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Magnesium in PDB 4no1: Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2

Enzymatic activity of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2

All present enzymatic activity of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2, PDB code: 4no1 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.440, 301.330, 144.910, 90.00, 113.06, 90.00
R / Rfree (%) 19 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2 (pdb code 4no1). 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-B(Oh)2, PDB code: 4no1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4no1

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Magnesium binding site 1 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


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-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:44.4
occ:1.00
 O G:ARG122 2.2 41.3 1.0
O G:MET125 2.3 37.6 1.0
O G:HOH441 2.4 40.9 1.0
O G:TYR119 2.6 36.8 1.0
OG1 G:THR8 2.7 33.9 1.0
O G:ALA123 3.4 42.3 1.0
C G:ARG122 3.4 38.9 1.0
CG2 G:THR8 3.4 36.8 1.0
C G:MET125 3.4 39.4 1.0
C G:ALA123 3.6 40.4 1.0
CB G:THR8 3.6 36.4 1.0
CA G:ALA123 3.6 39.2 1.0
C G:TYR119 3.7 34.4 1.0
N G:ALA123 4.0 38.1 1.0
N G:MET125 4.1 43.8 1.0
CA G:MET125 4.3 43.7 1.0
N G:ARG126 4.3 37.1 1.0
N G:THR8 4.4 38.0 1.0
CA G:ARG126 4.4 34.8 1.0
CA G:TYR119 4.5 33.8 1.0
N G:TYR124 4.5 42.8 1.0
CA G:ARG122 4.6 40.5 1.0
CD G:PRO127 4.6 29.8 1.0
N G:ARG122 4.6 38.8 1.0
CA G:THR8 4.6 38.1 1.0
N G:THR120 4.7 31.8 1.0
CB G:MET125 4.8 49.4 1.0
CA G:THR120 4.9 30.9 1.0
C G:TYR124 4.9 43.8 1.0
C G:ARG126 5.0 32.9 1.0
CB G:TYR119 5.0 31.8 1.0

Magnesium binding site 2 out of 8 in 4no1

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Magnesium binding site 2 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


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-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:60.7
occ:1.00
 O N:HOH335 2.0 36.5 1.0
O N:HOH337 2.2 47.7 1.0
OE1 H:GLN91 2.2 42.2 1.0
CD H:GLN91 3.4 40.9 1.0
O N:ASN92 3.8 44.1 1.0
OD1 N:ASP51 3.9 37.2 1.0
NE2 H:GLN91 3.9 37.7 1.0
O H:HOH406 3.9 31.2 1.0
OD2 N:ASP51 4.3 34.8 1.0
CG N:ASP51 4.6 34.4 1.0
O N:HOH323 4.6 38.0 1.0
CG H:GLN91 4.6 38.8 1.0
C N:ASN92 4.7 42.7 1.0
CB H:GLN91 4.9 36.9 1.0
ND1 H:HIS116 5.0 40.9 1.0

Magnesium binding site 3 out of 8 in 4no1

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Magnesium binding site 3 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


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-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:65.6
occ:1.00
 O I:SER180 2.6 34.5 1.0
O I:ASP177 2.6 38.3 1.0
O I:ALA174 2.6 40.7 1.0
C I:ALA174 3.6 40.9 1.0
C I:SER180 3.7 35.0 1.0
C I:ASP177 3.8 38.8 1.0
O I:HOH408 3.8 41.3 1.0
CA I:ASP175 3.9 40.8 1.0
OXT I:ASP204 4.1 41.0 1.0
N I:ASP175 4.2 41.0 1.0
C I:ASP175 4.4 39.2 1.0
OD1 I:ASP175 4.5 44.3 1.0
N I:ASP177 4.5 39.7 1.0
O I:ALA178 4.5 37.6 1.0
O I:ASP175 4.6 36.8 1.0
CA I:GLY181 4.6 34.0 1.0
N I:SER180 4.6 36.5 1.0
N I:GLY181 4.6 32.7 1.0
N I:ALA178 4.6 36.6 1.0
CA I:ALA178 4.6 35.6 1.0
C I:ALA178 4.6 35.4 1.0
CA I:ASP177 4.7 39.8 1.0
CA I:SER180 4.7 36.8 1.0
CA I:ALA174 4.8 40.4 1.0
NH2 Y:ARG19 4.9 45.4 1.0
NH1 Y:ARG19 4.9 43.3 1.0
C I:ASP204 5.0 41.1 1.0
CB I:ALA174 5.0 40.3 1.0

