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Magnesium in PDB 4no8: Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide

Enzymatic activity of Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide

All present enzymatic activity of Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide, PDB code: 4no8 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.150, 300.350, 144.830, 90.00, 112.48, 90.00
R / Rfree (%) 19.3 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide (pdb code 4no8). 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 Z-Leu-Leu-Leu-Ketoamide, PDB code: 4no8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4no8

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Magnesium binding site 1 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide


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 Z-Leu-Leu-Leu-Ketoamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:59.4
occ:1.00
 O G:MET125 2.2 48.1 1.0
O G:ARG122 2.6 46.4 1.0
OG1 G:THR8 2.7 37.8 1.0
O G:TYR119 2.8 40.3 1.0
O G:ALA123 3.2 53.0 1.0
CG2 G:THR8 3.2 42.4 1.0
C G:MET125 3.3 48.4 1.0
CB G:THR8 3.5 41.0 1.0
C G:ALA123 3.6 46.9 1.0
CA G:ALA123 3.7 41.8 1.0
C G:ARG122 3.7 44.6 1.0
C G:TYR119 4.0 39.5 1.0
N G:THR8 4.1 41.5 1.0
N G:MET125 4.2 48.3 1.0
N G:ALA123 4.2 42.0 1.0
N G:ARG126 4.2 45.7 1.0
CA G:ARG126 4.3 42.5 1.0
CA G:MET125 4.3 49.5 1.0
CA G:THR8 4.4 42.4 1.0
N G:TYR124 4.6 51.8 1.0
CD G:PRO127 4.6 33.4 1.0
CA G:TYR119 4.7 37.3 1.0
CB G:MET125 4.9 54.0 1.0
C G:TYR124 4.9 50.3 1.0
C G:ARG126 4.9 40.0 1.0
CA G:ARG122 5.0 44.9 1.0

Magnesium binding site 2 out of 8 in 4no8

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Magnesium binding site 2 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide


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 Z-Leu-Leu-Leu-Ketoamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:55.7
occ:1.00
 OE1 H:GLN91 2.4 42.8 1.0
O N:HOH305 3.3 50.3 1.0
OD1 N:ASP51 3.4 49.9 1.0
O N:ASN92 3.4 45.7 1.0
CD H:GLN91 3.5 44.4 1.0
OD2 N:ASP51 3.7 38.1 1.0
NE2 H:GLN91 3.9 42.4 1.0
CG N:ASP51 4.0 43.5 1.0
C N:ASN92 4.5 46.0 1.0
CG H:GLN91 4.8 42.4 1.0

Magnesium binding site 3 out of 8 in 4no8

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Magnesium binding site 3 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide


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 Z-Leu-Leu-Leu-Ketoamide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:77.8
occ:1.00
 O I:ASP177 2.3 42.3 1.0
O I:SER180 2.8 42.2 1.0
O I:ALA174 3.1 51.7 1.0
C I:ASP177 3.4 43.8 1.0
OXT I:ASP204 3.7 46.2 1.0
CA I:ALA178 3.8 39.6 1.0
O I:ALA178 3.9 48.1 1.0
C I:ALA178 3.9 41.7 1.0
N I:ALA178 4.0 40.8 1.0
C I:SER180 4.0 46.4 1.0
NH1 Y:ARG19 4.0 59.8 1.0
C I:ALA174 4.3 49.2 1.0
O I:ASP204 4.4 52.5 1.0
C I:ASP204 4.5 48.7 1.0
CA I:ASP177 4.5 46.0 1.0
N I:SER180 4.5 47.3 1.0
N I:ASP177 4.5 45.6 1.0
NH2 Y:ARG19 4.6 55.2 1.0
CA I:ASP175 4.7 50.8 1.0
N I:LEU179 4.7 42.8 1.0
CZ Y:ARG19 4.8 57.6 1.0
C I:ASP175 4.8 50.7 1.0
O I:ASP175 4.9 54.6 1.0
CA I:SER180 4.9 47.6 1.0
N I:GLY181 4.9 43.5 1.0
CG2 Y:VAL26 4.9 46.5 1.0
N I:ASP175 5.0 49.3 1.0
CA I:GLY181 5.0 40.7 1.0

Magnesium binding site 4 out of 8 in 4no8

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Magnesium binding site 4 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide


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 Z-Leu-Leu-Leu-Ketoamide within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:58.4
occ:1.00
 O W:ASP204 2.3 52.0 1.0
O K:ASP168 2.3 47.4 1.0
O K:ALA165 2.4 40.9 1.0
O K:SER171 2.6 38.8 1.0
C W:ASP204 3.1 54.1 1.0
C K:ASP168 3.3 43.0 1.0
C K:ALA165 3.5 44.0 1.0
CA W:ASP204 3.6 52.7 1.0
CA K:ALA169 3.6 38.6 1.0
C K:SER171 3.8 40.3 1.0
N K:ALA169 3.8 41.6 1.0
O K:ALA169 3.8 48.1 1.0
C K:ALA169 3.8 42.8 1.0
O K:HIS166 3.9 45.5 1.0
OXT W:ASP204 4.0 56.9 1.0
CB W:ASP204 4.0 51.4 1.0
NH1 K:ARG19 4.1 56.9 1.0
C K:HIS166 4.3 44.5 1.0
N K:SER171 4.3 39.3 1.0
CA K:ALA165 4.3 44.8 1.0
N K:ASP168 4.4 42.6 1.0
CA K:ASP168 4.4 40.8 1.0
N K:HIS166 4.5 44.5 1.0
CZ K:ARG19 4.5 56.4 1.0
CA K:SER171 4.6 37.4 1.0
CA K:HIS166 4.6 44.8 1.0
N K:TYR170 4.6 43.4 1.0
O K:ALA164 4.7 39.5 1.0
NH2 K:ARG19 4.8 58.8 1.0
N K:GLY172 4.8 42.4 1.0
C K:ARG167 4.8 43.9 1.0
CA K:GLY172 4.9 44.3 1.0
N K:ARG167 4.9 43.7 1.0
CB K:SER171 5.0 34.8 1.0
CB K:ALA169 5.0 33.8 1.0
N W:ASP204 5.0 53.1 1.0

Magnesium binding site 5 out of 8 in 4no8

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Magnesium binding site 5 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide


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 Z-Leu-Leu-Leu-Ketoamide within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:63.9
occ:1.00
 O N:ILE163 2.9 41.0 1.0
O N:SER169 3.0 39.4 1.0
O N:ASP166 3.5 41.0 1.0
CD1 a:LEU34 3.6 44.6 1.0
NH1 N:ARG19 3.6 42.1 1.0
C N:ILE163 4.0 39.7 1.0
CZ N:ARG19 4.1 38.8 1.0
C N:SER169 4.2 36.9 1.0
NH2 N:ARG19 4.2 37.1 1.0
CG2 N:ILE163 4.2 34.1 1.0
CA N:GLY167 4.4 39.0 1.0
C N:ASP166 4.4 38.2 1.0
CA N:GLY170 4.5 41.4 1.0
O N:GLY167 4.6 38.0 1.0
C N:GLY167 4.8 37.4 1.0
N N:GLY167 4.8 37.9 1.0
CA N:ILE163 4.8 37.6 1.0
O N:LYS164 4.8 52.1 1.0
N N:GLY170 4.8 38.3 1.0
CG a:LEU34 4.9 47.2 1.0
N N:LYS164 5.0 40.9 1.0

Magnesium binding site 6 out of 8 in 4no8

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Magnesium binding site 6 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide


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 Z-Leu-Leu-Leu-Ketoamide within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:59.5
occ:1.00
 O V:ASP166 2.1 51.1 1.0
O V:SER169 2.1 46.2 1.0
OXT L:ASP222 2.2 56.9 1.0
O V:ILE163 2.4 48.7 1.0
O V:HOH402 2.7 47.3 1.0
C V:ASP166 3.1 48.6 1.0
C L:ASP222 3.2 54.8 1.0
C V:SER169 3.3 47.6 1.0
C V:ILE163 3.4 48.0 1.0
NH1 V:ARG19 3.8 59.4 1.0
CA V:LEU167 3.8 49.1 1.0
N V:LEU167 3.8 49.3 1.0
O V:GLY162 3.8 45.5 1.0
CA L:ASP222 3.9 53.7 1.0
O L:ASP222 4.0 53.0 1.0
N V:SER169 4.0 48.2 1.0
N V:ASP166 4.1 46.3 1.0
CA V:ILE163 4.1 49.5 1.0
CA V:ASP166 4.1 45.8 1.0
CA V:SER169 4.2 47.1 1.0
C V:LEU167 4.2 47.9 1.0
CZ V:ARG19 4.3 62.5 1.0
N V:GLY170 4.3 48.0 1.0
CB L:ASP222 4.3 53.4 1.0
CA V:GLY170 4.4 51.4 1.0
O V:LEU167 4.4 49.9 1.0
N V:TRP164 4.4 48.6 1.0
NH2 V:ARG19 4.5 65.5 1.0
C V:TRP164 4.5 50.3 1.0
CB V:SER169 4.6 46.5 1.0
O V:TRP164 4.7 46.8 1.0
CA V:TRP164 4.7 50.6 1.0
N V:ASN165 4.8 49.2 1.0
C V:GLY162 4.8 45.7 1.0
N V:GLY168 4.8 47.2 1.0
C V:ASN165 4.8 47.3 1.0
CB V:ASP166 4.9 44.8 1.0
N V:ILE163 4.9 48.1 1.0

