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Magnesium in PDB 4qlq: Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8

Enzymatic activity of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8

All present enzymatic activity of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8, PDB code: 4qlq was solved by G.De Bruin, E.Huber, B.Xin, E.Van Rooden, K.Al-Ayed, K.Kim, A.Kisselev, C.Driessen, G.Van Der Marel, M.Groll, H.Overkleeft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.650, 299.590, 144.820, 90.00, 112.85, 90.00
R / Rfree (%) 19.9 / 21.5

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 4qlq

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Magnesium binding site 1 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8


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 Tripeptidic Epoxyketone Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:54.5
occ:1.00
 O G:MET125 2.3 45.7 1.0
O G:ARG122 2.5 47.4 1.0
O G:TYR119 2.5 42.1 1.0
OG1 G:THR8 2.6 42.3 1.0
CG2 G:THR8 3.4 40.5 1.0
O G:ALA123 3.4 52.8 1.0
C G:ARG122 3.5 46.8 1.0
C G:MET125 3.5 51.5 1.0
CB G:THR8 3.6 43.2 1.0
C G:ALA123 3.6 50.8 1.0
CA G:ALA123 3.6 47.9 1.0
C G:TYR119 3.7 42.3 1.0
N G:ALA123 4.0 47.2 1.0
N G:MET125 4.1 50.5 1.0
CA G:MET125 4.4 54.6 1.0
N G:THR8 4.4 44.0 1.0
N G:ARG126 4.4 51.7 1.0
CA G:TYR119 4.4 41.7 1.0
CA G:ARG126 4.5 47.1 1.0
N G:TYR124 4.5 51.6 1.0
CA G:THR8 4.6 44.2 1.0
N G:ARG122 4.6 44.8 1.0
CD G:PRO127 4.7 37.9 1.0
N G:THR120 4.7 41.9 1.0
CA G:ARG122 4.7 48.9 1.0
CB G:MET125 4.8 60.3 1.0
CA G:THR120 4.8 42.3 1.0
C G:THR120 4.9 44.5 1.0

Magnesium binding site 2 out of 8 in 4qlq

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Magnesium binding site 2 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8


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 Tripeptidic Epoxyketone Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:69.2
occ:1.00
 OE1 H:GLN91 2.7 64.3 1.0
O N:HOH311 2.8 50.6 1.0
O N:HOH310 3.1 50.1 1.0
O N:ASN92 3.6 57.9 1.0
CD H:GLN91 3.8 59.3 1.0
OD1 N:ASP51 4.0 49.9 1.0
OD2 N:ASP51 4.2 51.5 1.0
NE2 H:GLN91 4.3 60.1 1.0
O H:HOH409 4.5 40.7 1.0
CG N:ASP51 4.5 50.6 1.0
C N:ASN92 4.7 54.3 1.0

Magnesium binding site 3 out of 8 in 4qlq

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Magnesium binding site 3 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8


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 Tripeptidic Epoxyketone Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:58.8
occ:1.00
 O I:ASP177 2.4 45.8 1.0
O I:SER180 2.4 49.4 1.0
O I:ALA174 2.5 48.1 1.0
C I:ALA174 3.5 47.6 1.0
C I:ASP177 3.6 45.2 1.0
C I:SER180 3.6 48.3 1.0
O I:HOH414 3.9 42.8 1.0
O I:HOH432 3.9 50.5 1.0
CA I:ASP175 4.0 47.1 1.0
N I:ASP175 4.1 47.8 1.0
N I:ASP177 4.3 46.1 1.0
OXT I:ASP204 4.3 48.9 1.0
C I:ASP175 4.4 46.0 1.0
N I:SER180 4.4 47.3 1.0
CA I:ASP177 4.5 45.8 1.0
N I:ALA178 4.5 43.5 1.0
CA I:SER180 4.5 47.5 1.0
N I:GLY181 4.5 45.1 1.0
CA I:ALA174 4.5 44.9 1.0
CA I:ALA178 4.5 42.5 1.0
C I:ALA178 4.6 44.3 1.0
O I:ALA178 4.6 45.2 1.0
CA I:GLY181 4.6 41.6 1.0
O I:ASP175 4.6 46.2 1.0
OD1 I:ASP175 4.6 51.3 1.0
CB I:ALA174 4.7 43.9 1.0
CB I:SER180 4.9 47.9 1.0
CB I:ASP177 5.0 48.4 1.0
N I:ARG176 5.0 43.2 1.0

Magnesium binding site 4 out of 8 in 4qlq

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Magnesium binding site 4 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8


