Magnesium in PDB 4r02: Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)

Enzymatic activity of Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)

All present enzymatic activity of Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide):
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide), PDB code: 4r02 was solved by C.Voss, C.Scholz, S.Knorr, P.Beck, M.Stein, A.Zall, U.Kuckelkorn, P.-M.Kloetzel, M.Groll, K.Hamacher, B.Schmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 137.240, 300.870, 146.290, 90.00, 113.20, 90.00
R / Rfree (%) 17 / 20.7

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide) (pdb code 4r02). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide), PDB code: 4r02:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 4r02

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Magnesium binding site 1 out of 11 in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)


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 BSC4999 (Alpha-Keto Phenylamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:40.2
occ:1.00
 O G:MET125 2.2 38.5 1.0
O G:ARG122 2.2 35.4 1.0
O G:TYR119 2.3 30.7 1.0
O G:HOH422 2.5 41.6 1.0
OG1 G:THR8 2.7 37.0 1.0
CG2 G:THR8 3.3 37.3 1.0
C G:ARG122 3.4 37.1 1.0
C G:MET125 3.4 41.1 1.0
C G:TYR119 3.4 31.2 1.0
CB G:THR8 3.6 37.4 1.0
O G:ALA123 3.8 42.7 1.0
CA G:ALA123 3.9 39.2 1.0
C G:ALA123 4.0 40.4 1.0
N G:ALA123 4.1 37.6 1.0
N G:MET125 4.2 41.9 1.0
CA G:TYR119 4.2 31.4 1.0
CA G:MET125 4.3 44.6 1.0
N G:ARG122 4.4 37.1 1.0
N G:ARG126 4.4 38.3 1.0
N G:THR120 4.4 30.7 1.0
CA G:ARG122 4.5 38.7 1.0
CA G:ARG126 4.5 36.0 1.0
N G:THR8 4.5 38.8 1.0
CA G:THR120 4.6 31.8 1.0
CB G:MET125 4.6 52.6 1.0
CD G:PRO127 4.6 33.3 1.0
C G:THR120 4.7 33.1 1.0
CA G:THR8 4.7 38.6 1.0
O G:HOH413 4.7 40.4 1.0
N G:GLN121 4.7 33.3 1.0
N G:TYR124 4.7 41.5 1.0
CB G:TYR119 4.8 31.3 1.0
C G:ARG126 4.9 34.5 1.0
C G:GLN121 5.0 34.8 1.0

Magnesium binding site 2 out of 11 in 4r02

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Magnesium binding site 2 out of 11 in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)


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 BSC4999 (Alpha-Keto Phenylamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:54.7
occ:1.00
 O I:HOH427 2.2 64.3 1.0
O I:HOH444 2.4 54.3 1.0
O I:ASP177 2.4 43.4 1.0
O I:ALA174 2.4 47.6 1.0
O I:SER180 2.4 48.2 1.0
C I:ALA174 3.4 46.0 1.0
C I:ASP177 3.5 44.1 1.0
O I:HOH445 3.5 64.4 1.0
C I:SER180 3.6 46.4 1.0
O I:HOH446 3.8 58.5 1.0
CA I:ASP175 3.9 48.1 1.0
N I:ASP175 4.1 47.9 1.0
N I:ASP177 4.2 43.6 1.0
C I:ASP175 4.2 47.4 1.0
OXT I:ASP204 4.3 50.6 1.0
N I:SER180 4.4 44.0 1.0
CA I:ASP177 4.4 45.0 1.0
N I:ALA178 4.5 44.5 1.0
O I:ASP175 4.5 50.1 1.0
O I:HOH429 4.5 40.9 1.0
CA I:SER180 4.5 46.1 1.0
O I:ALA178 4.5 47.0 1.0
CA I:ALA174 4.5 42.5 1.0
C I:ALA178 4.5 45.6 1.0
N I:GLY181 4.5 44.2 1.0
CA I:ALA178 4.6 45.0 1.0
CA I:GLY181 4.6 46.2 1.0
OD1 I:ASP175 4.7 55.1 1.0
N I:ARG176 4.8 44.2 1.0
CB I:ALA174 4.8 41.2 1.0
CB I:ASP177 4.8 46.2 1.0
CB I:SER180 5.0 49.4 1.0
NH1 Y:ARG19 5.0 45.1 1.0

Magnesium binding site 3 out of 11 in 4r02

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Magnesium binding site 3 out of 11 in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)


