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Magnesium in PDB 4qby: Ycp in Complex with Boc-Ala-Ala-Ala-Cho

Enzymatic activity of Ycp in Complex with Boc-Ala-Ala-Ala-Cho

All present enzymatic activity of Ycp in Complex with Boc-Ala-Ala-Ala-Cho:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Boc-Ala-Ala-Ala-Cho, PDB code: 4qby was solved by M.Arciniega, P.Beck, O.Lange, M.Groll, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.990, 300.130, 144.800, 90.00, 112.51, 90.00
R / Rfree (%) 17.8 / 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 Boc-Ala-Ala-Ala-Cho (pdb code 4qby). 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 Boc-Ala-Ala-Ala-Cho, PDB code: 4qby:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 4qby

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Magnesium binding site 1 out of 11 in the Ycp in Complex with Boc-Ala-Ala-Ala-Cho


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

b:53.7
occ:1.00
 O G:MET125 2.2 62.2 1.0
O G:TYR119 2.7 54.5 1.0
O G:ARG122 2.7 53.4 1.0
OG1 G:THR8 2.8 53.3 1.0
O G:ALA123 3.1 68.3 1.0
CG2 G:THR8 3.2 47.8 1.0
C G:MET125 3.4 59.7 1.0
C G:ALA123 3.5 63.5 1.0
CB G:THR8 3.6 48.9 1.0
CA G:ALA123 3.7 61.3 1.0
C G:ARG122 3.8 59.2 1.0
C G:TYR119 3.8 56.2 1.0
N G:MET125 4.1 57.4 1.0
N G:ARG126 4.2 58.3 1.0
N G:ALA123 4.2 60.1 1.0
CA G:ARG126 4.2 52.8 1.0
N G:THR8 4.3 52.7 1.0
CA G:MET125 4.3 59.3 1.0
N G:TYR124 4.5 65.4 1.0
CD G:PRO127 4.6 50.5 1.0
CA G:THR8 4.6 52.6 1.0
CA G:TYR119 4.6 52.7 1.0
C G:TYR124 4.8 61.4 1.0
C G:ARG126 4.9 53.9 1.0
N G:THR120 4.9 56.4 1.0
CB G:MET125 4.9 65.0 1.0

Magnesium binding site 2 out of 11 in 4qby

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Magnesium binding site 2 out of 11 in the Ycp in Complex with Boc-Ala-Ala-Ala-Cho


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 Boc-Ala-Ala-Ala-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:60.8
occ:1.00
 OE1 H:GLN91 2.8 74.4 1.0
OD1 N:ASP51 3.0 52.3 1.0
OD2 N:ASP51 3.5 51.8 1.0
CG N:ASP51 3.7 50.4 1.0
CD H:GLN91 3.7 75.0 1.0
O N:ASN92 3.8 60.3 1.0
NE2 H:GLN91 4.0 83.2 1.0
C N:ASN92 4.9 60.0 1.0
OG N:SER48 5.0 57.5 1.0
ND1 H:HIS116 5.0 58.0 1.0

Magnesium binding site 3 out of 11 in 4qby

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Magnesium binding site 3 out of 11 in the Ycp in Complex with Boc-Ala-Ala-Ala-Cho


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

b:42.3
occ:1.00
 O I:ASP177 2.3 52.9 1.0
O I:SER180 2.9 58.2 1.0
O I:ALA174 3.0 62.3 1.0
C I:ASP177 3.4 55.2 1.0
OXT I:ASP204 3.9 63.8 1.0
CA I:ALA178 4.0 50.2 1.0
O I:ALA178 4.0 50.7 1.0
C I:SER180 4.0 58.6 1.0
C I:ALA178 4.1 51.8 1.0
C I:ALA174 4.1 61.1 1.0
N I:ALA178 4.1 52.6 1.0
CA I:ASP175 4.2 69.3 1.0
O I:ASP204 4.3 74.1 1.0
O I:ASP175 4.4 77.8 1.0
NH1 Y:ARG19 4.4 73.3 1.0
C I:ASP175 4.5 70.8 1.0
N I:ASP177 4.5 60.6 1.0
CA I:ASP177 4.5 59.7 1.0
N I:SER180 4.5 55.1 1.0
C I:ASP204 4.6 63.6 1.0
NH2 Y:ARG19 4.6 75.5 1.0
N I:ASP175 4.6 64.0 1.0
OD1 I:ASP175 4.8 64.1 1.0
N I:LEU179 4.8 52.0 1.0
CA I:SER180 4.8 58.1 1.0
CZ Y:ARG19 4.9 74.0 1.0
N I:GLY181 4.9 58.5 1.0
CA I:GLY181 5.0 56.7 1.0

Magnesium binding site 4 out of 11 in 4qby

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Magnesium binding site 4 out of 11 in the Ycp in Complex with Boc-Ala-Ala-Ala-Cho


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 Boc-Ala-Ala-Ala-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:67.3
occ:1.00
 MG Y:MG301 3.4 50.6 1.0
NE1 I:TRP182 3.5 59.1 1.0
OXT I:ASP204 3.6 63.8 1.0
NE I:ARG27 3.6 57.5 1.0
O Y:HIS166 3.6 55.8 1.0
C I:ASP204 3.7 63.6 1.0
O I:ASP204 3.8 74.1 1.0
CA Y:ALA169 3.8 47.3 1.0
CD1 I:TRP182 3.8 59.7 1.0
O I:ALA178 3.9 50.7 1.0
CE2 I:TRP182 4.1 55.6 1.0
CB Y:ALA169 4.1 46.2 1.0
CD I:ARG27 4.3 55.0 1.0
N Y:ALA169 4.3 52.7 1.0
NH2 I:ARG27 4.3 56.9 1.0
O Y:ARG167 4.4 53.7 1.0
CZ I:ARG27 4.4 55.5 1.0
CA I:ASP204 4.6 65.2 1.0
CG I:TRP182 4.6 58.7 1.0
O Y:ASP168 4.6 61.4 1.0
CZ2 I:TRP182 4.7 54.9 1.0
C Y:ASP168 4.7 56.7 1.0
CD2 I:TRP182 4.7 55.7 1.0
C Y:HIS166 4.8 56.3 1.0
C Y:ALA169 4.9 46.3 1.0
O Y:ALA169 4.9 50.1 1.0
C Y:ARG167 5.0 57.3 1.0

Magnesium binding site 5 out of 11 in 4qby

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Magnesium binding site 5 out of 11 in the Ycp in Complex with Boc-Ala-Ala-Ala-Cho


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 Boc-Ala-Ala-Ala-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:33.6
occ:1.00
 OE1 J:GLN118 3.1 52.9 1.0
OD2 J:ASP120 3.2 64.1 1.0
O J:THR124 3.6 56.8 1.0
CG J:ASP120 3.7 62.5 1.0
CB J:ASP120 3.8 57.0 1.0
N J:ASP120 4.1 55.0 1.0
CB J:THR124 4.2 47.0 1.0
CG2 J:THR124 4.3 43.5 1.0
CD J:GLN118 4.3 57.0 1.0
CE1 J:HIS133 4.4 50.6 1.0
O J:GLN118 4.5 52.0 1.0
OD1 J:ASP120 4.6 67.1 1.0
CA J:ASP120 4.6 53.3 1.0
C J:THR124 4.6 51.9 1.0
CG1 I:VAL35 4.7 47.6 1.0
C J:ILE119 4.8 54.3 1.0
CG2 J:VAL126 4.9 53.8 1.0
CD2 I:LEU28 4.9 54.0 1.0
C J:GLN118 5.0 54.1 1.0

Magnesium binding site 6 out of 11 in 4qby

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Magnesium binding site 6 out of 11 in the Ycp in Complex with Boc-Ala-Ala-Ala-Cho