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 Tripeptidic Epoxyketone Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:51.7
occ:1.00
 O K:ASP168 2.4 42.9 1.0
O K:SER171 2.4 52.6 1.0
O W:ASP204 2.4 56.9 1.0
O K:ALA165 2.5 45.2 1.0
C W:ASP204 3.2 51.8 1.0
C K:ASP168 3.4 41.1 1.0
NH1 K:ARG19 3.6 50.4 1.0
C K:SER171 3.6 51.3 1.0
C K:ALA165 3.6 46.3 1.0
CA W:ASP204 3.7 47.7 1.0
CA K:ALA169 3.8 38.1 1.0
C K:ALA169 3.9 43.0 1.0
O K:ALA169 3.9 45.2 1.0
N K:ALA169 4.0 39.5 1.0
OXT W:ASP204 4.0 53.7 1.0
CB W:ASP204 4.0 46.5 1.0
N K:SER171 4.1 51.2 1.0
CZ K:ARG19 4.3 52.0 1.0
CA K:ALA165 4.4 45.8 1.0
O K:HIS166 4.4 42.0 1.0
CA K:SER171 4.4 49.4 1.0
NH2 K:ARG19 4.5 56.0 1.0
CA K:ASP168 4.6 39.7 1.0
N K:ASP168 4.6 39.7 1.0
N K:TYR170 4.6 46.2 1.0
C K:HIS166 4.6 42.4 1.0
N K:GLY172 4.6 50.2 1.0
N K:HIS166 4.6 43.5 1.0
CA K:GLY172 4.7 49.8 1.0
O K:ALA164 4.7 46.0 1.0
CA K:HIS166 4.8 42.6 1.0
CB K:SER171 4.9 46.1 1.0
CG W:ASP204 5.0 49.6 1.0

Magnesium binding site 5 out of 8 in 4qlq

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Magnesium binding site 5 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8


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 Tripeptidic Epoxyketone Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:48.4
occ:1.00
 O N:ILE163 2.5 48.0 1.0
O N:SER169 2.7 54.7 1.0
O N:ASP166 2.9 49.8 1.0
CD1 a:LEU34 3.5 46.3 1.0
NH1 N:ARG19 3.6 54.2 1.0
C N:ILE163 3.7 53.5 1.0
C N:SER169 3.8 51.6 1.0
C N:ASP166 3.9 47.5 1.0
CG2 N:ILE163 4.0 46.6 1.0
CA N:GLY167 4.2 44.4 1.0
CA N:ILE163 4.3 53.2 1.0
CZ N:ARG19 4.4 55.9 1.0
O N:GLY167 4.4 47.0 1.0
CA N:GLY170 4.5 54.8 1.0
N N:GLY167 4.5 45.7 1.0
C N:GLY167 4.5 44.8 1.0
N N:GLY170 4.6 51.2 1.0
NH2 N:ARG19 4.7 50.5 1.0
N N:LYS164 4.8 56.0 1.0
N N:SER169 4.8 46.0 1.0
CB N:ILE163 4.8 50.2 1.0
CA N:SER169 4.8 47.0 1.0
CG a:LEU34 4.9 47.0 1.0
O N:LYS164 4.9 53.8 1.0
C N:LYS164 4.9 57.7 1.0
CA N:LYS164 5.0 59.7 1.0

Magnesium binding site 6 out of 8 in 4qlq

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Magnesium binding site 6 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8


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 Tripeptidic Epoxyketone Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:54.8
occ:1.00
 O V:ASP166 2.2 47.6 1.0
O V:SER169 2.2 49.0 1.0
OXT L:ASP222 2.2 48.1 1.0
O V:ILE163 2.3 45.6 1.0
C L:ASP222 3.1 55.4 1.0
C V:ASP166 3.1 44.1 1.0
C V:ILE163 3.4 47.8 1.0
C V:SER169 3.4 50.6 1.0
CA L:ASP222 3.8 52.6 1.0
CA V:LEU167 3.8 44.5 1.0
O V:GLY162 3.8 45.6 1.0
N V:LEU167 3.8 45.3 1.0
NH1 V:ARG19 3.9 44.0 1.0
O L:ASP222 3.9 62.7 1.0
N V:ASP166 4.0 49.5 1.0
CA V:ILE163 4.1 49.6 1.0
N V:SER169 4.1 43.7 1.0
CA V:ASP166 4.2 44.7 1.0
CB L:ASP222 4.2 46.5 1.0
C V:LEU167 4.2 43.4 1.0
CA V:SER169 4.3 47.3 1.0
N V:TRP164 4.3 46.2 1.0
C V:TRP164 4.3 52.6 1.0
N V:GLY170 4.3 52.8 1.0
CZ V:ARG19 4.4 46.2 1.0
CA V:GLY170 4.4 53.2 1.0
O V:TRP164 4.4 53.6 1.0
NH2 V:ARG19 4.5 48.7 1.0
CA V:TRP164 4.5 48.3 1.0
O V:LEU167 4.6 44.3 1.0
N V:ASN165 4.6 53.5 1.0
CB V:SER169 4.7 47.5 1.0
C V:GLY162 4.8 45.5 1.0
C V:ASN165 4.8 50.9 1.0
N V:GLY168 4.8 40.5 1.0
CB V:ASP166 4.9 43.4 1.0
N V:ILE163 5.0 45.8 1.0
CD2 V:LEU167 5.0 45.4 1.0