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 BSC4999 (Alpha-Keto Phenylamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:82.2
occ:1.00
 O I:HOH446 2.2 58.5 1.0
O Y:HOH403 2.6 37.2 1.0
NE I:ARG27 3.3 42.9 1.0
OXT I:ASP204 3.4 50.6 1.0
O I:HOH443 3.5 39.2 1.0
CD I:ARG27 3.6 41.4 1.0
O I:ASP204 3.8 48.7 1.0
C I:ASP204 3.8 50.2 1.0
O I:HOH427 3.8 64.3 1.0
O I:ALA178 3.8 47.0 1.0
CD1 I:TRP182 3.9 40.6 1.0
NE1 I:TRP182 3.9 40.3 1.0
CZ I:ARG27 4.4 41.8 1.0
CG I:TRP182 4.4 41.5 1.0
CE2 I:TRP182 4.4 40.7 1.0
MG Y:MG302 4.4 42.8 1.0
CA Y:ALA169 4.4 37.9 1.0
O Y:HIS166 4.6 40.4 1.0
CD2 I:TRP182 4.6 41.0 1.0
NH2 I:ARG27 4.7 40.0 1.0
CB Y:ALA169 4.7 37.0 1.0
O I:SER180 4.8 48.2 1.0
O I:HOH429 4.8 40.9 1.0
CG I:ARG27 4.8 39.4 1.0
CA I:ASP204 4.9 48.9 1.0

Magnesium binding site 4 out of 11 in 4r02

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Magnesium binding site 4 out of 11 in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)


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 BSC4999 (Alpha-Keto Phenylamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:61.7
occ:1.00
 O J:HOH301 1.8 36.0 1.0
O J:THR124 2.9 37.0 1.0
O J:GLN118 3.7 36.6 1.0
OE1 J:GLN118 3.7 48.3 1.0
N J:ASP120 3.8 33.6 1.0
C J:THR124 3.8 36.4 1.0
CB J:THR124 3.9 37.6 1.0
CG2 J:THR124 4.0 36.7 1.0
CG J:GLN118 4.1 41.6 1.0
CB J:ASP120 4.1 35.2 1.0
C J:GLN118 4.2 37.4 1.0
CG J:ASP120 4.2 38.2 1.0
OD2 J:ASP120 4.3 40.9 1.0
CD J:GLN118 4.3 43.7 1.0
CA J:ILE119 4.4 33.3 1.0
C J:ILE119 4.5 34.2 1.0
CA J:THR124 4.5 37.2 1.0
N J:ILE119 4.6 34.8 1.0
CA J:ASP120 4.6 34.4 1.0
CB J:GLN118 4.7 39.6 1.0
CE1 J:HIS133 4.7 39.2 1.0
N J:LYS125 4.7 36.3 1.0
CG2 J:VAL126 4.7 48.4 1.0
OD1 J:ASP120 4.8 41.5 1.0
O I:HOH478 4.8 61.8 1.0
CG1 I:VAL35 4.9 40.6 1.0
N J:VAL126 4.9 37.8 1.0
CA J:LYS125 4.9 37.1 1.0
OG1 J:THR124 5.0 38.6 1.0
CD2 I:LEU28 5.0 38.8 1.0

Magnesium binding site 5 out of 11 in 4r02

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Magnesium binding site 5 out of 11 in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)


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 BSC4999 (Alpha-Keto Phenylamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:47.9
occ:1.00
 O K:ASP168 2.2 42.7 1.0
O K:SER171 2.3 45.4 1.0
O W:ASP204 2.3 48.4 1.0
O K:ALA165 2.3 42.7 1.0
O K:HOH434 2.4 46.9 1.0
C W:ASP204 3.3 49.2 1.0
C K:ASP168 3.3 40.9 1.0
C K:ALA165 3.4 42.0 1.0
C K:SER171 3.4 43.7 1.0
O K:ALA169 3.7 39.9 1.0
CA K:ALA169 3.8 39.5 1.0
CA W:ASP204 3.8 48.7 1.0
C K:ALA169 3.8 40.1 1.0
NH1 K:ARG19 3.8 44.4 1.0
O K:HOH401 3.9 71.6 1.0
N K:ALA169 3.9 40.2 1.0
CB W:ASP204 4.0 50.5 1.0
N K:SER171 4.0 43.5 1.0
CA K:ALA165 4.0 40.8 1.0
OXT W:ASP204 4.2 47.8 1.0
CA K:SER171 4.2 43.0 1.0
CA K:ASP168 4.4 40.6 1.0
N K:GLY172 4.4 45.0 1.0
N K:ASP168 4.5 37.2 1.0
CZ K:ARG19 4.5 42.6 1.0
N K:TYR170 4.5 40.3 1.0
O K:HIS166 4.5 41.5 1.0
N K:HIS166 4.5 40.5 1.0
O K:ALA164 4.5 43.5 1.0
CA K:GLY172 4.6 45.7 1.0
C K:HIS166 4.6 41.0 1.0
CB K:SER171 4.6 42.0 1.0
O W:HOH339 4.6 51.8 1.0
NH2 K:ARG19 4.8 43.8 1.0
CA K:HIS166 4.8 40.8 1.0
CB K:ALA165 4.9 39.3 1.0
CG W:ASP204 4.9 53.5 1.0

