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Magnesium in PDB 4qzz: Ycp in Complex with Omuralide

Enzymatic activity of Ycp in Complex with Omuralide

All present enzymatic activity of Ycp in Complex with Omuralide:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Omuralide, PDB code: 4qzz was solved by E.M.Huber, W.Heinemeyer, 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 (°) 135.960, 301.960, 145.050, 90.00, 113.14, 90.00
R / Rfree (%) 17.9 / 20.8

Other elements in 4qzz:

The structure of Ycp in Complex with Omuralide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with Omuralide (pdb code 4qzz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Ycp in Complex with Omuralide, PDB code: 4qzz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4qzz

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Magnesium binding site 1 out of 7 in the Ycp in Complex with Omuralide


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

b:40.1
occ:1.00
 O G:MET125 2.2 49.8 1.0
OG1 G:THR8 2.6 39.7 1.0
O G:ARG122 2.6 43.9 1.0
O G:TYR119 2.8 34.8 1.0
O G:ALA123 3.2 50.9 1.0
CG2 G:THR8 3.3 42.3 1.0
C G:MET125 3.3 47.4 1.0
CB G:THR8 3.5 41.4 1.0
C G:ALA123 3.5 47.8 1.0
CA G:ALA123 3.6 45.8 1.0
C G:ARG122 3.7 45.4 1.0
C G:TYR119 4.0 35.4 1.0
N G:ALA123 4.1 45.8 1.0
N G:THR8 4.1 44.4 1.0
N G:ARG126 4.2 42.5 1.0
CA G:ARG126 4.2 40.8 1.0
N G:MET125 4.2 49.4 1.0
CA G:MET125 4.3 50.9 1.0
CA G:THR8 4.4 42.9 1.0
N G:TYR124 4.5 48.5 1.0
CD G:PRO127 4.6 38.5 1.0
CA G:TYR119 4.8 34.5 1.0
C G:ARG126 4.9 39.5 1.0
C G:TYR124 4.9 48.2 1.0
CB G:ALA123 4.9 44.8 1.0
CA G:ARG122 5.0 47.0 1.0
CB G:MET125 5.0 55.3 1.0

Magnesium binding site 2 out of 7 in 4qzz

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Magnesium binding site 2 out of 7 in the Ycp in Complex with Omuralide


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 Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:34.7
occ:1.00
 OE1 J:GLN118 3.3 40.6 1.0
O J:THR124 3.3 37.5 1.0
CB J:ASP120 3.7 37.1 1.0
CG J:ASP120 3.8 40.3 1.0
N J:ASP120 3.8 33.5 1.0
OD2 J:ASP120 3.9 46.7 1.0
CB J:THR124 4.1 36.9 1.0
CD J:GLN118 4.1 36.5 1.0
CG2 J:THR124 4.2 36.8 1.0
CG J:GLN118 4.2 35.9 1.0
O J:GLN118 4.3 34.1 1.0
CE1 J:HIS133 4.3 36.1 1.0
C J:THR124 4.3 36.6 1.0
CA J:ASP120 4.4 34.6 1.0
OD1 J:ASP120 4.4 43.6 1.0
C J:ILE119 4.5 32.8 1.0
C J:GLN118 4.7 33.1 1.0
CA J:ILE119 4.7 31.5 1.0
CG1 I:VAL35 4.8 43.1 1.0
CA J:THR124 4.8 36.3 1.0
N J:ILE119 4.9 31.3 1.0
ND1 J:HIS133 5.0 36.6 1.0
CB J:GLN118 5.0 34.5 1.0

Magnesium binding site 3 out of 7 in 4qzz

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Magnesium binding site 3 out of 7 in the Ycp in Complex with Omuralide


