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

Magnesium in PDB 4nnw: Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde

Protein crystallography data

The structure of Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde, PDB code: 4nnw 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.640, 301.290, 145.120, 90.00, 113.71, 90.00
R / Rfree (%) 19.5 / 20.8

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 4nnw

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


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

b:43.8
occ:1.00
 O G:MET125 2.2 41.8 1.0
O G:ARG122 2.4 38.0 1.0
O G:TYR119 2.4 31.5 1.0
OG1 G:THR8 2.6 38.4 1.0
CG2 G:THR8 3.3 37.3 1.0
C G:MET125 3.4 45.1 1.0
C G:ARG122 3.5 36.8 1.0
CB G:THR8 3.6 40.0 1.0
O G:ALA123 3.6 43.8 1.0
C G:TYR119 3.6 30.4 1.0
CA G:ALA123 3.8 35.8 1.0
C G:ALA123 3.8 39.7 1.0
N G:ALA123 4.1 34.9 1.0
N G:MET125 4.2 47.2 1.0
CA G:MET125 4.3 49.2 1.0
N G:ARG126 4.3 40.6 1.0
CA G:TYR119 4.3 30.6 1.0
CA G:ARG126 4.4 37.3 1.0
CD G:PRO127 4.5 30.7 1.0
N G:THR8 4.5 39.1 1.0
N G:ARG122 4.6 38.6 1.0
N G:THR120 4.6 28.5 1.0
CA G:ARG122 4.7 38.8 1.0
CA G:THR8 4.7 39.6 1.0
N G:TYR124 4.7 43.8 1.0
CB G:MET125 4.7 56.6 1.0
CA G:THR120 4.7 29.5 1.0
C G:THR120 4.8 30.8 1.0
CB G:TYR119 4.8 29.9 1.0
C G:ARG126 4.9 36.6 1.0
N G:GLN121 5.0 31.5 1.0
N G:PRO127 5.0 34.3 1.0

Magnesium binding site 2 out of 8 in 4nnw

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


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

b:65.6
occ:1.00
 OE1 H:GLN91 2.7 44.7 1.0
OD1 N:ASP51 2.8 35.1 1.0
O N:ASN92 3.4 42.4 1.0
CD H:GLN91 3.4 45.5 1.0
NE2 H:GLN91 3.5 46.1 1.0
CG N:ASP51 3.5 31.3 1.0
OD2 N:ASP51 3.5 33.7 1.0
O H:HOH406 3.7 32.8 1.0
CE1 H:PHE88 4.5 23.6 1.0
C N:ASN92 4.6 42.6 1.0
CZ H:PHE88 4.7 22.3 1.0
O N:HOH319 4.7 31.8 1.0
CG H:GLN91 4.9 41.8 1.0

Magnesium binding site 3 out of 8 in 4nnw

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


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

b:42.8
occ:1.00
 O I:ASP177 2.3 38.9 1.0
O I:ALA174 2.4 40.5 1.0
O I:HOH430 2.4 36.9 1.0
O I:SER180 2.7 41.3 1.0
C I:ASP177 3.4 39.5 1.0
C I:ALA174 3.5 39.0 1.0
O I:HOH429 3.5 54.2 1.0
C I:SER180 3.8 40.9 1.0
CA I:ASP175 4.0 40.2 1.0
N I:ASP175 4.2 39.5 1.0
N I:ASP177 4.2 37.9 1.0
N I:ALA178 4.3 37.1 1.0
CA I:ALA178 4.3 35.4 1.0
OXT I:ASP204 4.3 46.6 1.0
O I:HOH416 4.3 33.2 1.0
C I:ASP175 4.3 38.6 1.0
CA I:ASP177 4.4 40.2 1.0
C I:ALA178 4.4 37.9 1.0
N I:SER180 4.5 41.4 1.0
O I:ALA178 4.5 38.8 1.0
O I:ASP175 4.6 41.4 1.0
CA I:ALA174 4.6 37.5 1.0
CA I:SER180 4.6 41.2 1.0
N I:GLY181 4.7 37.8 1.0
OD1 I:ASP175 4.7 43.0 1.0
CA I:GLY181 4.7 36.4 1.0
CB I:ASP177 4.9 42.4 1.0
CB I:ALA174 4.9 38.9 1.0
N I:LEU179 4.9 39.1 1.0
N I:ARG176 5.0 34.6 1.0
NH2 Y:ARG19 5.0 55.8 1.0