Magnesium binding site 6 out of 11 in 4r02

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Magnesium binding site 6 out of 11 in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)


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 BSC4999 (Alpha-Keto Phenylamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg303

b:49.7
occ:1.00
 O K:HOH484 2.5 42.5 1.0
O K:ILE82 2.7 38.5 1.0
O K:HOH436 2.8 54.9 1.0
O K:HOH502 3.0 50.5 1.0
C K:ILE82 3.6 36.6 1.0
CB K:ASN85 3.7 36.1 1.0
N K:LEU86 3.7 33.8 1.0
CA K:ILE82 3.8 35.4 1.0
CG2 K:ILE82 4.1 35.2 1.0
CB K:LEU86 4.1 36.1 1.0
C K:ASN85 4.1 33.6 1.0
CA K:LEU86 4.2 35.0 1.0
O K:HOH406 4.2 68.9 1.0
CH2 K:TRP58 4.4 30.7 1.0
CA K:ASN85 4.4 34.3 1.0
CB K:ILE82 4.5 35.0 1.0
O K:LYS81 4.5 36.6 1.0
O K:HOH456 4.5 44.4 1.0
O K:HOH464 4.6 40.2 1.0
O K:ASN85 4.8 33.6 1.0
CG K:ASN85 4.8 37.7 1.0
N K:ASN85 4.9 33.2 1.0
N K:LEU83 4.9 35.8 1.0
CG1 K:ILE82 4.9 34.7 1.0
OD1 K:ASN85 4.9 41.5 1.0
N K:ILE82 5.0 34.9 1.0

Magnesium binding site 7 out of 11 in 4r02

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Magnesium binding site 7 out of 11 in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)


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 BSC4999 (Alpha-Keto Phenylamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:48.6
occ:1.00
 O N:HOH305 1.9 50.5 1.0
O N:SER169 2.3 39.6 1.0
O N:ASP166 2.4 37.0 1.0
O N:ILE163 2.5 35.9 1.0
C N:SER169 3.4 37.7 1.0
C N:ASP166 3.5 36.1 1.0
C N:ILE163 3.6 37.0 1.0
CD1 a:LEU34 3.8 37.2 1.0
NH1 N:ARG19 3.8 40.9 1.0
CA N:GLY167 3.9 35.4 1.0
CG2 N:ILE163 4.0 34.0 1.0
O a:HOH411 4.0 61.4 1.0
N N:GLY167 4.1 35.9 1.0
O N:GLY167 4.1 34.8 1.0
CA N:ILE163 4.1 35.8 1.0
C N:GLY167 4.1 34.9 1.0
N N:SER169 4.2 35.4 1.0
CA N:SER169 4.3 35.6 1.0
N N:GLY170 4.4 38.2 1.0
CA N:GLY170 4.4 38.7 1.0
CZ N:ARG19 4.5 41.7 1.0
O a:HOH425 4.5 57.7 1.0
CA N:ASP166 4.6 36.2 1.0
N N:ASP166 4.6 36.0 1.0
CB N:SER169 4.7 35.0 1.0
CB N:ILE163 4.7 35.0 1.0
N N:LYS164 4.7 37.9 1.0
CG a:LEU34 4.9 38.4 1.0
N N:SER168 4.9 33.8 1.0
C N:LYS164 5.0 39.5 1.0
NH2 N:ARG19 5.0 43.8 1.0

Magnesium binding site 8 out of 11 in 4r02

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Magnesium binding site 8 out of 11 in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)


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 BSC4999 (Alpha-Keto Phenylamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:82.3
occ:1.00
 O H:HOH320 2.0 61.7 1.0
O N:HOH347 2.1 50.7 1.0
O N:HOH317 2.3 51.8 1.0
O N:HOH309 2.5 54.9 1.0
OD1 N:ASP51 3.2 43.4 1.0
OD2 N:ASP51 3.5 43.3 1.0
O N:ASN92 3.5 52.9 1.0
NE2 H:GLN91 3.5 71.7 1.0
CG N:ASP51 3.7 42.5 1.0
O N:HOH329 3.9 43.1 1.0
O H:HOH321 4.6 41.2 1.0
C N:ASN92 4.6 50.3 1.0
CD H:GLN91 4.6 70.2 1.0
O N:HOH379 4.7 63.8 1.0
OG N:SER48 4.8 35.7 1.0
O H:HOH333 4.9 50.0 1.0
OE1 H:GLN91 4.9 79.6 1.0