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 Boc-Ala-Ala-Ala-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:45.4
occ:1.00
 O K:ASP168 2.3 50.4 1.0
O K:ALA165 2.4 58.5 1.0
O W:ASP204 2.6 58.0 1.0
O K:SER171 2.9 54.4 1.0
C W:ASP204 3.2 60.2 1.0
C K:ASP168 3.2 49.0 1.0
O K:HIS166 3.5 53.0 1.0
C K:ALA165 3.5 57.1 1.0
CA K:ALA169 3.5 51.0 1.0
CA W:ASP204 3.5 60.5 1.0
N K:ALA169 3.7 50.4 1.0
C K:ALA169 3.8 54.2 1.0
CB W:ASP204 3.8 61.4 1.0
O K:ALA169 3.8 56.1 1.0
NH1 K:ARG19 3.8 81.1 1.0
C K:SER171 4.0 58.6 1.0
C K:HIS166 4.0 56.5 1.0
OXT W:ASP204 4.1 63.9 1.0
CA K:ALA165 4.4 55.2 1.0
N K:HIS166 4.4 57.0 1.0
N K:SER171 4.4 56.0 1.0
N K:ASP168 4.4 45.7 1.0
CA K:ASP168 4.4 48.1 1.0
CA K:HIS166 4.5 57.4 1.0
N K:TYR170 4.6 56.5 1.0
C K:ARG167 4.6 47.7 1.0
O K:ALA164 4.6 56.5 1.0
CZ K:ARG19 4.6 73.4 1.0
CA K:SER171 4.7 55.4 1.0
O K:ARG167 4.8 49.5 1.0
N K:ARG167 4.8 52.3 1.0
CB K:ALA169 4.8 45.4 1.0
CG W:ASP204 4.9 60.8 1.0
N W:ASP204 4.9 60.8 1.0
N K:GLY172 5.0 61.4 1.0

Magnesium binding site 7 out of 11 in 4qby

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Magnesium binding site 7 out of 11 in the Ycp in Complex with Boc-Ala-Ala-Ala-Cho


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

b:54.7
occ:1.00
 O K:ILE82 2.9 60.5 1.0
CB K:ASN85 3.7 50.1 1.0
C K:ILE82 3.7 60.9 1.0
N K:LEU86 3.7 53.0 1.0
CA K:ILE82 3.8 59.0 1.0
CG2 K:ILE82 3.9 59.3 1.0
C K:ASN85 4.1 52.7 1.0
CA K:LEU86 4.2 48.8 1.0
CB K:LEU86 4.3 45.6 1.0
CB K:ILE82 4.4 57.9 1.0
CH2 K:TRP58 4.4 43.4 1.0
CA K:ASN85 4.4 50.2 1.0
O K:LYS81 4.7 49.6 1.0
O K:ASN85 4.8 56.8 1.0
CG K:ASN85 4.8 50.8 1.0
N K:ASN85 4.9 49.9 1.0
OD1 K:ASN85 4.9 48.7 1.0
CG1 K:ILE82 5.0 55.4 1.0
N K:LEU83 5.0 56.7 1.0

Magnesium binding site 8 out of 11 in 4qby

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Magnesium binding site 8 out of 11 in the Ycp in Complex with Boc-Ala-Ala-Ala-Cho


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 Boc-Ala-Ala-Ala-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:48.9
occ:1.00
 O N:SER169 2.7 52.2 1.0
O N:ILE163 2.7 50.9 1.0
O N:ASP166 3.0 54.5 1.0
NH1 N:ARG19 3.5 49.1 1.0
C N:SER169 3.8 53.5 1.0
C N:ILE163 3.8 53.5 1.0
CD1 a:LEU34 3.8 57.1 1.0
CG2 N:ILE163 3.9 48.9 1.0
C N:ASP166 4.1 50.1 1.0
CZ N:ARG19 4.2 53.9 1.0
CA N:GLY170 4.2 55.2 1.0
CA N:GLY167 4.3 48.5 1.0
O N:GLY167 4.4 47.0 1.0
N N:GLY170 4.4 55.4 1.0
NH2 N:ARG19 4.5 63.1 1.0
CA N:ILE163 4.5 52.8 1.0
C N:GLY167 4.6 47.9 1.0
N N:GLY167 4.6 48.2 1.0
O N:LYS164 4.8 61.2 1.0
N N:LYS164 4.8 58.4 1.0
CB N:ILE163 4.9 49.2 1.0
CA N:SER169 4.9 52.0 1.0
C N:LYS164 5.0 58.5 1.0
N N:SER169 5.0 55.8 1.0

Magnesium binding site 9 out of 11 in 4qby

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Magnesium binding site 9 out of 11 in the Ycp in Complex with Boc-Ala-Ala-Ala-Cho


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 Boc-Ala-Ala-Ala-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:68.8
occ:1.00
 OXT L:ASP222 1.9 84.9 1.0
O V:ASP166 2.0 61.6 1.0
O V:SER169 2.1 54.7 1.0
O V:ILE163 2.2 59.7 1.0
C L:ASP222 3.0 79.8 1.0
C V:ASP166 3.1 58.5 1.0
C V:ILE163 3.3 62.6 1.0
C V:SER169 3.4 52.4 1.0
CA L:ASP222 3.6 72.2 1.0
NH1 V:ARG19 3.7 74.4 1.0
CA V:LEU167 3.7 51.7 1.0
N V:LEU167 3.8 55.9 1.0
O V:GLY162 3.9 59.1 1.0
CB L:ASP222 3.9 67.5 1.0
O V:TRP164 4.0 67.9 1.0
O L:ASP222 4.0 83.9 1.0
CA V:ILE163 4.1 62.5 1.0
N V:SER169 4.1 50.9 1.0
C V:LEU167 4.2 49.4 1.0
CZ V:ARG19 4.2 65.5 1.0
CA V:SER169 4.3 50.9 1.0
CA V:ASP166 4.3 57.8 1.0
N V:ASP166 4.3 58.7 1.0
N V:GLY170 4.3 52.8 1.0
C V:TRP164 4.3 68.3 1.0
N V:TRP164 4.3 65.2 1.0
CA V:GLY170 4.3 53.9 1.0
O V:LEU167 4.4 46.7 1.0
NH2 V:ARG19 4.5 73.4 1.0
CA V:TRP164 4.6 64.6 1.0
CB V:SER169 4.7 51.5 1.0
N V:GLY168 4.8 51.3 1.0
C V:GLY162 4.9 58.5 1.0
CD2 V:LEU167 4.9 47.4 1.0
N V:ASN165 5.0 69.0 1.0
CG L:ASP222 5.0 66.4 1.0
N V:ILE163 5.0 61.4 1.0

Magnesium binding site 10 out of 11 in 4qby

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Magnesium binding site 10 out of 11 in the Ycp in Complex with Boc-Ala-Ala-Ala-Cho


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 Boc-Ala-Ala-Ala-Cho within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:50.6
occ:1.00
 O Y:ALA165 2.4 51.6 1.0
O I:ASP204 2.5 74.1 1.0
O Y:ASP168 2.5 61.4 1.0
O Y:SER171 2.8 53.8 1.0
C I:ASP204 3.1 63.6 1.0
MG I:MG302 3.4 67.3 1.0
C Y:ASP168 3.4 56.7 1.0
CA I:ASP204 3.4 65.2 1.0
C Y:ALA165 3.5 54.3 1.0
O Y:HIS166 3.6 55.8 1.0
CA Y:ALA169 3.6 47.3 1.0
NH1 Y:ARG19 3.6 73.3 1.0
CB I:ASP204 3.7 69.2 1.0
O Y:ALA169 3.8 50.1 1.0
C Y:ALA169 3.8 46.3 1.0
N Y:ALA169 3.9 52.7 1.0
C Y:SER171 4.0 57.4 1.0
OXT I:ASP204 4.0 63.8 1.0
C Y:HIS166 4.2 56.3 1.0
CA Y:ALA165 4.4 57.4 1.0
N Y:HIS166 4.4 54.0 1.0
CZ Y:ARG19 4.5 74.0 1.0
N Y:SER171 4.5 54.3 1.0
CA Y:HIS166 4.5 54.5 1.0
N Y:ASP168 4.6 57.4 1.0
CA Y:ASP168 4.6 58.0 1.0
N Y:TYR170 4.7 48.2 1.0
CA Y:SER171 4.8 55.4 1.0
NH2 Y:ARG19 4.8 75.5 1.0
C Y:ARG167 4.8 57.3 1.0
O Y:ALA164 4.8 58.8 1.0
CG I:ASP204 4.8 70.8 1.0
N I:ASP204 4.9 61.2 1.0
CB Y:ALA169 4.9 46.2 1.0
O Y:ARG167 4.9 53.7 1.0
N Y:GLY172 4.9 59.8 1.0
N Y:ARG167 5.0 56.0 1.0

Reference:

M.Arciniega, P.Beck, O.F.Lange, M.Groll, R.Huber. Differential Global Structural Changes in the Core Particle of Yeast and Mouse Proteasome Induced By Ligand Binding. Proc.Natl.Acad.Sci.Usa V. 111 9479 2014.
ISSN: ISSN 0027-8424
PubMed: 24979800
DOI: 10.1073/PNAS.1408018111
Page generated: Tue Aug 20 01:52:47 2024

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