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Magnesium in PDB 4nnw: Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde

Protein crystallography data

The structure of Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde, PDB code: 4nnw 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.640, 301.290, 145.120, 90.00, 113.71, 90.00
R / Rfree (%) 19.5 / 20.8

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 4nnw

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Magnesium binding site 1 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde


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

b:43.8
occ:1.00
 O G:MET125 2.2 41.8 1.0
O G:ARG122 2.4 38.0 1.0
O G:TYR119 2.4 31.5 1.0
OG1 G:THR8 2.6 38.4 1.0
CG2 G:THR8 3.3 37.3 1.0
C G:MET125 3.4 45.1 1.0
C G:ARG122 3.5 36.8 1.0
CB G:THR8 3.6 40.0 1.0
O G:ALA123 3.6 43.8 1.0
C G:TYR119 3.6 30.4 1.0
CA G:ALA123 3.8 35.8 1.0
C G:ALA123 3.8 39.7 1.0
N G:ALA123 4.1 34.9 1.0
N G:MET125 4.2 47.2 1.0
CA G:MET125 4.3 49.2 1.0
N G:ARG126 4.3 40.6 1.0
CA G:TYR119 4.3 30.6 1.0
CA G:ARG126 4.4 37.3 1.0
CD G:PRO127 4.5 30.7 1.0
N G:THR8 4.5 39.1 1.0
N G:ARG122 4.6 38.6 1.0
N G:THR120 4.6 28.5 1.0
CA G:ARG122 4.7 38.8 1.0
CA G:THR8 4.7 39.6 1.0
N G:TYR124 4.7 43.8 1.0
CB G:MET125 4.7 56.6 1.0
CA G:THR120 4.7 29.5 1.0
C G:THR120 4.8 30.8 1.0
CB G:TYR119 4.8 29.9 1.0
C G:ARG126 4.9 36.6 1.0
N G:GLN121 5.0 31.5 1.0
N G:PRO127 5.0 34.3 1.0

Magnesium binding site 2 out of 8 in 4nnw

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Magnesium binding site 2 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde


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-Ketoaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:65.6
occ:1.00
 OE1 H:GLN91 2.7 44.7 1.0
OD1 N:ASP51 2.8 35.1 1.0
O N:ASN92 3.4 42.4 1.0
CD H:GLN91 3.4 45.5 1.0
NE2 H:GLN91 3.5 46.1 1.0
CG N:ASP51 3.5 31.3 1.0
OD2 N:ASP51 3.5 33.7 1.0
O H:HOH406 3.7 32.8 1.0
CE1 H:PHE88 4.5 23.6 1.0
C N:ASN92 4.6 42.6 1.0
CZ H:PHE88 4.7 22.3 1.0
O N:HOH319 4.7 31.8 1.0
CG H:GLN91 4.9 41.8 1.0

Magnesium binding site 3 out of 8 in 4nnw

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Magnesium binding site 3 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde


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

b:42.8
occ:1.00
 O I:ASP177 2.3 38.9 1.0
O I:ALA174 2.4 40.5 1.0
O I:HOH430 2.4 36.9 1.0
O I:SER180 2.7 41.3 1.0
C I:ASP177 3.4 39.5 1.0
C I:ALA174 3.5 39.0 1.0
O I:HOH429 3.5 54.2 1.0
C I:SER180 3.8 40.9 1.0
CA I:ASP175 4.0 40.2 1.0
N I:ASP175 4.2 39.5 1.0
N I:ASP177 4.2 37.9 1.0
N I:ALA178 4.3 37.1 1.0
CA I:ALA178 4.3 35.4 1.0
OXT I:ASP204 4.3 46.6 1.0
O I:HOH416 4.3 33.2 1.0
C I:ASP175 4.3 38.6 1.0
CA I:ASP177 4.4 40.2 1.0
C I:ALA178 4.4 37.9 1.0
N I:SER180 4.5 41.4 1.0
O I:ALA178 4.5 38.8 1.0
O I:ASP175 4.6 41.4 1.0
CA I:ALA174 4.6 37.5 1.0
CA I:SER180 4.6 41.2 1.0
N I:GLY181 4.7 37.8 1.0
OD1 I:ASP175 4.7 43.0 1.0
CA I:GLY181 4.7 36.4 1.0
CB I:ASP177 4.9 42.4 1.0
CB I:ALA174 4.9 38.9 1.0
N I:LEU179 4.9 39.1 1.0
N I:ARG176 5.0 34.6 1.0
NH2 Y:ARG19 5.0 55.8 1.0

Magnesium binding site 4 out of 8 in 4nnw

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Magnesium binding site 4 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde


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

b:45.5
occ:1.00
 O K:ALA165 2.3 43.0 1.0
O K:ASP168 2.3 38.9 1.0
O W:ASP204 2.5 44.4 1.0
O K:SER171 2.9 41.7 1.0
C W:ASP204 3.2 40.6 1.0
C K:ASP168 3.2 37.3 1.0
C K:ALA165 3.4 42.6 1.0
CA W:ASP204 3.6 39.2 1.0
CA K:ALA169 3.7 32.6 1.0
N K:ALA169 3.8 33.4 1.0
O K:HIS166 3.8 43.1 1.0
NH1 K:ARG19 3.9 42.6 1.0
C K:SER171 4.0 40.9 1.0
OXT W:ASP204 4.0 42.9 1.0
C K:ALA169 4.0 36.0 1.0
C K:HIS166 4.1 42.4 1.0
CB W:ASP204 4.1 37.5 1.0
O K:ALA169 4.2 38.8 1.0
N K:ASP168 4.2 41.0 1.0
CA K:ALA165 4.3 41.0 1.0
N K:HIS166 4.3 42.7 1.0
CA K:ASP168 4.3 38.8 1.0
CA K:HIS166 4.4 41.9 1.0
N K:SER171 4.5 41.9 1.0
O K:ALA164 4.5 42.7 1.0
CZ K:ARG19 4.7 44.7 1.0
N K:ARG167 4.7 41.6 1.0
C K:ARG167 4.7 40.0 1.0
CA K:SER171 4.8 39.9 1.0
N K:TYR170 4.8 37.4 1.0
N K:GLY172 4.9 41.8 1.0
CA K:GLY172 5.0 43.8 1.0

Magnesium binding site 5 out of 8 in 4nnw

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Magnesium binding site 5 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde


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

b:34.3
occ:1.00
 O N:SER169 2.6 33.3 1.0
O N:ILE163 2.7 31.4 1.0
O N:ASP166 2.9 33.2 1.0
NH1 N:ARG19 3.4 27.1 1.0
CD1 a:LEU34 3.6 33.5 1.0
C N:SER169 3.8 31.7 1.0
C N:ASP166 3.9 31.6 1.0
C N:ILE163 3.9 32.5 1.0
CG2 N:ILE163 4.0 25.4 1.0
CA N:GLY167 4.2 27.9 1.0
CZ N:ARG19 4.2 25.8 1.0
O N:GLY167 4.3 28.4 1.0
N N:GLY167 4.4 29.1 1.0
C N:GLY167 4.4 27.5 1.0
CA N:GLY170 4.4 31.6 1.0
CA N:ILE163 4.5 30.9 1.0
N N:GLY170 4.6 30.7 1.0
NH2 N:ARG19 4.6 21.0 1.0
N N:SER169 4.7 29.7 1.0
CA N:SER169 4.8 29.6 1.0
CB N:ILE163 4.9 29.1 1.0
CG a:LEU34 4.9 35.8 1.0
N N:LYS164 5.0 34.8 1.0
N N:ASP166 5.0 32.3 1.0
O N:LYS164 5.0 34.6 1.0

Magnesium binding site 6 out of 8 in 4nnw

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Magnesium binding site 6 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde


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

b:46.1
occ:1.00
 O V:ASP166 2.2 39.0 1.0
OXT L:ASP222 2.2 41.5 1.0
O V:SER169 2.3 44.4 1.0
O V:ILE163 2.3 42.8 1.0
C L:ASP222 3.1 43.8 1.0
C V:ASP166 3.2 38.9 1.0
C V:ILE163 3.3 43.9 1.0
C V:SER169 3.5 41.7 1.0
CA L:ASP222 3.8 41.5 1.0
CA V:LEU167 3.8 33.5 1.0
NH1 V:ARG19 3.8 49.7 1.0
N V:LEU167 3.9 36.5 1.0
O L:ASP222 3.9 45.9 1.0
O V:GLY162 3.9 38.8 1.0
N V:ASP166 4.0 43.2 1.0
CA V:ILE163 4.1 44.7 1.0
CA V:ASP166 4.2 39.9 1.0
N V:TRP164 4.3 42.5 1.0
C V:TRP164 4.3 40.0 1.0
N V:SER169 4.3 33.9 1.0
CB L:ASP222 4.3 39.1 1.0
CZ V:ARG19 4.3 46.6 1.0
C V:LEU167 4.3 32.2 1.0
O V:TRP164 4.4 36.5 1.0
NH2 V:ARG19 4.4 43.5 1.0
N V:GLY170 4.4 44.0 1.0
CA V:SER169 4.4 36.5 1.0
CA V:GLY170 4.4 46.5 1.0
CA V:TRP164 4.5 41.1 1.0
N V:ASN165 4.6 40.5 1.0
O V:LEU167 4.7 32.3 1.0
CB V:SER169 4.8 37.3 1.0
C V:ASN165 4.8 42.2 1.0
C V:GLY162 4.8 39.9 1.0
CD2 V:LEU167 4.9 29.6 1.0
N V:GLY168 4.9 32.0 1.0

Magnesium binding site 7 out of 8 in 4nnw

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Magnesium binding site 7 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde


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

b:36.0
occ:1.00
 O Y:ASP168 2.3 36.8 1.0
O Y:SER171 2.3 39.1 1.0
O I:ASP204 2.4 42.1 1.0
O Y:ALA165 2.4 42.4 1.0
O Y:HOH415 2.8 35.7 1.0
C I:ASP204 3.2 43.0 1.0
C Y:ASP168 3.3 36.4 1.0
NH1 Y:ARG19 3.4 59.0 1.0
C Y:SER171 3.5 38.7 1.0
C Y:ALA165 3.5 42.4 1.0
CA Y:ALA169 3.7 33.6 1.0
CA I:ASP204 3.8 39.8 1.0
C Y:ALA169 3.8 33.1 1.0
O Y:ALA169 3.9 34.0 1.0
N Y:ALA169 3.9 36.3 1.0
CB I:ASP204 4.0 37.2 1.0
N Y:SER171 4.1 39.8 1.0
OXT I:ASP204 4.1 46.6 1.0
CZ Y:ARG19 4.2 53.1 1.0
CA Y:ALA165 4.2 40.6 1.0
CA Y:SER171 4.3 39.1 1.0
O Y:HIS166 4.4 36.5 1.0
N Y:GLY172 4.4 36.4 1.0
CA Y:ASP168 4.5 35.0 1.0
N Y:ASP168 4.5 37.9 1.0
N Y:TYR170 4.5 34.1 1.0
N Y:HIS166 4.5 42.0 1.0
CA Y:GLY172 4.6 36.3 1.0
C Y:HIS166 4.6 37.8 1.0
NH2 Y:ARG19 4.6 55.8 1.0
O Y:ALA164 4.7 42.3 1.0
CB Y:SER171 4.8 38.6 1.0
CA Y:HIS166 4.8 39.0 1.0
CG I:ASP204 5.0 41.5 1.0

Magnesium binding site 8 out of 8 in 4nnw

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Magnesium binding site 8 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-Ketoaldehyde


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

b:50.0
occ:1.00
 O Z:THR192 2.5 42.3 1.0
O Z:VAL198 2.5 34.8 1.0
O Z:HIS195 3.0 32.1 1.0
CG2 Z:THR192 3.5 31.6 1.0
C Z:THR192 3.5 41.8 1.0
C Z:VAL198 3.7 34.8 1.0
CA Z:THR192 3.8 38.6 1.0
NH2 Z:ARG28 3.8 28.3 1.0
C Z:HIS195 4.0 33.0 1.0
O Z:ASP222 4.1 39.2 1.0
CB Z:THR192 4.2 34.9 1.0
CA Z:ILE196 4.3 32.6 1.0
O Z:ILE196 4.3 34.4 1.0
OD1 Z:ASP222 4.4 37.7 1.0
C Z:ILE196 4.4 33.4 1.0
N Z:VAL198 4.6 35.8 1.0
CA Z:GLY199 4.6 35.0 1.0
N Z:ILE196 4.6 32.7 1.0
N Z:GLY199 4.6 33.6 1.0
CA Z:VAL198 4.7 34.0 1.0
N Z:GLU193 4.7 43.7 1.0
NH2 H:ARG19 4.8 45.8 1.0
CZ Z:ARG28 4.9 31.1 1.0
N Z:HIS195 4.9 35.1 1.0
C Z:ASP222 4.9 36.5 1.0
O Z:LYS220 5.0 41.4 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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