Magnesium binding site 4 out of 8 in 4nnw

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


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

b:45.5
occ:1.00
 O K:ALA165 2.3 43.0 1.0
O K:ASP168 2.3 38.9 1.0
O W:ASP204 2.5 44.4 1.0
O K:SER171 2.9 41.7 1.0
C W:ASP204 3.2 40.6 1.0
C K:ASP168 3.2 37.3 1.0
C K:ALA165 3.4 42.6 1.0
CA W:ASP204 3.6 39.2 1.0
CA K:ALA169 3.7 32.6 1.0
N K:ALA169 3.8 33.4 1.0
O K:HIS166 3.8 43.1 1.0
NH1 K:ARG19 3.9 42.6 1.0
C K:SER171 4.0 40.9 1.0
OXT W:ASP204 4.0 42.9 1.0
C K:ALA169 4.0 36.0 1.0
C K:HIS166 4.1 42.4 1.0
CB W:ASP204 4.1 37.5 1.0
O K:ALA169 4.2 38.8 1.0
N K:ASP168 4.2 41.0 1.0
CA K:ALA165 4.3 41.0 1.0
N K:HIS166 4.3 42.7 1.0
CA K:ASP168 4.3 38.8 1.0
CA K:HIS166 4.4 41.9 1.0
N K:SER171 4.5 41.9 1.0
O K:ALA164 4.5 42.7 1.0
CZ K:ARG19 4.7 44.7 1.0
N K:ARG167 4.7 41.6 1.0
C K:ARG167 4.7 40.0 1.0
CA K:SER171 4.8 39.9 1.0
N K:TYR170 4.8 37.4 1.0
N K:GLY172 4.9 41.8 1.0
CA K:GLY172 5.0 43.8 1.0

Magnesium binding site 5 out of 8 in 4nnw

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


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-Ketoaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:34.3
occ:1.00
 O N:SER169 2.6 33.3 1.0
O N:ILE163 2.7 31.4 1.0
O N:ASP166 2.9 33.2 1.0
NH1 N:ARG19 3.4 27.1 1.0
CD1 a:LEU34 3.6 33.5 1.0
C N:SER169 3.8 31.7 1.0
C N:ASP166 3.9 31.6 1.0
C N:ILE163 3.9 32.5 1.0
CG2 N:ILE163 4.0 25.4 1.0
CA N:GLY167 4.2 27.9 1.0
CZ N:ARG19 4.2 25.8 1.0
O N:GLY167 4.3 28.4 1.0
N N:GLY167 4.4 29.1 1.0
C N:GLY167 4.4 27.5 1.0
CA N:GLY170 4.4 31.6 1.0
CA N:ILE163 4.5 30.9 1.0
N N:GLY170 4.6 30.7 1.0
NH2 N:ARG19 4.6 21.0 1.0
N N:SER169 4.7 29.7 1.0
CA N:SER169 4.8 29.6 1.0
CB N:ILE163 4.9 29.1 1.0
CG a:LEU34 4.9 35.8 1.0
N N:LYS164 5.0 34.8 1.0
N N:ASP166 5.0 32.3 1.0
O N:LYS164 5.0 34.6 1.0

Magnesium binding site 6 out of 8 in 4nnw

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


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

b:46.1
occ:1.00
 O V:ASP166 2.2 39.0 1.0
OXT L:ASP222 2.2 41.5 1.0
O V:SER169 2.3 44.4 1.0
O V:ILE163 2.3 42.8 1.0
C L:ASP222 3.1 43.8 1.0
C V:ASP166 3.2 38.9 1.0
C V:ILE163 3.3 43.9 1.0
C V:SER169 3.5 41.7 1.0
CA L:ASP222 3.8 41.5 1.0
CA V:LEU167 3.8 33.5 1.0
NH1 V:ARG19 3.8 49.7 1.0
N V:LEU167 3.9 36.5 1.0
O L:ASP222 3.9 45.9 1.0
O V:GLY162 3.9 38.8 1.0
N V:ASP166 4.0 43.2 1.0
CA V:ILE163 4.1 44.7 1.0
CA V:ASP166 4.2 39.9 1.0
N V:TRP164 4.3 42.5 1.0
C V:TRP164 4.3 40.0 1.0
N V:SER169 4.3 33.9 1.0
CB L:ASP222 4.3 39.1 1.0
CZ V:ARG19 4.3 46.6 1.0
C V:LEU167 4.3 32.2 1.0
O V:TRP164 4.4 36.5 1.0
NH2 V:ARG19 4.4 43.5 1.0
N V:GLY170 4.4 44.0 1.0
CA V:SER169 4.4 36.5 1.0
CA V:GLY170 4.4 46.5 1.0
CA V:TRP164 4.5 41.1 1.0
N V:ASN165 4.6 40.5 1.0
O V:LEU167 4.7 32.3 1.0
CB V:SER169 4.8 37.3 1.0
C V:ASN165 4.8 42.2 1.0
C V:GLY162 4.8 39.9 1.0
CD2 V:LEU167 4.9 29.6 1.0
N V:GLY168 4.9 32.0 1.0

