
C Y:ASP168 3.2 27.1 1.0
CA Y:ALA169 3.4 28.7 1.0
OXT I:ASP204 3.6 40.2 1.0
CA I:ASP204 3.6 36.6 1.0
N Y:ALA169 3.6 27.9 1.0
C Y:ALA169 3.6 29.2 1.0
C Y:ALA165 3.7 30.1 1.0
O Y:ALA169 3.8 29.3 1.0
C Y:SER171 3.9 30.9 1.0
NH1 Y:ARG19 4.0 29.9 1.0
O Y:HIS166 4.1 32.4 1.0
CB I:ASP204 4.1 35.6 1.0
N Y:SER171 4.3 28.6 1.0
C Y:HIS166 4.4 30.6 1.0
CA Y:ASP168 4.4 26.2 1.0
N Y:TYR170 4.4 29.4 1.0
N Y:ASP168 4.5 27.9 1.0
CZ Y:ARG19 4.5 31.3 1.0
CA Y:ALA165 4.6 29.9 1.0
CA Y:SER171 4.6 28.9 1.0
N Y:HIS166 4.6 29.8 1.0
NH2 Y:ARG19 4.7 32.0 1.0
CB Y:ALA169 4.7 27.7 1.0
CA Y:HIS166 4.7 29.5 1.0
O Y:ALA164 4.8 31.7 1.0
N Y:GLY172 4.8 33.6 1.0
C Y:ARG167 4.9 29.6 1.0
CB Y:SER171 4.9 28.2 1.0
CA Y:GLY172 4.9 33.5 1.0
N I:ASP204 5.0 35.7 1.0

Magnesium binding site 8 out of 8 in 4nnn

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Magnesium binding site 8 out of 8 in the Ycp in Complex with MG132


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ycp in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:98.0
occ:1.00
 O Z:HOH408 2.0 53.1 1.0
O Z:HOH415 2.1 36.8 1.0
O Z:VAL198 2.3 33.9 1.0
O Z:THR192 2.4 37.9 1.0
O Z:HIS195 2.5 31.5 1.0
C Z:THR192 3.3 37.3 1.0
C Z:VAL198 3.5 33.0 1.0
CG2 Z:THR192 3.5 31.6 1.0
CA Z:THR192 3.6 34.7 1.0
C Z:HIS195 3.6 30.9 1.0
NH2 Z:ARG28 3.7 30.2 1.0
CA Z:ILE196 4.0 29.8 1.0
O Z:ILE196 4.1 30.0 1.0
C Z:ILE196 4.1 29.7 1.0
CB Z:THR192 4.2 33.3 1.0
N Z:VAL198 4.2 32.1 1.0
O Z:ASP222 4.3 42.4 1.0
N Z:ILE196 4.3 30.1 1.0
CA Z:VAL198 4.3 31.3 1.0
N Z:GLY199 4.5 32.0 1.0
N Z:GLU193 4.6 33.7 1.0
CA Z:GLY199 4.6 33.2 1.0
CB Z:VAL198 4.7 29.3 1.0
N Z:HIS195 4.7 31.6 1.0
O Z:ALA191 4.7 36.4 1.0
CA Z:HIS195 4.8 30.8 1.0
CZ Z:ARG28 4.8 31.0 1.0
NH2 H:ARG19 4.8 32.5 1.0
N Z:GLN197 4.9 30.0 1.0
N Z:THR192 4.9 35.5 1.0
OG1 Z:THR192 4.9 33.3 1.0
OD1 Z:ASP222 4.9 40.8 1.0

Reference:

M.L.Stein, H.Cui, P.Beck, C.Dubiella, C.Voss, A.Kruger, B.Schmidt, M.Groll. Systematic Comparison of Peptidic Proteasome Inhibitors Highlights the Alpha-Ketoamide Electrophile As An Auspicious Reversible Lead Motif. Angew.Chem.Int.Ed.Engl. V. 53 1679 2014.
ISSN: ISSN 1433-7851
PubMed: 24403024
DOI: 10.1002/ANIE.201308984
Page generated: Mon Aug 19 23:44:14 2024

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