Atomistry » Magnesium » PDB 4nlz-4nxm » 4no8
Atomistry »
  Magnesium »
    PDB 4nlz-4nxm »
      4no8 »

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

Go back to Magnesium Binding Sites List in 4no8
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

Go back to Magnesium Binding Sites List in 4no8
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

Go back to Magnesium Binding Sites List in 4no8
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

Go back to Magnesium Binding Sites List in 4no8
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

Go back to Magnesium Binding Sites List in 4no8
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

Go back to Magnesium Binding Sites List in 4no8
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

Go back to Magnesium Binding Sites List in 4no8
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

Go back to Magnesium Binding Sites List in 4no8
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 Dec 14 19:15:14 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