Magnesium binding site 7 out of 8 in 4no8

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Magnesium binding site 7 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide


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 Z-Leu-Leu-Leu-Ketoamide within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:55.4
occ:1.00
 O Y:ASP168 2.4 52.4 1.0
O I:ASP204 2.4 52.5 1.0
O Y:ALA165 2.5 41.0 1.0
O Y:SER171 2.8 47.0 1.0
C I:ASP204 3.2 48.7 1.0
C Y:ASP168 3.2 48.2 1.0
CA Y:ALA169 3.5 43.5 1.0
C Y:ALA165 3.6 39.9 1.0
CA I:ASP204 3.7 45.8 1.0
N Y:ALA169 3.7 45.5 1.0
O Y:HIS166 3.8 40.7 1.0
C Y:ALA169 3.8 44.7 1.0
O Y:ALA169 3.9 50.3 1.0
C Y:SER171 4.0 49.4 1.0
OXT I:ASP204 4.0 46.2 1.0
CB I:ASP204 4.1 44.6 1.0
C Y:HIS166 4.2 41.2 1.0
NH1 Y:ARG19 4.2 59.8 1.0
N Y:ASP168 4.3 50.8 1.0
CA Y:ASP168 4.4 48.0 1.0
N Y:SER171 4.5 46.4 1.0
CA Y:ALA165 4.5 42.7 1.0
N Y:HIS166 4.5 38.3 1.0
CA Y:HIS166 4.6 38.3 1.0
N Y:TYR170 4.7 45.9 1.0
CZ Y:ARG19 4.7 57.6 1.0
C Y:ARG167 4.7 48.5 1.0
O Y:ALA164 4.7 44.7 1.0
CA Y:SER171 4.8 46.4 1.0
N Y:ARG167 4.8 43.0 1.0
CB Y:ALA169 4.8 43.1 1.0
NH2 Y:ARG19 4.9 55.2 1.0
N I:ASP204 5.0 47.8 1.0

Magnesium binding site 8 out of 8 in 4no8

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Magnesium binding site 8 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoamide


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 Z-Leu-Leu-Leu-Ketoamide within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:58.5
occ:1.00
 O Z:VAL198 2.6 40.0 1.0
O Z:THR192 2.7 51.1 1.0
O Z:HIS195 3.3 49.3 1.0
CG2 Z:THR192 3.5 40.8 1.0
NH2 Z:ARG28 3.6 54.1 1.0
O Z:ASP222 3.6 57.4 1.0
C Z:THR192 3.7 50.4 1.0
C Z:VAL198 3.8 43.8 1.0
CA Z:THR192 4.0 49.5 1.0
O Z:ILE196 4.1 57.5 1.0
OD1 Z:ASP222 4.2 65.1 1.0
NH2 H:ARG19 4.3 65.8 1.0
C Z:HIS195 4.3 46.7 1.0
CB Z:THR192 4.4 45.1 1.0
CA Z:ILE196 4.4 50.1 1.0
CA Z:GLY199 4.4 42.7 1.0
C Z:ILE196 4.5 52.1 1.0
C Z:ASP222 4.5 63.4 1.0
N Z:GLY199 4.5 42.6 1.0
CZ Z:ARG28 4.5 53.7 1.0
O Z:LYS220 4.6 50.6 1.0
N Z:VAL198 4.7 46.4 1.0
NH1 Z:ARG28 4.7 51.5 1.0
CA Z:VAL198 4.8 44.1 1.0
N Z:ILE196 4.9 49.4 1.0
N Z:GLU193 4.9 50.1 1.0
OXT Z:ASP222 4.9 66.0 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 23:44:13 2024

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