Magnesium binding site 9 out of 11 in 4r02

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Magnesium binding site 9 out of 11 in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:42.6
occ:1.00
 O V:SER169 2.2 44.6 1.0
O V:ASP166 2.2 40.7 1.0
O V:ILE163 2.3 39.1 1.0
O V:HOH403 2.5 48.7 1.0
OXT L:ASP222 2.6 48.5 1.0
C L:ASP222 3.3 55.2 1.0
C V:ASP166 3.3 40.0 1.0
C V:ILE163 3.3 40.8 1.0
C V:SER169 3.4 41.8 1.0
O V:GLY162 3.7 39.3 1.0
CA L:ASP222 3.9 54.5 1.0
NH1 V:ARG19 3.9 50.8 1.0
CA V:ILE163 4.0 41.8 1.0
O L:ASP222 4.0 60.9 1.0
CA V:LEU167 4.0 40.4 1.0
N V:LEU167 4.1 40.0 1.0
N V:ASP166 4.1 42.6 1.0
N V:SER169 4.2 38.9 1.0
CA V:SER169 4.2 39.5 1.0
N V:TRP164 4.3 41.9 1.0
CB L:ASP222 4.3 55.6 1.0
N V:GLY170 4.3 42.1 1.0
CA V:ASP166 4.3 41.3 1.0
CA V:GLY170 4.3 43.0 1.0
C V:LEU167 4.3 40.6 1.0
C V:TRP164 4.4 44.7 1.0
O V:LEU167 4.5 39.7 1.0
CZ V:ARG19 4.6 51.8 1.0
CA V:TRP164 4.6 43.2 1.0
O V:TRP164 4.6 44.5 1.0
CB V:SER169 4.6 38.2 1.0
N V:ASN165 4.7 45.6 1.0
C V:GLY162 4.7 39.8 1.0
NH2 V:ARG19 4.8 53.1 1.0
N V:ILE163 4.8 41.9 1.0
C V:ASN165 4.9 43.8 1.0
CB V:ASP166 5.0 41.1 1.0

Magnesium binding site 10 out of 11 in 4r02

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Magnesium binding site 10 out of 11 in the Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Ycp in Complex with BSC4999 (Alpha-Keto Phenylamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:42.8
occ:1.00
 O Y:ASP168 2.2 40.7 1.0
O Y:SER171 2.3 40.3 1.0
O Y:ALA165 2.3 40.0 1.0
O I:ASP204 2.3 48.7 1.0
O Y:HOH403 2.4 37.2 1.0
C I:ASP204 3.2 50.2 1.0
C Y:ASP168 3.3 38.2 1.0
C Y:ALA165 3.4 38.1 1.0
C Y:SER171 3.5 40.1 1.0
CA I:ASP204 3.7 48.9 1.0
CA Y:ALA169 3.8 37.9 1.0
O Y:ALA169 3.8 39.8 1.0
C Y:ALA169 3.8 39.1 1.0
NH1 Y:ARG19 3.8 45.1 1.0
CB I:ASP204 3.9 49.2 1.0
N Y:ALA169 3.9 38.4 1.0
N Y:SER171 4.0 39.9 1.0
CA Y:ALA165 4.1 37.7 1.0
OXT I:ASP204 4.2 50.6 1.0
CA Y:SER171 4.3 39.9 1.0
MG I:MG302 4.4 82.2 1.0
CZ Y:ARG19 4.4 46.1 1.0
CA Y:ASP168 4.4 35.8 1.0
O Y:HIS166 4.4 40.4 1.0
N Y:ASP168 4.4 26.2 1.0
N Y:HIS166 4.5 37.1 1.0
N Y:GLY172 4.5 41.5 1.0
N Y:TYR170 4.5 40.0 1.0
C Y:HIS166 4.5 38.9 1.0
O Y:ALA164 4.5 37.8 1.0
NH2 Y:ARG19 4.7 48.8 1.0
CA Y:GLY172 4.7 41.7 1.0
CB Y:SER171 4.7 38.5 1.0
CA Y:HIS166 4.8 37.5 1.0
CG I:ASP204 4.9 51.7 1.0
CB Y:ALA165 4.9 36.3 1.0
O I:HOH427 5.0 64.3 1.0

Reference:

C.Voss, C.Scholz, S.Knorr, P.Beck, M.L.Stein, A.Zall, U.Kuckelkorn, P.M.Kloetzel, M.Groll, K.Hamacher, B.Schmidt. Alpha-Keto Phenylamides As P1'-Extended Proteasome Inhibitors. Chemmedchem 2014.
ISSN: ESSN 1860-7187
PubMed: 25087721
DOI: 10.1002/CMDC.201402244
Page generated: Mon Dec 14 19:29:23 2020

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