Magnesium binding site 4 out of 8 in 4no1

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Magnesium binding site 4 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


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-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:42.5
occ:1.00
 O K:ASP168 2.2 39.7 1.0
O K:ALA165 2.3 35.6 1.0
O W:ASP204 2.4 36.3 1.0
O K:SER171 2.4 39.7 1.0
O K:HOH428 2.5 52.0 1.0
C K:ASP168 3.2 38.5 1.0
C W:ASP204 3.2 36.3 1.0
C K:ALA165 3.4 36.5 1.0
C K:SER171 3.6 39.6 1.0
CA K:ALA169 3.6 39.8 1.0
CA W:ASP204 3.8 37.1 1.0
N K:ALA169 3.8 40.5 1.0
C K:ALA169 3.9 39.3 1.0
NH1 K:ARG19 3.9 46.0 1.0
O K:ALA169 3.9 39.8 1.0
OXT W:ASP204 4.1 35.1 1.0
O K:HIS166 4.1 41.5 1.0
CB W:ASP204 4.1 37.3 1.0
N K:SER171 4.1 40.2 1.0
CA K:ALA165 4.2 37.5 1.0
C K:HIS166 4.3 39.0 1.0
N K:ASP168 4.3 37.4 1.0
CA K:ASP168 4.3 37.1 1.0
CA K:SER171 4.4 38.1 1.0
N K:HIS166 4.4 37.3 1.0
O K:ALA164 4.4 37.9 1.0
CZ K:ARG19 4.5 44.8 1.0
N K:TYR170 4.6 38.9 1.0
CA K:HIS166 4.6 37.8 1.0
N K:GLY172 4.6 39.7 1.0
CA K:GLY172 4.7 38.5 1.0
NH2 K:ARG19 4.8 45.7 1.0
CB K:SER171 4.8 35.9 1.0
C K:ARG167 4.8 38.2 1.0
N K:ARG167 4.9 38.3 1.0

Magnesium binding site 5 out of 8 in 4no1

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Magnesium binding site 5 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


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-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:42.0
occ:1.00
 O N:SER169 2.5 31.1 1.0
O N:ILE163 2.6 35.3 1.0
O N:ASP166 2.7 35.2 1.0
NH1 N:ARG19 3.5 40.4 1.0
CD1 a:LEU34 3.5 33.6 1.0
C N:SER169 3.7 32.0 1.0
C N:ILE163 3.7 36.2 1.0
C N:ASP166 3.8 35.3 1.0
CG2 N:ILE163 4.0 36.2 1.0
CA N:GLY167 4.2 35.2 1.0
CZ N:ARG19 4.3 38.9 1.0
O N:GLY167 4.3 34.3 1.0
CA N:ILE163 4.4 36.4 1.0
N N:GLY167 4.4 35.6 1.0
C N:GLY167 4.5 33.7 1.0
CA N:GLY170 4.5 32.0 1.0
N N:GLY170 4.5 31.7 1.0
NH2 N:ARG19 4.6 39.0 1.0
N N:SER169 4.6 32.5 1.0
CA N:SER169 4.7 31.2 1.0
N N:LYS164 4.8 38.1 1.0
CB N:ILE163 4.8 37.5 1.0
CG a:LEU34 4.9 33.3 1.0
O N:LYS164 4.9 43.2 1.0
N N:ASP166 4.9 35.9 1.0
C N:LYS164 4.9 41.2 1.0
CA N:ASP166 4.9 35.7 1.0

Magnesium binding site 6 out of 8 in 4no1

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Magnesium binding site 6 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


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-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:48.9
occ:1.00
 O V:ASP166 2.2 35.6 1.0
O V:ILE163 2.2 40.7 1.0
OXT L:ASP222 2.3 45.1 1.0
O V:SER169 2.4 45.0 1.0
C L:ASP222 3.1 47.4 1.0
C V:ASP166 3.2 36.2 1.0
C V:ILE163 3.3 41.5 1.0
C V:SER169 3.5 42.3 1.0
O V:GLY162 3.7 32.4 1.0
CA L:ASP222 3.8 47.1 1.0
O L:ASP222 3.9 51.1 1.0
N V:LEU167 3.9 35.9 1.0
CA V:LEU167 3.9 35.8 1.0
NH1 V:ARG19 4.0 41.3 1.0
N V:ASP166 4.0 41.3 1.0
CA V:ILE163 4.0 42.9 1.0
C V:TRP164 4.1 46.0 1.0
N V:TRP164 4.2 42.8 1.0
O V:TRP164 4.2 48.0 1.0
CA V:ASP166 4.2 37.8 1.0
CB L:ASP222 4.3 46.4 1.0
N V:SER169 4.3 37.5 1.0
CA V:TRP164 4.4 44.7 1.0
C V:LEU167 4.4 36.0 1.0
CA V:SER169 4.4 38.7 1.0
N V:GLY170 4.4 44.5 1.0
CA V:GLY170 4.5 46.8 1.0
N V:ASN165 4.5 45.0 1.0
CZ V:ARG19 4.5 41.8 1.0
O V:LEU167 4.6 37.6 1.0
NH2 V:ARG19 4.7 41.5 1.0
C V:GLY162 4.7 38.7 1.0
C V:ASN165 4.7 42.5 1.0
CB V:SER169 4.7 37.9 1.0
N V:ILE163 4.9 40.9 1.0
CB V:ASP166 5.0 36.8 1.0

Magnesium binding site 7 out of 8 in 4no1

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Magnesium binding site 7 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


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-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:42.7
occ:1.00
 O Y:ASP168 2.2 36.9 1.0
O Y:SER171 2.3 41.7 1.0
O Y:ALA165 2.4 32.8 1.0
O I:ASP204 2.4 41.9 1.0
O Y:HOH402 2.5 33.6 1.0
C Y:ASP168 3.2 33.5 1.0
C I:ASP204 3.3 41.1 1.0
C Y:ALA165 3.5 33.0 1.0
C Y:SER171 3.5 38.6 1.0
CA Y:ALA169 3.6 35.0 1.0
C Y:ALA169 3.8 36.6 1.0
NH1 Y:ARG19 3.8 43.3 1.0
N Y:ALA169 3.8 34.1 1.0
CA I:ASP204 3.8 40.9 1.0
O Y:ALA169 3.9 38.5 1.0
N Y:SER171 4.0 37.7 1.0
CB I:ASP204 4.1 41.2 1.0
OXT I:ASP204 4.1 41.0 1.0
O Y:HIS166 4.2 33.0 1.0
CA Y:ALA165 4.2 34.5 1.0
CA Y:SER171 4.3 36.4 1.0
CZ Y:ARG19 4.4 43.5 1.0
CA Y:ASP168 4.4 30.7 1.0
N Y:ASP168 4.4 26.6 1.0
C Y:HIS166 4.4 32.5 1.0
O Y:ALA164 4.5 32.4 1.0
N Y:TYR170 4.5 38.2 1.0
N Y:HIS166 4.5 31.1 1.0
N Y:GLY172 4.5 37.9 1.0
CA Y:GLY172 4.6 36.5 1.0
NH2 Y:ARG19 4.7 45.4 1.0
CA Y:HIS166 4.7 29.9 1.0
CB Y:SER171 4.7 33.7 1.0
C Y:ARG167 4.9 32.4 1.0

Magnesium binding site 8 out of 8 in 4no1

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Magnesium binding site 8 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


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-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:68.3
occ:1.00
 O Z:VAL198 2.4 38.6 1.0
O Z:THR192 2.7 42.3 1.0
O Z:HIS195 2.9 36.8 1.0
NH2 Z:ARG28 3.6 47.0 1.0
CG2 Z:THR192 3.6 40.9 1.0
C Z:VAL198 3.6 38.4 1.0
C Z:THR192 3.6 43.1 1.0
CA Z:THR192 3.9 44.2 1.0
O Z:ASP222 3.9 53.5 1.0
C Z:HIS195 4.0 35.9 1.0
O Z:ILE196 4.1 41.2 1.0
CA Z:ILE196 4.2 37.2 1.0
C Z:ILE196 4.3 37.2 1.0
OD1 Z:ASP222 4.3 42.0 1.0
CB Z:THR192 4.4 42.5 1.0
N Z:VAL198 4.4 34.9 1.0
NH2 H:ARG19 4.4 48.7 1.0
N Z:GLY199 4.5 38.2 1.0
CA Z:GLY199 4.5 39.5 1.0
CA Z:VAL198 4.5 35.4 1.0
N Z:ILE196 4.6 35.9 1.0
CZ Z:ARG28 4.6 49.6 1.0
C Z:ASP222 4.7 49.5 1.0
NH1 Z:ARG28 4.9 51.3 1.0
N Z:GLU193 4.9 41.9 1.0
O Z:LYS220 4.9 43.5 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

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