Magnesium binding site 7 out of 8 in 4nnw

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


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

b:36.0
occ:1.00
 O Y:ASP168 2.3 36.8 1.0
O Y:SER171 2.3 39.1 1.0
O I:ASP204 2.4 42.1 1.0
O Y:ALA165 2.4 42.4 1.0
O Y:HOH415 2.8 35.7 1.0
C I:ASP204 3.2 43.0 1.0
C Y:ASP168 3.3 36.4 1.0
NH1 Y:ARG19 3.4 59.0 1.0
C Y:SER171 3.5 38.7 1.0
C Y:ALA165 3.5 42.4 1.0
CA Y:ALA169 3.7 33.6 1.0
CA I:ASP204 3.8 39.8 1.0
C Y:ALA169 3.8 33.1 1.0
O Y:ALA169 3.9 34.0 1.0
N Y:ALA169 3.9 36.3 1.0
CB I:ASP204 4.0 37.2 1.0
N Y:SER171 4.1 39.8 1.0
OXT I:ASP204 4.1 46.6 1.0
CZ Y:ARG19 4.2 53.1 1.0
CA Y:ALA165 4.2 40.6 1.0
CA Y:SER171 4.3 39.1 1.0
O Y:HIS166 4.4 36.5 1.0
N Y:GLY172 4.4 36.4 1.0
CA Y:ASP168 4.5 35.0 1.0
N Y:ASP168 4.5 37.9 1.0
N Y:TYR170 4.5 34.1 1.0
N Y:HIS166 4.5 42.0 1.0
CA Y:GLY172 4.6 36.3 1.0
C Y:HIS166 4.6 37.8 1.0
NH2 Y:ARG19 4.6 55.8 1.0
O Y:ALA164 4.7 42.3 1.0
CB Y:SER171 4.8 38.6 1.0
CA Y:HIS166 4.8 39.0 1.0
CG I:ASP204 5.0 41.5 1.0

Magnesium binding site 8 out of 8 in 4nnw

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


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

b:50.0
occ:1.00
 O Z:THR192 2.5 42.3 1.0
O Z:VAL198 2.5 34.8 1.0
O Z:HIS195 3.0 32.1 1.0
CG2 Z:THR192 3.5 31.6 1.0
C Z:THR192 3.5 41.8 1.0
C Z:VAL198 3.7 34.8 1.0
CA Z:THR192 3.8 38.6 1.0
NH2 Z:ARG28 3.8 28.3 1.0
C Z:HIS195 4.0 33.0 1.0
O Z:ASP222 4.1 39.2 1.0
CB Z:THR192 4.2 34.9 1.0
CA Z:ILE196 4.3 32.6 1.0
O Z:ILE196 4.3 34.4 1.0
OD1 Z:ASP222 4.4 37.7 1.0
C Z:ILE196 4.4 33.4 1.0
N Z:VAL198 4.6 35.8 1.0
CA Z:GLY199 4.6 35.0 1.0
N Z:ILE196 4.6 32.7 1.0
N Z:GLY199 4.6 33.6 1.0
CA Z:VAL198 4.7 34.0 1.0
N Z:GLU193 4.7 43.7 1.0
NH2 H:ARG19 4.8 45.8 1.0
CZ Z:ARG28 4.9 31.1 1.0
N Z:HIS195 4.9 35.1 1.0
C Z:ASP222 4.9 36.5 1.0
O Z:LYS220 5.0 41.4 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 23:44:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy