Magnesium in PDB 5c1b: P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
Enzymatic activity of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
All present enzymatic activity of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide:
3.6.4.6;
Protein crystallography data
The structure of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide, PDB code: 5c1b
was solved by
P.Haenzelmann,
H.Schindelin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.14 /
3.08
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
140.715,
180.664,
254.958,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
19.8 /
24
|
Other elements in 5c1b:
The structure of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Magnesium atom in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
(pdb code 5c1b). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the
P97-DELTA709-728 in Complex with A UFD1-Shp Peptide, PDB code: 5c1b:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 12 in 5c1b
Go back to
Magnesium Binding Sites List in 5c1b
Magnesium binding site 1 out
of 12 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg903
b:0.2
occ:1.00
|
O2G
|
A:AGS901
|
2.1
|
0.7
|
1.0
|
|
OG1
|
A:THR252
|
2.1
|
97.0
|
1.0
|
|
O
|
A:HOH1003
|
2.1
|
93.8
|
1.0
|
|
O
|
A:HOH1002
|
2.1
|
0.1
|
1.0
|
|
O
|
A:HOH1001
|
2.1
|
0.3
|
1.0
|
|
O2B
|
A:AGS901
|
2.1
|
84.4
|
1.0
|
|
PG
|
A:AGS901
|
2.7
|
0.5
|
1.0
|
|
O3G
|
A:AGS901
|
2.8
|
0.2
|
1.0
|
|
HOG2
|
A:AGS901
|
2.9
|
0.0
|
1.0
|
|
O3B
|
A:AGS901
|
3.1
|
0.9
|
1.0
|
|
PB
|
A:AGS901
|
3.1
|
95.6
|
1.0
|
|
H21
|
A:AGS901
|
3.1
|
0.9
|
1.0
|
|
CB
|
A:THR252
|
3.3
|
89.0
|
1.0
|
|
OD1
|
A:ASP304
|
3.3
|
0.1
|
1.0
|
|
HB
|
A:THR252
|
3.4
|
0.8
|
1.0
|
|
OD2
|
A:ASP304
|
3.4
|
0.7
|
1.0
|
|
H
|
A:THR252
|
3.6
|
0.1
|
1.0
|
|
O1A
|
A:AGS901
|
3.7
|
0.1
|
1.0
|
|
CG
|
A:ASP304
|
3.8
|
0.3
|
1.0
|
|
HG21
|
A:THR252
|
3.9
|
98.3
|
1.0
|
|
CG2
|
A:THR252
|
4.1
|
81.9
|
1.0
|
|
O1B
|
A:AGS901
|
4.1
|
88.4
|
1.0
|
|
O3A
|
A:AGS901
|
4.2
|
0.6
|
1.0
|
|
PA
|
A:AGS901
|
4.3
|
92.2
|
1.0
|
|
N
|
A:THR252
|
4.3
|
88.4
|
1.0
|
|
O2A
|
A:AGS901
|
4.3
|
71.8
|
1.0
|
|
CA
|
A:THR252
|
4.4
|
85.9
|
1.0
|
|
HG23
|
A:THR252
|
4.4
|
98.3
|
1.0
|
|
S1G
|
A:AGS901
|
4.6
|
0.7
|
1.0
|
|
HZ1
|
A:LYS251
|
4.6
|
0.6
|
1.0
|
|
HB2
|
A:LYS251
|
4.7
|
0.5
|
1.0
|
|
HA
|
A:THR252
|
4.7
|
0.1
|
1.0
|
|
HG3
|
A:GLU305
|
4.8
|
0.2
|
1.0
|
|
HE2
|
A:PHE302
|
4.9
|
88.4
|
1.0
|
|
HG22
|
A:THR252
|
5.0
|
98.3
|
1.0
|
|
Magnesium binding site 2 out
of 12 in 5c1b
Go back to
Magnesium Binding Sites List in 5c1b
Magnesium binding site 2 out
of 12 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg904
b:86.3
occ:1.00
|
O2G
|
A:AGS902
|
2.0
|
55.3
|
1.0
|
|
O1B
|
A:AGS902
|
2.0
|
91.9
|
1.0
|
|
OG1
|
A:THR525
|
2.1
|
78.9
|
1.0
|
|
O
|
A:HOH1004
|
2.1
|
0.6
|
1.0
|
|
O
|
A:HOH1005
|
2.1
|
89.0
|
1.0
|
|
O1A
|
A:AGS902
|
2.1
|
89.4
|
1.0
|
|
HOG2
|
A:AGS902
|
2.4
|
66.3
|
1.0
|
|
HB
|
A:THR525
|
3.1
|
81.8
|
1.0
|
|
CB
|
A:THR525
|
3.1
|
68.1
|
1.0
|
|
PB
|
A:AGS902
|
3.3
|
78.3
|
1.0
|
|
PA
|
A:AGS902
|
3.4
|
88.8
|
1.0
|
|
PG
|
A:AGS902
|
3.4
|
97.7
|
1.0
|
|
H
|
A:THR525
|
3.5
|
0.1
|
1.0
|
|
OD2
|
A:ASP577
|
3.8
|
84.3
|
1.0
|
|
O3B
|
A:AGS902
|
3.8
|
97.4
|
1.0
|
|
O3A
|
A:AGS902
|
3.8
|
71.0
|
1.0
|
|
HG21
|
A:THR525
|
3.9
|
86.2
|
1.0
|
|
O2A
|
A:AGS902
|
4.0
|
0.8
|
1.0
|
|
CG2
|
A:THR525
|
4.1
|
71.9
|
1.0
|
|
N
|
A:THR525
|
4.1
|
89.2
|
1.0
|
|
HD2
|
B:ARG635
|
4.2
|
0.9
|
1.0
|
|
CA
|
A:THR525
|
4.2
|
77.1
|
1.0
|
|
OD1
|
A:ASP577
|
4.2
|
84.6
|
1.0
|
|
CG
|
A:ASP577
|
4.4
|
79.7
|
1.0
|
|
O3G
|
A:AGS902
|
4.5
|
88.8
|
1.0
|
|
H5'1
|
A:AGS902
|
4.5
|
0.5
|
1.0
|
|
O2B
|
A:AGS902
|
4.5
|
75.1
|
1.0
|
|
HG23
|
A:THR525
|
4.5
|
86.2
|
1.0
|
|
S1G
|
A:AGS902
|
4.6
|
95.8
|
1.0
|
|
HA
|
A:THR525
|
4.6
|
92.5
|
1.0
|
|
O5'
|
A:AGS902
|
4.6
|
92.5
|
1.0
|
|
HB2
|
A:LYS524
|
4.7
|
0.4
|
1.0
|
|
H5'2
|
A:AGS902
|
4.8
|
0.5
|
1.0
|
|
C5'
|
A:AGS902
|
4.8
|
88.8
|
1.0
|
|
H21
|
A:AGS902
|
4.9
|
0.6
|
1.0
|
|
HG22
|
A:THR525
|
4.9
|
86.2
|
1.0
|
|
HH11
|
B:ARG635
|
4.9
|
0.7
|
1.0
|
|
HG3
|
A:GLU578
|
5.0
|
0.4
|
1.0
|
|
HG2
|
A:GLU578
|
5.0
|
0.4
|
1.0
|
|
Magnesium binding site 3 out
of 12 in 5c1b
Go back to
Magnesium Binding Sites List in 5c1b
Magnesium binding site 3 out
of 12 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg903
b:0.2
occ:1.00
|
O2G
|
B:AGS901
|
2.0
|
0.8
|
1.0
|
|
O2B
|
B:AGS901
|
2.0
|
78.6
|
1.0
|
|
O
|
B:HOH1001
|
2.1
|
0.7
|
1.0
|
|
OG1
|
B:THR252
|
2.1
|
94.8
|
1.0
|
|
O
|
B:HOH1003
|
2.1
|
0.5
|
1.0
|
|
O
|
B:HOH1002
|
2.1
|
0.9
|
1.0
|
|
HOG2
|
B:AGS901
|
2.5
|
0.4
|
1.0
|
|
PB
|
B:AGS901
|
3.2
|
72.8
|
1.0
|
|
OD2
|
B:ASP304
|
3.2
|
0.0
|
1.0
|
|
OD1
|
B:ASP304
|
3.2
|
0.5
|
1.0
|
|
PG
|
B:AGS901
|
3.3
|
0.3
|
1.0
|
|
CB
|
B:THR252
|
3.3
|
69.1
|
1.0
|
|
HB
|
B:THR252
|
3.4
|
83.0
|
1.0
|
|
H
|
B:THR252
|
3.5
|
92.4
|
1.0
|
|
O3B
|
B:AGS901
|
3.5
|
0.1
|
1.0
|
|
CG
|
B:ASP304
|
3.6
|
0.7
|
1.0
|
|
O3A
|
B:AGS901
|
3.7
|
0.9
|
1.0
|
|
O2A
|
B:AGS901
|
3.8
|
93.0
|
1.0
|
|
HG21
|
B:THR252
|
4.1
|
71.2
|
1.0
|
|
O3G
|
B:AGS901
|
4.2
|
0.5
|
1.0
|
|
N
|
B:THR252
|
4.2
|
77.0
|
1.0
|
|
CG2
|
B:THR252
|
4.2
|
59.4
|
1.0
|
|
PA
|
B:AGS901
|
4.3
|
82.8
|
1.0
|
|
CA
|
B:THR252
|
4.3
|
61.9
|
1.0
|
|
O1B
|
B:AGS901
|
4.4
|
63.9
|
1.0
|
|
HZ1
|
B:LYS251
|
4.4
|
0.1
|
1.0
|
|
HG23
|
B:THR252
|
4.5
|
71.2
|
1.0
|
|
HB2
|
B:LYS251
|
4.5
|
73.0
|
1.0
|
|
HA
|
B:THR252
|
4.6
|
74.2
|
1.0
|
|
O1A
|
B:AGS901
|
4.7
|
72.0
|
1.0
|
|
S1G
|
B:AGS901
|
4.7
|
0.3
|
1.0
|
|
HG3
|
B:GLU305
|
4.8
|
0.7
|
1.0
|
|
HE2
|
B:PHE302
|
4.8
|
90.2
|
1.0
|
|
H21
|
B:AGS901
|
4.8
|
0.7
|
1.0
|
|
HZ
|
B:PHE302
|
4.8
|
80.1
|
1.0
|
|
Magnesium binding site 4 out
of 12 in 5c1b
Go back to
Magnesium Binding Sites List in 5c1b
Magnesium binding site 4 out
of 12 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg904
b:99.2
occ:1.00
|
O2B
|
B:AGS902
|
2.0
|
95.8
|
1.0
|
|
O2G
|
B:AGS902
|
2.0
|
70.6
|
1.0
|
|
OG1
|
B:THR525
|
2.1
|
86.2
|
1.0
|
|
O2A
|
B:AGS902
|
2.1
|
98.3
|
1.0
|
|
O
|
B:HOH1004
|
2.1
|
0.2
|
1.0
|
|
O
|
B:HOH1005
|
2.1
|
0.0
|
1.0
|
|
HOG2
|
B:AGS902
|
2.3
|
84.7
|
1.0
|
|
HB
|
B:THR525
|
3.1
|
93.5
|
1.0
|
|
CB
|
B:THR525
|
3.1
|
77.9
|
1.0
|
|
PB
|
B:AGS902
|
3.3
|
92.9
|
1.0
|
|
PA
|
B:AGS902
|
3.4
|
95.7
|
1.0
|
|
PG
|
B:AGS902
|
3.4
|
0.3
|
1.0
|
|
H
|
B:THR525
|
3.5
|
94.8
|
1.0
|
|
OD2
|
B:ASP577
|
3.7
|
77.9
|
1.0
|
|
O3B
|
B:AGS902
|
3.8
|
72.1
|
1.0
|
|
O3A
|
B:AGS902
|
3.9
|
0.3
|
1.0
|
|
HG21
|
B:THR525
|
3.9
|
94.1
|
1.0
|
|
O1A
|
B:AGS902
|
4.1
|
99.3
|
1.0
|
|
N
|
B:THR525
|
4.1
|
79.0
|
1.0
|
|
CG2
|
B:THR525
|
4.1
|
78.5
|
1.0
|
|
HD2
|
C:ARG635
|
4.1
|
0.3
|
1.0
|
|
CA
|
B:THR525
|
4.2
|
78.7
|
1.0
|
|
OD1
|
B:ASP577
|
4.2
|
85.2
|
1.0
|
|
O3G
|
B:AGS902
|
4.3
|
72.8
|
1.0
|
|
H5'2
|
B:AGS902
|
4.4
|
0.6
|
1.0
|
|
CG
|
B:ASP577
|
4.4
|
85.9
|
1.0
|
|
O1B
|
B:AGS902
|
4.5
|
86.4
|
1.0
|
|
HG23
|
B:THR525
|
4.5
|
94.1
|
1.0
|
|
HA
|
B:THR525
|
4.5
|
94.4
|
1.0
|
|
O5'
|
B:AGS902
|
4.6
|
0.1
|
1.0
|
|
HB2
|
B:LYS524
|
4.6
|
89.6
|
1.0
|
|
S1G
|
B:AGS902
|
4.7
|
91.2
|
1.0
|
|
HH11
|
C:ARG635
|
4.8
|
0.3
|
1.0
|
|
HG22
|
B:THR525
|
4.9
|
94.1
|
1.0
|
|
C5'
|
B:AGS902
|
4.9
|
0.8
|
1.0
|
|
H21
|
B:AGS902
|
5.0
|
87.4
|
1.0
|
|
Magnesium binding site 5 out
of 12 in 5c1b
Go back to
Magnesium Binding Sites List in 5c1b
Magnesium binding site 5 out
of 12 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg904
b:0.5
occ:1.00
|
O2G
|
C:AGS902
|
2.1
|
0.8
|
1.0
|
|
O
|
C:HOH1001
|
2.1
|
0.2
|
1.0
|
|
O2B
|
C:AGS902
|
2.1
|
94.3
|
1.0
|
|
OG1
|
C:THR252
|
2.1
|
93.6
|
1.0
|
|
O
|
C:HOH1002
|
2.1
|
0.4
|
1.0
|
|
O
|
C:HOH1003
|
2.1
|
0.9
|
1.0
|
|
HOG2
|
C:AGS902
|
2.8
|
0.9
|
1.0
|
|
PG
|
C:AGS902
|
3.1
|
0.8
|
1.0
|
|
O3B
|
C:AGS902
|
3.1
|
0.7
|
1.0
|
|
PB
|
C:AGS902
|
3.1
|
83.0
|
1.0
|
|
CB
|
C:THR252
|
3.3
|
81.6
|
1.0
|
|
OD1
|
C:ASP304
|
3.4
|
98.4
|
1.0
|
|
OD2
|
C:ASP304
|
3.4
|
1.0
|
1.0
|
|
HB
|
C:THR252
|
3.5
|
97.9
|
1.0
|
|
O2A
|
C:AGS902
|
3.6
|
90.8
|
1.0
|
|
H
|
C:THR252
|
3.6
|
89.3
|
1.0
|
|
O3G
|
C:AGS902
|
3.8
|
75.6
|
1.0
|
|
CG
|
C:ASP304
|
3.8
|
97.2
|
1.0
|
|
HG21
|
C:THR252
|
4.1
|
84.1
|
1.0
|
|
O1B
|
C:AGS902
|
4.1
|
80.0
|
1.0
|
|
N
|
C:THR252
|
4.2
|
74.4
|
1.0
|
|
O3A
|
C:AGS902
|
4.2
|
0.1
|
1.0
|
|
CG2
|
C:THR252
|
4.2
|
70.1
|
1.0
|
|
CA
|
C:THR252
|
4.3
|
81.7
|
1.0
|
|
PA
|
C:AGS902
|
4.4
|
81.5
|
1.0
|
|
HG23
|
C:THR252
|
4.5
|
84.1
|
1.0
|
|
H21
|
C:AGS902
|
4.5
|
90.7
|
1.0
|
|
HZ3
|
C:LYS251
|
4.5
|
0.9
|
1.0
|
|
HB2
|
C:LYS251
|
4.6
|
79.5
|
1.0
|
|
HA
|
C:THR252
|
4.7
|
98.0
|
1.0
|
|
S1G
|
C:AGS902
|
4.7
|
0.7
|
1.0
|
|
O1A
|
C:AGS902
|
4.7
|
82.7
|
1.0
|
|
HG3
|
C:GLU305
|
4.9
|
99.8
|
1.0
|
|
Magnesium binding site 6 out
of 12 in 5c1b
Go back to
Magnesium Binding Sites List in 5c1b
Magnesium binding site 6 out
of 12 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg905
b:0.3
occ:1.00
|
O2B
|
C:AGS903
|
2.0
|
0.8
|
1.0
|
|
O2G
|
C:AGS903
|
2.1
|
0.0
|
1.0
|
|
O
|
C:HOH1004
|
2.1
|
0.8
|
1.0
|
|
O
|
C:HOH1005
|
2.1
|
0.6
|
1.0
|
|
O2A
|
C:AGS903
|
2.1
|
93.8
|
1.0
|
|
OG1
|
C:THR525
|
2.1
|
83.8
|
1.0
|
|
HOG2
|
C:AGS903
|
2.3
|
0.6
|
1.0
|
|
HB
|
C:THR525
|
3.0
|
0.0
|
1.0
|
|
CB
|
C:THR525
|
3.1
|
92.5
|
1.0
|
|
PB
|
C:AGS903
|
3.2
|
92.7
|
1.0
|
|
PG
|
C:AGS903
|
3.4
|
1.0
|
1.0
|
|
PA
|
C:AGS903
|
3.4
|
96.7
|
1.0
|
|
H
|
C:THR525
|
3.5
|
0.6
|
1.0
|
|
O3B
|
C:AGS903
|
3.7
|
83.9
|
1.0
|
|
O3A
|
C:AGS903
|
3.7
|
0.4
|
1.0
|
|
OD2
|
C:ASP577
|
3.8
|
84.9
|
1.0
|
|
HG21
|
C:THR525
|
3.8
|
0.5
|
1.0
|
|
HD2
|
D:ARG635
|
4.0
|
0.5
|
1.0
|
|
CG2
|
C:THR525
|
4.1
|
89.6
|
1.0
|
|
N
|
C:THR525
|
4.2
|
92.2
|
1.0
|
|
O1A
|
C:AGS903
|
4.2
|
0.9
|
1.0
|
|
CA
|
C:THR525
|
4.2
|
92.2
|
1.0
|
|
O3G
|
C:AGS903
|
4.2
|
79.8
|
1.0
|
|
H5'2
|
C:AGS903
|
4.4
|
0.3
|
1.0
|
|
OD1
|
C:ASP577
|
4.4
|
91.6
|
1.0
|
|
HG23
|
C:THR525
|
4.5
|
0.5
|
1.0
|
|
O1B
|
C:AGS903
|
4.5
|
99.0
|
1.0
|
|
H5'1
|
C:AGS903
|
4.5
|
0.3
|
1.0
|
|
O5'
|
C:AGS903
|
4.5
|
0.1
|
1.0
|
|
CG
|
C:ASP577
|
4.5
|
92.0
|
1.0
|
|
HA
|
C:THR525
|
4.6
|
0.7
|
1.0
|
|
HH11
|
D:ARG635
|
4.7
|
0.1
|
1.0
|
|
C5'
|
C:AGS903
|
4.7
|
0.8
|
1.0
|
|
S1G
|
C:AGS903
|
4.8
|
1.0
|
1.0
|
|
HB2
|
C:LYS524
|
4.8
|
0.9
|
1.0
|
|
HG22
|
C:THR525
|
4.8
|
0.5
|
1.0
|
|
H21
|
C:AGS903
|
5.0
|
95.8
|
1.0
|
|
CD
|
D:ARG635
|
5.0
|
0.4
|
1.0
|
|
Magnesium binding site 7 out
of 12 in 5c1b
Go back to
Magnesium Binding Sites List in 5c1b
Magnesium binding site 7 out
of 12 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg904
b:0.3
occ:1.00
|
O2G
|
D:AGS902
|
2.1
|
0.6
|
1.0
|
|
O
|
D:HOH1004
|
2.1
|
0.3
|
1.0
|
|
O
|
D:HOH1003
|
2.1
|
0.3
|
1.0
|
|
O2B
|
D:AGS902
|
2.1
|
99.2
|
1.0
|
|
O
|
D:HOH1001
|
2.1
|
0.2
|
1.0
|
|
OG1
|
D:THR252
|
2.1
|
0.5
|
1.0
|
|
HOG2
|
D:AGS902
|
2.8
|
0.5
|
1.0
|
|
PG
|
D:AGS902
|
3.0
|
0.3
|
1.0
|
|
O3B
|
D:AGS902
|
3.0
|
0.5
|
1.0
|
|
PB
|
D:AGS902
|
3.1
|
91.6
|
1.0
|
|
CB
|
D:THR252
|
3.4
|
96.6
|
1.0
|
|
OD1
|
D:ASP304
|
3.4
|
0.3
|
1.0
|
|
HB
|
D:THR252
|
3.4
|
0.9
|
1.0
|
|
OD2
|
D:ASP304
|
3.5
|
0.9
|
1.0
|
|
O3G
|
D:AGS902
|
3.6
|
1.0
|
1.0
|
|
H
|
D:THR252
|
3.6
|
99.4
|
1.0
|
|
O2A
|
D:AGS902
|
3.8
|
91.2
|
1.0
|
|
CG
|
D:ASP304
|
3.9
|
89.4
|
1.0
|
|
HG21
|
D:THR252
|
4.0
|
0.2
|
1.0
|
|
O1B
|
D:AGS902
|
4.1
|
80.2
|
1.0
|
|
O3A
|
D:AGS902
|
4.2
|
0.6
|
1.0
|
|
CG2
|
D:THR252
|
4.2
|
91.8
|
1.0
|
|
N
|
D:THR252
|
4.3
|
82.8
|
1.0
|
|
H21
|
D:AGS902
|
4.3
|
0.8
|
1.0
|
|
PA
|
D:AGS902
|
4.3
|
93.1
|
1.0
|
|
CA
|
D:THR252
|
4.4
|
78.8
|
1.0
|
|
O1A
|
D:AGS902
|
4.4
|
81.3
|
1.0
|
|
HG23
|
D:THR252
|
4.5
|
0.2
|
1.0
|
|
HZ2
|
D:LYS251
|
4.5
|
0.3
|
1.0
|
|
HB2
|
D:LYS251
|
4.6
|
81.0
|
1.0
|
|
S1G
|
D:AGS902
|
4.7
|
0.5
|
1.0
|
|
HA
|
D:THR252
|
4.7
|
94.6
|
1.0
|
|
HG3
|
D:GLU305
|
4.9
|
0.4
|
1.0
|
|
HE2
|
D:PHE302
|
5.0
|
87.3
|
1.0
|
|
Magnesium binding site 8 out
of 12 in 5c1b
Go back to
Magnesium Binding Sites List in 5c1b
Magnesium binding site 8 out
of 12 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg905
b:0.5
occ:1.00
|
O2G
|
D:AGS903
|
2.0
|
82.3
|
1.0
|
|
O2B
|
D:AGS903
|
2.0
|
98.9
|
1.0
|
|
O
|
D:HOH1002
|
2.1
|
0.0
|
1.0
|
|
O
|
D:HOH1005
|
2.1
|
0.1
|
1.0
|
|
OG1
|
D:THR525
|
2.1
|
90.8
|
1.0
|
|
O2A
|
D:AGS903
|
2.1
|
0.1
|
1.0
|
|
HOG2
|
D:AGS903
|
2.5
|
98.8
|
1.0
|
|
HB
|
D:THR525
|
3.0
|
0.1
|
1.0
|
|
CB
|
D:THR525
|
3.1
|
84.2
|
1.0
|
|
PB
|
D:AGS903
|
3.2
|
87.0
|
1.0
|
|
PA
|
D:AGS903
|
3.3
|
98.0
|
1.0
|
|
PG
|
D:AGS903
|
3.4
|
0.8
|
1.0
|
|
H
|
D:THR525
|
3.4
|
98.3
|
1.0
|
|
OD2
|
D:ASP577
|
3.7
|
92.4
|
1.0
|
|
O3B
|
D:AGS903
|
3.7
|
84.7
|
1.0
|
|
O3A
|
D:AGS903
|
3.7
|
92.7
|
1.0
|
|
HG21
|
D:THR525
|
3.9
|
86.5
|
1.0
|
|
O1A
|
D:AGS903
|
3.9
|
92.9
|
1.0
|
|
N
|
D:THR525
|
4.0
|
81.9
|
1.0
|
|
CG2
|
D:THR525
|
4.1
|
72.0
|
1.0
|
|
OD1
|
D:ASP577
|
4.1
|
100.0
|
1.0
|
|
CA
|
D:THR525
|
4.1
|
83.8
|
1.0
|
|
HD2
|
E:ARG635
|
4.2
|
0.6
|
1.0
|
|
O3G
|
D:AGS903
|
4.3
|
84.2
|
1.0
|
|
H21
|
D:AGS903
|
4.3
|
0.1
|
1.0
|
|
CG
|
D:ASP577
|
4.4
|
97.2
|
1.0
|
|
O1B
|
D:AGS903
|
4.5
|
84.6
|
1.0
|
|
H5'2
|
D:AGS903
|
4.5
|
0.3
|
1.0
|
|
HG23
|
D:THR525
|
4.5
|
86.5
|
1.0
|
|
HA
|
D:THR525
|
4.5
|
0.5
|
1.0
|
|
HB2
|
D:LYS524
|
4.6
|
0.8
|
1.0
|
|
H5'1
|
D:AGS903
|
4.6
|
0.3
|
1.0
|
|
O5'
|
D:AGS903
|
4.6
|
66.5
|
1.0
|
|
S1G
|
D:AGS903
|
4.7
|
95.1
|
1.0
|
|
C5'
|
D:AGS903
|
4.8
|
91.1
|
1.0
|
|
HG22
|
D:THR525
|
4.9
|
86.5
|
1.0
|
|
Magnesium binding site 9 out
of 12 in 5c1b
Go back to
Magnesium Binding Sites List in 5c1b
Magnesium binding site 9 out
of 12 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg903
b:0.3
occ:1.00
|
O2G
|
E:AGS901
|
2.1
|
0.9
|
1.0
|
|
O
|
E:HOH1001
|
2.1
|
0.7
|
1.0
|
|
OG1
|
E:THR252
|
2.1
|
0.5
|
1.0
|
|
O
|
E:HOH1002
|
2.1
|
0.5
|
1.0
|
|
O2B
|
E:AGS901
|
2.1
|
81.6
|
1.0
|
|
O
|
E:HOH1003
|
2.1
|
0.4
|
1.0
|
|
HOG2
|
E:AGS901
|
2.8
|
0.2
|
1.0
|
|
PG
|
E:AGS901
|
3.0
|
0.1
|
1.0
|
|
O3B
|
E:AGS901
|
3.0
|
0.9
|
1.0
|
|
PB
|
E:AGS901
|
3.1
|
91.7
|
1.0
|
|
O1A
|
E:AGS901
|
3.2
|
0.8
|
1.0
|
|
OD1
|
E:ASP304
|
3.4
|
0.2
|
1.0
|
|
CB
|
E:THR252
|
3.4
|
0.3
|
1.0
|
|
OD2
|
E:ASP304
|
3.5
|
1.0
|
1.0
|
|
HB
|
E:THR252
|
3.6
|
0.9
|
1.0
|
|
H
|
E:THR252
|
3.6
|
0.4
|
1.0
|
|
O3G
|
E:AGS901
|
3.8
|
88.5
|
1.0
|
|
CG
|
E:ASP304
|
3.9
|
0.2
|
1.0
|
|
HG21
|
E:THR252
|
4.1
|
0.6
|
1.0
|
|
O1B
|
E:AGS901
|
4.1
|
88.8
|
1.0
|
|
O3A
|
E:AGS901
|
4.2
|
0.1
|
1.0
|
|
N
|
E:THR252
|
4.2
|
95.3
|
1.0
|
|
HZ1
|
E:LYS251
|
4.2
|
0.5
|
1.0
|
|
PA
|
E:AGS901
|
4.3
|
94.0
|
1.0
|
|
CG2
|
E:THR252
|
4.3
|
87.2
|
1.0
|
|
H21
|
E:AGS901
|
4.3
|
0.2
|
1.0
|
|
CA
|
E:THR252
|
4.4
|
98.9
|
1.0
|
|
HB2
|
E:LYS251
|
4.4
|
1.0
|
1.0
|
|
HG23
|
E:THR252
|
4.5
|
0.6
|
1.0
|
|
HA
|
E:THR252
|
4.7
|
0.7
|
1.0
|
|
S1G
|
E:AGS901
|
4.7
|
0.6
|
1.0
|
|
HG3
|
E:GLU305
|
4.8
|
0.3
|
1.0
|
|
HZ3
|
E:LYS251
|
5.0
|
0.5
|
1.0
|
|
NZ
|
E:LYS251
|
5.0
|
95.4
|
1.0
|
|
O2A
|
E:AGS901
|
5.0
|
81.8
|
1.0
|
|
Magnesium binding site 10 out
of 12 in 5c1b
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Magnesium Binding Sites List in 5c1b
Magnesium binding site 10 out
of 12 in the P97-DELTA709-728 in Complex with A UFD1-Shp Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of P97-DELTA709-728 in Complex with A UFD1-Shp Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg904
b:0.3
occ:1.00
|
O2G
|
E:AGS902
|
2.0
|
96.7
|
1.0
|
|
O2B
|
E:AGS902
|
2.1
|
0.8
|
1.0
|
|
O
|
E:HOH1004
|
2.1
|
99.6
|
1.0
|
|
O1A
|
E:AGS902
|
2.1
|
97.6
|
1.0
|
|
O
|
E:HOH1005
|
2.1
|
83.0
|
1.0
|
|
OG1
|
E:THR525
|
2.1
|
0.6
|
1.0
|
|
HOG2
|
E:AGS902
|
2.3
|
0.0
|
1.0
|
|
HB
|
E:THR525
|
3.1
|
1.0
|
1.0
|
|
CB
|
E:THR525
|
3.2
|
0.6
|
1.0
|
|
PB
|
E:AGS902
|
3.3
|
94.3
|
1.0
|
|
PA
|
E:AGS902
|
3.4
|
92.7
|
1.0
|
|
PG
|
E:AGS902
|
3.4
|
0.2
|
1.0
|
|
H
|
E:THR525
|
3.5
|
0.3
|
1.0
|
|
OD2
|
E:ASP577
|
3.8
|
84.0
|
1.0
|
|
O3B
|
E:AGS902
|
3.8
|
0.5
|
1.0
|
|
O3A
|
E:AGS902
|
3.8
|
57.0
|
1.0
|
|
HG21
|
E:THR525
|
3.9
|
0.6
|
1.0
|
|
O2A
|
E:AGS902
|
4.0
|
0.7
|
1.0
|
|
HD2
|
F:ARG635
|
4.0
|
0.4
|
1.0
|
|
CG2
|
E:THR525
|
4.1
|
0.3
|
1.0
|
|
N
|
E:THR525
|
4.2
|
1.0
|
1.0
|
|
H5'1
|
E:AGS902
|
4.2
|
0.8
|
1.0
|
|
CA
|
E:THR525
|
4.2
|
0.9
|
1.0
|
|
O3G
|
E:AGS902
|
4.3
|
74.2
|
1.0
|
|
H21
|
E:AGS902
|
4.3
|
89.1
|
1.0
|
|
OD1
|
E:ASP577
|
4.4
|
86.1
|
1.0
|
|
O1B
|
E:AGS902
|
4.5
|
68.7
|
1.0
|
|
CG
|
E:ASP577
|
4.5
|
81.1
|
1.0
|
|
HG23
|
E:THR525
|
4.5
|
0.6
|
1.0
|
|
O5'
|
E:AGS902
|
4.6
|
78.7
|
1.0
|
|
HA
|
E:THR525
|
4.6
|
0.9
|
1.0
|
|
S1G
|
E:AGS902
|
4.7
|
95.2
|
1.0
|
|
C5'
|
E:AGS902
|
4.7
|
89.8
|
1.0
|
|
HB2
|
E:LYS524
|
4.7
|
93.5
|
1.0
|
|
H5'2
|
E:AGS902
|
4.7
|
0.8
|
1.0
|
|
HH11
|
F:ARG635
|
4.8
|
0.5
|
1.0
|
|
HG22
|
E:THR525
|
4.9
|
0.6
|
1.0
|
|
CD
|
F:ARG635
|
5.0
|
87.0
|
1.0
|
|
Reference:
P.Hanzelmann,
H.Schindelin.
Characterization of An Additional Binding Surface on the P97 N-Terminal Domain Involved in Bipartite Cofactor Interactions. Structure V. 24 140 2016.
ISSN: ISSN 0969-2126
PubMed: 26712280
DOI: 10.1016/J.STR.2015.10.027
Page generated: Sun Sep 29 01:52:18 2024
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