Magnesium binding site 7 out of 8 in 4qlq

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Magnesium binding site 7 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8


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 Tripeptidic Epoxyketone Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:49.5
occ:1.00
 O Y:ASP168 2.3 41.3 1.0
O Y:SER171 2.3 51.7 1.0
O Y:HOH408 2.4 44.5 1.0
O Y:ALA165 2.4 42.8 1.0
O I:ASP204 2.5 63.2 1.0
C I:ASP204 3.3 49.8 1.0
C Y:ASP168 3.3 39.1 1.0
C Y:SER171 3.5 49.2 1.0
C Y:ALA165 3.5 42.3 1.0
NH1 Y:ARG19 3.6 63.8 1.0
CA I:ASP204 3.8 49.1 1.0
CA Y:ALA169 3.8 40.6 1.0
C Y:ALA169 3.9 40.9 1.0
N Y:ALA169 3.9 39.5 1.0
O Y:ALA169 4.0 39.8 1.0
N Y:SER171 4.0 45.2 1.0
CB I:ASP204 4.0 46.5 1.0
OXT I:ASP204 4.1 48.9 1.0
CA Y:ALA165 4.2 41.5 1.0
CZ Y:ARG19 4.3 61.5 1.0
CA Y:SER171 4.3 45.6 1.0
O Y:HIS166 4.4 41.5 1.0
CA Y:ASP168 4.5 37.4 1.0
N Y:ASP168 4.5 40.2 1.0
N Y:GLY172 4.5 47.9 1.0
N Y:TYR170 4.5 43.2 1.0
N Y:HIS166 4.6 41.1 1.0
C Y:HIS166 4.6 41.2 1.0
NH2 Y:ARG19 4.6 65.2 1.0
O Y:ALA164 4.6 42.4 1.0
CA Y:GLY172 4.6 46.1 1.0
CA Y:HIS166 4.8 39.4 1.0
CB Y:SER171 4.8 46.0 1.0

Magnesium binding site 8 out of 8 in 4qlq

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Magnesium binding site 8 out of 8 in the Ycp in Complex with Tripeptidic Epoxyketone Inhibitor 8


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 Tripeptidic Epoxyketone Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:57.9
occ:1.00
 O Z:THR192 2.6 45.3 1.0
O Z:VAL198 2.6 53.5 1.0
O Z:HIS195 2.8 43.9 1.0
C Z:THR192 3.6 46.5 1.0
CG2 Z:THR192 3.7 37.3 1.0
C Z:HIS195 3.8 42.2 1.0
C Z:VAL198 3.8 52.5 1.0
NH2 Z:ARG28 3.9 52.1 1.0
CA Z:THR192 3.9 44.4 1.0
CA Z:ILE196 4.0 39.8 1.0
O Z:ASP222 4.0 53.5 1.0
O Z:ILE196 4.1 41.3 1.0
C Z:ILE196 4.2 40.9 1.0
N Z:ILE196 4.3 39.4 1.0
NH2 H:ARG19 4.4 52.7 1.0
N Z:VAL198 4.5 49.6 1.0
CB Z:THR192 4.5 40.8 1.0
OD1 Z:ASP222 4.5 51.4 1.0
CA Z:VAL198 4.7 51.1 1.0
N Z:GLY199 4.7 50.2 1.0
N Z:HIS195 4.8 44.5 1.0
N Z:GLU193 4.8 47.2 1.0
CA Z:GLY199 4.8 50.2 1.0
C Z:ASP222 4.9 52.0 1.0
CA Z:HIS195 4.9 43.4 1.0
O Z:ALA191 5.0 43.2 1.0
N Z:GLN197 5.0 43.0 1.0
CZ Z:ARG28 5.0 53.0 1.0

Reference:

G.De Bruin, E.M.Huber, B.T.Xin, E.J.Van Rooden, K.Al-Ayed, K.B.Kim, A.F.Kisselev, C.Driessen, M.Van Der Stelt, G.A.Van Der Marel, M.Groll, H.S.Overkleeft. Structure-Based Design of Beta 1I or Beta 5I Specific Inhibitors of Human Immunoproteasomes J.Med.Chem. V. 57 6197 2014.
ISSN: ISSN 0022-2623
PubMed: 25006746
DOI: 10.1021/JM500716S
Page generated: Tue Aug 20 02:03:16 2024

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