Atomistry » Magnesium » PDB 4nlz-4nxm » 4no9
Atomistry »
  Magnesium »
    PDB 4nlz-4nxm »
      4no9 »

Magnesium in PDB 4no9: Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone

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

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

Protein crystallography data

The structure of Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone, PDB code: 4no9 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.490, 301.490, 144.390, 90.00, 114.15, 90.00
R / Rfree (%) 17.7 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone (pdb code 4no9). 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-Epoxyketone, PDB code: 4no9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4no9

Go back to Magnesium Binding Sites List in 4no9
Magnesium binding site 1 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone


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

b:58.3
occ:1.00
 O G:MET125 2.3 48.1 1.0
OG1 G:THR8 2.5 41.5 1.0
O G:ARG122 2.7 42.1 1.0
O G:TYR119 2.9 34.8 1.0
O G:ALA123 3.1 55.2 1.0
CG2 G:THR8 3.3 42.1 1.0
C G:MET125 3.4 50.7 1.0
CB G:THR8 3.5 41.9 1.0
C G:ALA123 3.5 50.9 1.0
CA G:ALA123 3.6 48.2 1.0
C G:ARG122 3.7 44.7 1.0
N G:MET125 4.1 56.5 1.0
N G:ALA123 4.1 45.3 1.0
C G:TYR119 4.1 37.9 1.0
N G:THR8 4.2 43.1 1.0
N G:ARG126 4.3 43.1 1.0
CA G:MET125 4.4 59.6 1.0
CA G:ARG126 4.4 40.8 1.0
CA G:THR8 4.4 43.2 1.0
N G:TYR124 4.4 53.5 1.0
CD G:PRO127 4.6 37.9 1.0
C G:TYR124 4.8 54.3 1.0
CB G:ALA123 4.8 50.1 1.0
CA G:TYR119 4.9 37.6 1.0
CB G:MET125 5.0 69.3 1.0

Magnesium binding site 2 out of 8 in 4no9

Go back to Magnesium Binding Sites List in 4no9
Magnesium binding site 2 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone


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-Epoxyketone within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:44.2
occ:1.00
 OE1 H:GLN91 2.3 49.5 1.0
OD1 N:ASP51 3.3 40.0 1.0
CD H:GLN91 3.3 46.6 1.0
O N:ASN92 3.5 50.7 1.0
OD2 N:ASP51 3.6 43.2 1.0
NE2 H:GLN91 3.7 48.1 1.0
CG N:ASP51 3.9 42.5 1.0
C N:ASN92 4.5 49.1 1.0
CG H:GLN91 4.7 42.7 1.0

Magnesium binding site 3 out of 8 in 4no9

Go back to Magnesium Binding Sites List in 4no9
Magnesium binding site 3 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone


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

b:60.9
occ:1.00
 O I:ASP177 2.6 43.8 1.0
O I:SER180 2.7 54.9 1.0
O I:ALA174 3.4 52.2 1.0
OXT I:ASP204 3.4 45.3 1.0
C I:ASP177 3.7 42.2 1.0
O I:ALA178 3.9 48.0 1.0
C I:SER180 4.0 51.4 1.0
CA I:ALA178 4.0 40.1 1.0
C I:ALA178 4.0 41.2 1.0
O I:ASP204 4.1 40.2 1.0
C I:ASP204 4.2 33.6 1.0
N I:ALA178 4.3 39.3 1.0
C I:ALA174 4.5 52.5 1.0
NH1 Y:ARG19 4.5 66.1 1.0
N I:SER180 4.6 45.6 1.0
NH2 Y:ARG19 4.6 67.6 1.0
CA I:ASP175 4.7 57.2 1.0
O I:ASP175 4.7 55.6 1.0
N I:ASP177 4.8 43.9 1.0
CA I:ASP177 4.8 42.7 1.0
N I:LEU179 4.8 41.5 1.0
C I:ASP175 4.8 53.7 1.0
N I:GLY181 4.9 49.5 1.0
CA I:GLY181 4.9 48.1 1.0
CA I:SER180 4.9 49.5 1.0
CZ Y:ARG19 4.9 63.4 1.0

Magnesium binding site 4 out of 8 in 4no9

Go back to Magnesium Binding Sites List in 4no9
Magnesium binding site 4 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone


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

b:50.6
occ:1.00
 O K:ASP168 2.3 54.1 1.0
O K:ALA165 2.4 50.5 1.0
O W:ASP204 2.5 54.7 1.0
O K:SER171 2.9 45.6 1.0
C W:ASP204 3.1 53.8 1.0
C K:ASP168 3.2 48.7 1.0
CA W:ASP204 3.4 52.9 1.0
C K:ALA165 3.5 51.1 1.0
O K:HIS166 3.6 50.5 1.0
CA K:ALA169 3.7 38.9 1.0
CB W:ASP204 3.8 53.5 1.0
N K:ALA169 3.8 42.0 1.0
NH1 K:ARG19 3.9 62.6 1.0
C K:ALA169 4.0 43.1 1.0
OXT W:ASP204 4.0 52.0 1.0
C K:HIS166 4.0 49.1 1.0
O K:ALA169 4.1 45.1 1.0
C K:SER171 4.1 46.3 1.0
N K:ASP168 4.3 52.0 1.0
N K:HIS166 4.4 50.1 1.0
CA K:ASP168 4.4 51.8 1.0
CA K:HIS166 4.4 50.0 1.0
CA K:ALA165 4.4 53.0 1.0
N K:SER171 4.5 47.2 1.0
O K:ALA164 4.6 52.3 1.0
C K:ARG167 4.7 49.8 1.0
N W:ASP204 4.8 50.6 1.0
N K:ARG167 4.8 46.6 1.0
CZ K:ARG19 4.8 64.4 1.0
N K:TYR170 4.8 46.0 1.0
CA K:SER171 4.8 44.3 1.0

Magnesium binding site 5 out of 8 in 4no9

Go back to Magnesium Binding Sites List in 4no9
Magnesium binding site 5 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone


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

b:38.4
occ:1.00
 O N:ILE163 2.4 42.5 1.0
O N:SER169 2.6 41.8 1.0
O N:ASP166 2.9 43.8 1.0
CD1 a:LEU34 3.5 43.0 1.0
C N:ILE163 3.6 40.2 1.0
NH1 N:ARG19 3.7 32.8 1.0
CG2 N:ILE163 3.8 34.0 1.0
C N:SER169 3.8 41.0 1.0
C N:ASP166 3.9 42.6 1.0
CA N:GLY167 4.2 38.7 1.0
CA N:ILE163 4.3 37.7 1.0
CZ N:ARG19 4.4 32.2 1.0
N N:GLY167 4.5 40.0 1.0
O N:GLY167 4.5 40.1 1.0
CA N:GLY170 4.5 43.3 1.0
C N:GLY167 4.6 38.8 1.0
N N:GLY170 4.6 40.6 1.0
N N:LYS164 4.7 41.6 1.0
CB N:ILE163 4.7 36.0 1.0
N N:SER169 4.7 41.8 1.0
O N:LYS164 4.8 45.7 1.0
NH2 N:ARG19 4.8 30.5 1.0
CA N:SER169 4.8 40.2 1.0
C N:LYS164 4.8 44.7 1.0
CG a:LEU34 4.9 43.0 1.0
CA N:LYS164 4.9 42.6 1.0
N N:ASP166 5.0 45.9 1.0

Magnesium binding site 6 out of 8 in 4no9

Go back to Magnesium Binding Sites List in 4no9
Magnesium binding site 6 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone


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-Epoxyketone within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:59.9
occ:1.00
 O V:ASP166 2.2 40.5 1.0
OXT L:ASP222 2.2 57.2 1.0
O V:ILE163 2.4 49.6 1.0
O V:SER169 2.9 40.3 1.0
C L:ASP222 3.0 55.0 1.0
C V:ASP166 3.1 44.2 1.0
C V:ILE163 3.4 52.5 1.0
O V:TRP164 3.6 49.4 1.0
CA L:ASP222 3.6 53.6 1.0
C V:TRP164 3.8 49.3 1.0
N V:LEU167 3.8 43.4 1.0
O L:ASP222 3.8 58.3 1.0
CA V:LEU167 3.8 42.3 1.0
N V:ASP166 3.8 44.5 1.0
O V:GLY162 3.9 51.2 1.0
CA V:ASP166 4.1 44.4 1.0
C V:SER169 4.1 44.3 1.0
N V:TRP164 4.2 51.5 1.0
CA V:TRP164 4.2 49.3 1.0
N V:ASN165 4.3 49.2 1.0
CB L:ASP222 4.3 53.6 1.0
NH1 V:ARG19 4.4 64.8 1.0
CA V:ILE163 4.4 53.1 1.0
C V:ASN165 4.5 45.5 1.0
O L:ARG221 4.5 47.3 1.0
C V:LEU167 4.5 39.1 1.0
CD2 V:LEU167 4.6 44.8 1.0
N V:SER169 4.7 42.3 1.0
N L:ASP222 4.8 50.8 1.0
CA V:ASN165 4.8 46.7 1.0
O V:LEU167 4.9 38.5 1.0
CZ V:ARG19 4.9 60.4 1.0
NH2 V:ARG19 4.9 61.1 1.0
CA V:SER169 4.9 42.6 1.0
C V:GLY162 5.0 50.0 1.0

Magnesium binding site 7 out of 8 in 4no9

Go back to Magnesium Binding Sites List in 4no9
Magnesium binding site 7 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone


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

b:51.2
occ:1.00
 O Y:ASP168 2.1 50.0 1.0
O Y:ALA165 2.5 51.1 1.0
O I:ASP204 2.5 40.2 1.0
O Y:SER171 2.8 40.5 1.0
C Y:ASP168 3.1 49.7 1.0
C I:ASP204 3.2 33.6 1.0
CA Y:ALA169 3.5 46.8 1.0
CA I:ASP204 3.6 44.5 1.0
C Y:ALA165 3.6 53.1 1.0
NH1 Y:ARG19 3.7 66.1 1.0
N Y:ALA169 3.7 48.7 1.0
C Y:ALA169 3.8 45.5 1.0
O Y:HIS166 3.8 45.5 1.0
O Y:ALA169 3.8 46.1 1.0
CB I:ASP204 3.9 49.7 1.0
C Y:SER171 3.9 41.7 1.0
OXT I:ASP204 4.1 45.3 1.0
C Y:HIS166 4.2 48.2 1.0
N Y:SER171 4.3 43.5 1.0
CA Y:ASP168 4.3 49.5 1.0
N Y:ASP168 4.3 50.6 1.0
CA Y:ALA165 4.5 52.9 1.0
N Y:HIS166 4.5 53.0 1.0
N Y:TYR170 4.5 47.0 1.0
CZ Y:ARG19 4.6 63.4 1.0
CA Y:HIS166 4.6 49.6 1.0
CA Y:SER171 4.7 40.3 1.0
O Y:ALA164 4.7 55.5 1.0
C Y:ARG167 4.7 49.2 1.0
CB Y:ALA169 4.9 45.3 1.0
N Y:ARG167 4.9 45.1 1.0
N I:ASP204 5.0 43.5 1.0
N Y:GLY172 5.0 43.2 1.0
NH2 Y:ARG19 5.0 67.6 1.0

Magnesium binding site 8 out of 8 in 4no9

Go back to Magnesium Binding Sites List in 4no9
Magnesium binding site 8 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Epoxyketone


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

b:46.0
occ:1.00
 O Z:THR192 2.4 52.7 1.0
O Z:VAL198 2.7 47.1 1.0
O Z:HIS195 2.7 43.8 1.0
C Z:THR192 3.4 54.0 1.0
CG2 Z:THR192 3.5 52.8 1.0
C Z:HIS195 3.8 45.0 1.0
CA Z:THR192 3.8 51.6 1.0
C Z:VAL198 3.9 47.4 1.0
O Z:ASP222 4.0 53.5 1.0
NH2 Z:ARG28 4.0 41.6 1.0
CA Z:ILE196 4.0 44.8 1.0
O Z:ILE196 4.3 47.2 1.0
C Z:ILE196 4.3 45.8 1.0
CB Z:THR192 4.3 52.0 1.0
N Z:ILE196 4.3 44.3 1.0
NH2 H:ARG19 4.4 65.2 1.0
OD1 Z:ASP222 4.5 59.7 1.0
N Z:VAL198 4.5 47.0 1.0
N Z:GLU193 4.6 55.2 1.0
CA Z:VAL198 4.7 47.4 1.0
N Z:HIS195 4.8 46.4 1.0
N Z:GLY199 4.8 43.9 1.0
CA Z:GLY199 4.9 42.9 1.0
CA Z:HIS195 4.9 44.4 1.0
C Z:ASP222 4.9 56.2 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 23:44:12 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy