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Magnesium in PDB 4r00: Ycp BETA5-C52F Mutant in Complex with Omuralide

Enzymatic activity of Ycp BETA5-C52F Mutant in Complex with Omuralide

All present enzymatic activity of Ycp BETA5-C52F Mutant in Complex with Omuralide:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-C52F Mutant in Complex with Omuralide, PDB code: 4r00 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.250, 301.240, 144.330, 90.00, 113.16, 90.00
R / Rfree (%) 18.4 / 21

Other elements in 4r00:

The structure of Ycp BETA5-C52F Mutant in Complex with Omuralide also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-C52F Mutant in Complex with Omuralide (pdb code 4r00). 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 BETA5-C52F Mutant in Complex with Omuralide, PDB code: 4r00:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4r00

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Magnesium binding site 1 out of 8 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:52.2
occ:1.00
 O G:MET125 2.3 49.2 1.0
OG1 G:THR8 2.6 41.4 1.0
O G:ARG122 2.7 42.2 1.0
O G:ALA123 3.0 52.9 1.0
O G:TYR119 3.0 38.6 1.0
CG2 G:THR8 3.3 44.3 1.0
C G:MET125 3.4 49.5 1.0
C G:ALA123 3.5 49.4 1.0
CB G:THR8 3.5 43.7 1.0
CA G:ALA123 3.6 47.7 1.0
C G:ARG122 3.8 45.1 1.0
N G:THR8 4.0 46.2 1.0
N G:ALA123 4.1 45.6 1.0
CA G:ARG126 4.1 43.5 1.0
N G:ARG126 4.2 44.5 1.0
N G:MET125 4.2 51.8 1.0
C G:TYR119 4.3 37.8 1.0
CA G:THR8 4.4 45.3 1.0
CA G:MET125 4.4 53.4 1.0
N G:TYR124 4.5 50.7 1.0
CD G:PRO127 4.6 40.6 1.0
CB G:ALA123 4.9 47.9 1.0
C G:TYR124 4.9 50.3 1.0
C G:ARG126 4.9 43.6 1.0
CA G:TYR119 5.0 35.6 1.0

Magnesium binding site 2 out of 8 in 4r00

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Magnesium binding site 2 out of 8 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:56.6
occ:1.00
 O I:ASP177 2.6 43.1 1.0
O I:SER180 2.7 44.5 1.0
O I:ALA174 2.9 43.0 1.0
OXT I:ASP204 3.6 63.6 1.0
C I:ASP177 3.8 43.4 1.0
C I:ALA174 3.9 45.2 1.0
C I:SER180 3.9 45.2 1.0
CA I:ASP175 4.1 46.1 1.0
NH1 Y:ARG19 4.2 56.8 1.0
C I:ASP175 4.4 47.1 1.0
O I:ASP175 4.4 51.1 1.0
O I:ALA178 4.4 47.5 1.0
O I:ASP204 4.4 56.6 1.0
C I:ASP204 4.4 57.9 1.0
N I:ASP175 4.4 46.3 1.0
CA I:ALA178 4.5 43.7 1.0
NH2 Y:ARG19 4.5 58.7 1.0
N I:ASP177 4.5 43.6 1.0
N I:ALA178 4.5 42.4 1.0
C I:ALA178 4.6 44.0 1.0
CA I:GLY181 4.7 47.2 1.0
CZ Y:ARG19 4.7 55.1 1.0
CA I:ASP177 4.7 43.2 1.0
N I:GLY181 4.8 46.4 1.0
N I:SER180 4.8 42.9 1.0
OD1 I:ASP175 4.8 51.9 1.0
CA I:SER180 4.9 44.1 1.0

Magnesium binding site 3 out of 8 in 4r00

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Magnesium binding site 3 out of 8 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:41.5
occ:1.00
 OE1 J:GLN118 3.3 38.7 1.0
O J:THR124 3.5 40.8 1.0
CB J:ASP120 3.7 36.3 1.0
CG J:ASP120 3.9 37.6 1.0
OD2 J:ASP120 4.0 41.9 1.0
N J:ASP120 4.0 34.3 1.0
CD J:GLN118 4.1 35.0 1.0
CB J:THR124 4.2 35.5 1.0
CG2 J:THR124 4.3 35.0 1.0
CG J:GLN118 4.3 34.6 1.0
CE1 J:HIS133 4.3 37.9 1.0
CA J:ASP120 4.4 34.4 1.0
O J:GLN118 4.5 34.5 1.0
C J:THR124 4.5 37.2 1.0
CG1 I:VAL35 4.6 44.2 1.0
OD1 J:ASP120 4.6 40.3 1.0
C J:ILE119 4.7 33.9 1.0
C J:GLN118 4.8 32.8 1.0
CA J:ILE119 4.9 31.8 1.0
ND1 J:HIS133 5.0 37.4 1.0
CD2 I:LEU28 5.0 44.3 1.0

Magnesium binding site 4 out of 8 in 4r00

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Magnesium binding site 4 out of 8 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:55.7
occ:1.00
 O K:ALA165 2.4 42.8 1.0
O K:ASP168 2.4 37.3 1.0
O W:ASP204 2.5 58.8 1.0
C W:ASP204 3.1 59.1 1.0
C K:ASP168 3.2 38.9 1.0
O K:HIS166 3.2 44.0 1.0
O K:SER171 3.4 45.4 1.0
CA W:ASP204 3.5 56.7 1.0
C K:ALA165 3.6 41.7 1.0
CA K:ALA169 3.6 41.0 1.0
N K:ALA169 3.7 39.8 1.0
C K:HIS166 3.8 43.5 1.0
OXT W:ASP204 4.0 64.2 1.0
CB W:ASP204 4.0 55.5 1.0
C K:ALA169 4.1 42.9 1.0
O K:ALA169 4.2 46.0 1.0
N K:ASP168 4.2 41.2 1.0
C K:ARG167 4.3 42.4 1.0
NH1 K:ARG19 4.3 57.6 1.0
CA K:ASP168 4.3 39.4 1.0
CA K:HIS166 4.3 42.9 1.0
N K:HIS166 4.4 41.3 1.0
O K:ARG167 4.4 43.8 1.0
N K:ARG167 4.5 43.1 1.0
C K:SER171 4.6 41.9 1.0
CA K:ALA165 4.6 42.3 1.0
O K:ALA164 4.7 42.4 1.0
N W:ASP204 4.8 56.1 1.0
NE1 W:TRP182 4.8 49.0 1.0
CB K:ALA169 4.9 39.7 1.0
CA K:ARG167 4.9 42.5 1.0
N K:SER171 4.9 39.7 1.0
N K:TYR170 5.0 42.9 1.0

Magnesium binding site 5 out of 8 in 4r00

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Magnesium binding site 5 out of 8 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:43.6
occ:1.00
 O N:SER169 2.5 37.8 1.0
O N:ILE163 2.8 40.6 1.0
O N:ASP166 2.9 43.0 1.0
NH1 N:ARG19 3.3 42.4 1.0
CD1 a:LEU34 3.7 45.9 1.0
C N:SER169 3.7 37.5 1.0
C N:ASP166 3.9 40.8 1.0
C N:ILE163 3.9 41.3 1.0
CZ N:ARG19 4.0 40.8 1.0
CA N:GLY167 4.0 39.7 1.0
CG2 N:ILE163 4.1 39.2 1.0
O N:GLY167 4.2 38.0 1.0
NH2 N:ARG19 4.3 41.5 1.0
C N:GLY167 4.3 38.3 1.0
N N:GLY167 4.4 39.2 1.0
CA N:GLY170 4.4 38.3 1.0
N N:GLY170 4.5 37.3 1.0
CA N:ILE163 4.5 39.9 1.0
N N:SER169 4.7 37.1 1.0
CA N:SER169 4.8 35.9 1.0
NE N:ARG19 4.9 40.7 1.0
CG a:LEU34 4.9 45.9 1.0
CB N:ILE163 5.0 38.9 1.0
N N:LYS164 5.0 42.6 1.0

Magnesium binding site 6 out of 8 in 4r00

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Magnesium binding site 6 out of 8 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:59.5
occ:1.00
 OXT L:ASP222 2.0 68.8 1.0
O V:ILE163 2.1 43.3 1.0
O V:ASP166 2.2 40.0 1.0
O V:SER169 2.4 40.5 1.0
C L:ASP222 3.1 65.1 1.0
C V:ASP166 3.2 40.8 1.0
C V:ILE163 3.3 45.1 1.0
C V:SER169 3.6 39.2 1.0
CA L:ASP222 3.7 63.6 1.0
CA V:LEU167 3.8 40.4 1.0
O V:GLY162 3.9 42.5 1.0
N V:LEU167 3.9 41.4 1.0
O V:TRP164 3.9 47.4 1.0
NH1 V:ARG19 3.9 56.0 1.0
O L:ASP222 4.1 65.9 1.0
C V:TRP164 4.1 46.0 1.0
CA V:ILE163 4.1 44.5 1.0
N V:ASP166 4.1 32.8 1.0
N V:TRP164 4.2 44.5 1.0
C V:LEU167 4.2 40.9 1.0
CA V:ASP166 4.3 38.2 1.0
CB L:ASP222 4.3 65.7 1.0
CA V:TRP164 4.3 45.1 1.0
N V:SER169 4.4 37.4 1.0
O V:LEU167 4.4 43.3 1.0
CA V:GLY170 4.5 43.0 1.0
N V:GLY170 4.5 39.9 1.0
CA V:SER169 4.5 38.3 1.0
CZ V:ARG19 4.5 52.9 1.0
N V:ASN165 4.6 43.5 1.0
NH2 V:ARG19 4.7 57.6 1.0
C V:ASN165 4.8 39.2 1.0
C V:GLY162 4.8 43.9 1.0
CB V:SER169 4.9 38.9 1.0
O L:ARG221 5.0 58.1 1.0
N V:GLY168 5.0 39.9 1.0
N V:ILE163 5.0 44.2 1.0

Magnesium binding site 7 out of 8 in 4r00

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Magnesium binding site 7 out of 8 in the Ycp BETA5-C52F Mutant 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 BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:51.2
occ:1.00
 O I:ASP204 2.3 56.6 1.0
O Y:ALA165 2.4 39.0 1.0
O Y:ASP168 2.4 36.8 1.0
O Y:SER171 2.9 43.1 1.0
C I:ASP204 3.1 57.9 1.0
C Y:ASP168 3.3 37.9 1.0
CA I:ASP204 3.5 55.9 1.0
C Y:ALA165 3.6 39.1 1.0
CA Y:ALA169 3.6 39.8 1.0
O Y:HIS166 3.7 45.0 1.0
N Y:ALA169 3.8 39.5 1.0
CB I:ASP204 3.9 56.5 1.0
O Y:ALA169 3.9 40.8 1.0
NH1 Y:ARG19 3.9 56.8 1.0
C Y:ALA169 3.9 39.7 1.0
OXT I:ASP204 4.0 63.6 1.0
C Y:SER171 4.1 39.4 1.0
C Y:HIS166 4.2 41.4 1.0
N Y:ASP168 4.4 39.1 1.0
CA Y:ALA165 4.4 39.0 1.0
CA Y:ASP168 4.4 37.3 1.0
N Y:HIS166 4.5 40.8 1.0
N Y:SER171 4.5 36.8 1.0
CA Y:HIS166 4.6 40.6 1.0
CZ Y:ARG19 4.6 55.1 1.0
C Y:ARG167 4.6 40.8 1.0
O Y:ALA164 4.7 39.1 1.0
N Y:TYR170 4.8 39.8 1.0
N Y:ARG167 4.8 40.8 1.0
CA Y:SER171 4.8 35.6 1.0
O Y:ARG167 4.9 42.9 1.0
N I:ASP204 4.9 54.5 1.0
NH2 Y:ARG19 4.9 58.7 1.0
CB Y:ALA169 5.0 39.2 1.0
CG I:ASP204 5.0 56.3 1.0

Magnesium binding site 8 out of 8 in 4r00

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Magnesium binding site 8 out of 8 in the Ycp BETA5-C52F Mutant in Complex with Omuralide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ycp BETA5-C52F Mutant in Complex with Omuralide within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:58.4
occ:1.00
 O Z:VAL198 2.6 49.9 1.0
O Z:THR192 3.1 53.2 1.0
O Z:ASP222 3.2 67.8 1.0
O Z:HIS195 3.2 41.8 1.0
NH2 Z:ARG28 3.5 56.1 1.0
O Z:ILE196 3.7 48.8 1.0
C Z:VAL198 3.8 50.3 1.0
CG2 Z:THR192 3.9 58.7 1.0
CA Z:ILE196 4.0 48.7 1.0
C Z:ILE196 4.0 46.7 1.0
NH2 H:ARG19 4.0 62.8 1.0
C Z:THR192 4.1 56.9 1.0
C Z:HIS195 4.1 47.2 1.0
OD1 Z:ASP222 4.2 68.4 1.0
C Z:ASP222 4.3 71.6 1.0
CA Z:THR192 4.4 57.2 1.0
CZ Z:ARG28 4.4 53.6 1.0
N Z:VAL198 4.5 46.6 1.0
N Z:ILE196 4.5 47.1 1.0
NH1 Z:ARG28 4.6 56.0 1.0
NH1 H:ARG19 4.7 59.1 1.0
CA Z:GLY199 4.7 51.2 1.0
N Z:GLY199 4.7 50.9 1.0
CA Z:VAL198 4.7 48.1 1.0
CZ H:ARG19 4.7 57.9 1.0
OXT Z:ASP222 4.8 68.9 1.0
CB Z:THR192 4.8 57.2 1.0
O Z:LYS220 4.9 60.2 1.0
N Z:GLN197 5.0 43.7 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: Tue Aug 20 02:42:34 2024

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