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

b:42.0
occ:1.00
 O K:ALA165 2.3 41.9 1.0
O K:ASP168 2.4 37.4 1.0
O W:ASP204 2.5 60.5 1.0
O K:SER171 3.1 39.6 1.0
C W:ASP204 3.1 58.2 1.0
C K:ASP168 3.3 38.0 1.0
C K:ALA165 3.4 41.1 1.0
CA W:ASP204 3.4 53.1 1.0
O K:HIS166 3.5 42.0 1.0
CA K:ALA169 3.7 39.9 1.0
C K:HIS166 3.8 41.0 1.0
CB W:ASP204 3.8 51.4 1.0
N K:ALA169 3.8 38.4 1.0
OXT W:ASP204 4.1 65.7 1.0
NH1 K:ARG19 4.1 53.3 1.0
C K:ALA169 4.1 40.8 1.0
O K:ALA169 4.1 41.9 1.0
N K:ASP168 4.2 39.6 1.0
N K:HIS166 4.3 41.0 1.0
CA K:HIS166 4.3 40.9 1.0
C K:SER171 4.3 39.4 1.0
C K:ARG167 4.4 40.2 1.0
CA K:ASP168 4.4 38.6 1.0
CA K:ALA165 4.4 40.3 1.0
N K:ARG167 4.5 40.8 1.0
O K:ARG167 4.6 41.4 1.0
O K:ALA164 4.6 39.5 1.0
N K:SER171 4.8 36.9 1.0
N W:ASP204 4.8 53.6 1.0
CZ K:ARG19 4.9 50.9 1.0
CA K:ARG167 5.0 40.3 1.0
N K:TYR170 5.0 41.0 1.0

Magnesium binding site 4 out of 7 in 4qzz

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Magnesium binding site 4 out of 7 in the Ycp in Complex with Omuralide


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

b:34.2
occ:1.00
 O N:SER169 2.6 35.0 1.0
O N:ILE163 2.8 35.8 1.0
O N:ASP166 2.9 39.3 1.0
NH1 N:ARG19 3.4 39.6 1.0
CD1 a:LEU34 3.6 44.0 1.0
C N:SER169 3.8 35.2 1.0
C N:ASP166 3.9 37.1 1.0
C N:ILE163 3.9 37.0 1.0
CA N:GLY167 4.0 37.7 1.0
CZ N:ARG19 4.1 38.4 1.0
CG2 N:ILE163 4.2 37.5 1.0
O N:GLY167 4.3 38.1 1.0
NH2 N:ARG19 4.4 38.5 1.0
N N:GLY167 4.4 36.8 1.0
C N:GLY167 4.4 37.2 1.0
CA N:GLY170 4.4 37.5 1.0
CA N:ILE163 4.6 37.3 1.0
N N:GLY170 4.6 36.0 1.0
N N:SER169 4.8 35.2 1.0
CA N:SER169 4.8 33.8 1.0
CG a:LEU34 4.9 43.6 1.0
N N:LYS164 4.9 38.7 1.0
NE N:ARG19 4.9 38.4 1.0
O N:LYS164 5.0 44.8 1.0
CB N:ILE163 5.0 36.5 1.0

Magnesium binding site 5 out of 7 in 4qzz

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Magnesium binding site 5 out of 7 in the Ycp in Complex with Omuralide


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

b:50.7
occ:1.00
 OXT L:ASP222 2.0 67.6 1.0
O V:ASP166 2.1 38.4 1.0
O V:ILE163 2.2 45.1 1.0
O V:SER169 2.4 40.2 1.0
C L:ASP222 3.1 65.5 1.0
C V:ASP166 3.2 38.9 1.0
C V:ILE163 3.3 45.4 1.0
C V:SER169 3.5 39.2 1.0
CA L:ASP222 3.7 62.9 1.0
CA V:LEU167 3.8 39.2 1.0
N V:LEU167 3.9 39.2 1.0
O V:GLY162 3.9 42.2 1.0
NH1 V:ARG19 3.9 59.3 1.0
O V:TRP164 4.0 45.7 1.0
O L:ASP222 4.1 70.0 1.0
N V:ASP166 4.1 39.9 1.0
CA V:ILE163 4.1 44.4 1.0
C V:TRP164 4.1 45.6 1.0
CB L:ASP222 4.2 62.2 1.0
CA V:ASP166 4.2 39.3 1.0
N V:TRP164 4.2 45.5 1.0
C V:LEU167 4.2 40.1 1.0
N V:SER169 4.3 37.5 1.0
CA V:TRP164 4.4 45.2 1.0
CA V:SER169 4.4 38.4 1.0
N V:GLY170 4.4 39.7 1.0
O V:LEU167 4.5 40.1 1.0
CA V:GLY170 4.5 42.9 1.0
CZ V:ARG19 4.6 54.8 1.0
N V:ASN165 4.6 44.5 1.0
C V:ASN165 4.8 42.1 1.0
NH2 V:ARG19 4.8 60.4 1.0
CB V:SER169 4.8 38.9 1.0
C V:GLY162 4.8 43.5 1.0
N V:GLY168 4.9 40.5 1.0
O L:ARG221 5.0 58.4 1.0
CB V:ASP166 5.0 38.5 1.0
N V:ILE163 5.0 44.4 1.0

Magnesium binding site 6 out of 7 in 4qzz

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Magnesium binding site 6 out of 7 in the Ycp in Complex with Omuralide


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

b:44.9
occ:1.00
 O Y:ASP168 2.4 44.2 1.0
O I:ASP204 2.4 52.7 1.0
O Y:ALA165 2.4 39.6 1.0
O Y:SER171 3.1 41.1 1.0
C I:ASP204 3.1 54.1 1.0
C Y:ASP168 3.3 40.6 1.0
CA I:ASP204 3.5 53.5 1.0
C Y:ALA165 3.6 38.6 1.0
CA Y:ALA169 3.6 40.6 1.0
O Y:HIS166 3.6 41.2 1.0
N Y:ALA169 3.8 40.9 1.0
CB I:ASP204 3.9 53.9 1.0
NH1 Y:ARG19 3.9 56.7 1.0
O Y:ALA169 4.0 42.4 1.0
C Y:ALA169 4.0 41.0 1.0
C Y:HIS166 4.0 39.4 1.0
OXT I:ASP204 4.0 53.8 1.0
C Y:SER171 4.3 40.1 1.0
N Y:ASP168 4.3 39.9 1.0
CA Y:ASP168 4.4 39.6 1.0
N Y:HIS166 4.4 38.9 1.0
C Y:ARG167 4.5 41.0 1.0
CA Y:HIS166 4.5 38.5 1.0
CA Y:ALA165 4.5 38.4 1.0
O Y:ARG167 4.6 43.1 1.0
N Y:ARG167 4.7 39.7 1.0
N Y:SER171 4.7 38.9 1.0
O Y:ALA164 4.7 38.5 1.0
CZ Y:ARG19 4.7 53.4 1.0
N Y:TYR170 4.9 40.5 1.0
N I:ASP204 4.9 51.7 1.0
CB Y:ALA169 4.9 40.6 1.0
NH2 Y:ARG19 5.0 53.6 1.0

Magnesium binding site 7 out of 7 in 4qzz

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Magnesium binding site 7 out of 7 in the Ycp in Complex with Omuralide


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

b:46.1
occ:1.00
 O Z:VAL198 2.6 48.7 1.0
O Z:THR192 2.9 50.4 1.0
O Z:HIS195 2.9 39.9 1.0
O Z:ASP222 3.4 68.1 1.0
NH2 Z:ARG28 3.6 56.0 1.0
O Z:ILE196 3.7 47.6 1.0
C Z:VAL198 3.8 48.5 1.0
CA Z:ILE196 3.8 44.6 1.0
C Z:HIS195 3.9 43.6 1.0
C Z:THR192 3.9 54.7 1.0
C Z:ILE196 3.9 43.9 1.0
CG2 Z:THR192 3.9 54.8 1.0
NH2 H:ARG19 4.2 61.8 1.0
CA Z:THR192 4.3 55.0 1.0
N Z:ILE196 4.3 43.6 1.0
N Z:VAL198 4.4 44.4 1.0
OD1 Z:ASP222 4.4 65.2 1.0
C Z:ASP222 4.5 69.5 1.0
CZ Z:ARG28 4.6 54.3 1.0
CA Z:VAL198 4.6 46.5 1.0
N Z:GLY199 4.7 49.4 1.0
CB Z:THR192 4.7 54.0 1.0
CA Z:GLY199 4.8 51.5 1.0
NH1 H:ARG19 4.8 57.9 1.0
NH1 Z:ARG28 4.8 56.0 1.0
N Z:GLN197 4.8 42.1 1.0
CZ H:ARG19 4.9 57.2 1.0

Reference:

E.M.Huber, W.Heinemeyer, M.Groll. Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and Onx 0914. Structure 2015.
ISSN: ISSN 0969-2126
PubMed: 25599643
DOI: 10.1016/J.STR.2014.11.019
Page generated: Mon Aug 11 23:00:02 2025

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