Magnesium in PDB 5ej8: Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
Enzymatic activity of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
All present enzymatic activity of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min:
2.2.1.9;
Protein crystallography data
The structure of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min, PDB code: 5ej8
was solved by
H.G.Song,
C.Dong,
Y.Z.Chen,
Y.R.Sun,
Z.H.Guo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
27.65 /
1.34
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.660,
90.760,
169.340,
83.25,
76.03,
64.32
|
|
R / Rfree (%)
|
13.3 /
16.4
|
Other elements in 5ej8:
The structure of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
15;
Binding sites:
The binding sites of Magnesium atom in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
(pdb code 5ej8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the
Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min, PDB code: 5ej8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 15 in 5ej8
Go back to
Magnesium Binding Sites List in 5ej8
Magnesium binding site 1 out
of 15 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:6.7
occ:0.45
|
MN
|
A:MN602
|
0.3
|
11.1
|
0.6
|
|
OD1
|
A:ASP442
|
2.0
|
9.6
|
1.0
|
|
O
|
A:HOH901
|
2.0
|
9.7
|
1.0
|
|
O1A
|
A:TD6601
|
2.1
|
9.0
|
1.0
|
|
OD1
|
A:ASN469
|
2.1
|
9.2
|
1.0
|
|
O
|
A:GLY471
|
2.2
|
11.7
|
1.0
|
|
O3B
|
A:TD6601
|
2.3
|
9.1
|
1.0
|
|
H
|
A:ASP442
|
2.9
|
10.6
|
1.0
|
|
CG
|
A:ASP442
|
3.0
|
9.1
|
1.0
|
|
CG
|
A:ASN469
|
3.1
|
9.8
|
1.0
|
|
HD21
|
A:ASN469
|
3.2
|
12.1
|
1.0
|
|
PA
|
A:TD6601
|
3.3
|
8.8
|
1.0
|
|
H
|
A:ASN469
|
3.4
|
12.1
|
1.0
|
|
PB
|
A:TD6601
|
3.4
|
9.5
|
1.0
|
|
C
|
A:GLY471
|
3.4
|
11.5
|
1.0
|
|
O3A
|
A:TD6601
|
3.4
|
8.6
|
1.0
|
|
ND2
|
A:ASN469
|
3.5
|
10.1
|
1.0
|
|
OD2
|
A:ASP442
|
3.6
|
10.4
|
1.0
|
|
H
|
A:GLN473
|
3.6
|
11.1
|
1.0
|
|
H
|
A:GLY471
|
3.6
|
13.5
|
1.0
|
|
HA2
|
A:GLY472
|
3.6
|
10.4
|
1.0
|
|
H
|
A:LEU443
|
3.6
|
9.8
|
1.0
|
|
N
|
A:ASP442
|
3.7
|
8.8
|
1.0
|
|
HA3
|
A:GLY441
|
3.9
|
12.6
|
1.0
|
|
HG2
|
A:GLN473
|
4.1
|
12.9
|
1.0
|
|
N
|
A:GLY471
|
4.1
|
11.3
|
1.0
|
|
O
|
A:VAL467
|
4.1
|
10.3
|
1.0
|
|
HG
|
A:LEU443
|
4.2
|
12.0
|
1.0
|
|
CB
|
A:ASP442
|
4.2
|
8.0
|
1.0
|
|
N
|
A:ASN469
|
4.2
|
10.1
|
1.0
|
|
O
|
A:HOH796
|
4.2
|
12.0
|
1.0
|
|
O7
|
A:TD6601
|
4.2
|
9.3
|
1.0
|
|
N
|
A:GLY472
|
4.3
|
8.4
|
1.0
|
|
CA
|
A:GLY472
|
4.3
|
8.6
|
1.0
|
|
HD22
|
A:ASN469
|
4.4
|
12.1
|
1.0
|
|
HA2
|
A:GLY441
|
4.4
|
12.6
|
1.0
|
|
N
|
A:GLN473
|
4.4
|
9.3
|
1.0
|
|
O2A
|
A:TD6601
|
4.4
|
9.8
|
1.0
|
|
CA
|
A:GLY471
|
4.4
|
11.0
|
1.0
|
|
O2B
|
A:TD6601
|
4.4
|
10.5
|
1.0
|
|
H
|
A:ASN470
|
4.4
|
12.5
|
1.0
|
|
CB
|
A:ASN469
|
4.4
|
11.7
|
1.0
|
|
CA
|
A:ASP442
|
4.4
|
8.2
|
1.0
|
|
N
|
A:LEU443
|
4.4
|
8.1
|
1.0
|
|
HB3
|
A:ASP442
|
4.4
|
9.7
|
1.0
|
|
O1B
|
A:TD6601
|
4.5
|
10.5
|
1.0
|
|
CA
|
A:GLY441
|
4.5
|
10.5
|
1.0
|
|
HA
|
A:ASN468
|
4.5
|
12.0
|
1.0
|
|
C
|
A:GLY441
|
4.5
|
9.1
|
1.0
|
|
N
|
A:ASN470
|
4.6
|
10.4
|
1.0
|
|
C
|
A:ASN469
|
4.6
|
10.4
|
1.0
|
|
CA
|
A:ASN469
|
4.6
|
11.1
|
1.0
|
|
HB2
|
A:GLN473
|
4.7
|
12.7
|
1.0
|
|
HA2
|
A:GLY471
|
4.8
|
13.2
|
1.0
|
|
CG
|
A:GLN473
|
4.9
|
10.7
|
1.0
|
|
C
|
A:GLY472
|
4.9
|
8.8
|
1.0
|
|
HB3
|
A:ASN469
|
4.9
|
14.0
|
1.0
|
|
HB2
|
A:ASP442
|
5.0
|
9.7
|
1.0
|
|
C
|
A:ASP442
|
5.0
|
8.1
|
1.0
|
|
HG3
|
A:GLN473
|
5.0
|
12.9
|
1.0
|
|
Magnesium binding site 2 out
of 15 in 5ej8
Go back to
Magnesium Binding Sites List in 5ej8
Magnesium binding site 2 out
of 15 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:29.6
occ:1.00
|
O
|
A:HOH718
|
2.0
|
27.0
|
1.0
|
|
O
|
A:HOH914
|
2.1
|
24.4
|
1.0
|
|
O
|
A:HOH1137
|
2.1
|
27.0
|
1.0
|
|
O
|
A:HOH828
|
2.2
|
32.7
|
1.0
|
|
O
|
A:HOH1016
|
2.3
|
42.3
|
1.0
|
|
OD2
|
A:ASP311
|
2.3
|
15.3
|
0.6
|
|
HZ1
|
A:LYS70
|
2.5
|
65.1
|
1.0
|
|
NZ
|
A:LYS70
|
3.1
|
54.3
|
1.0
|
|
HZ2
|
A:LYS70
|
3.1
|
65.1
|
1.0
|
|
HZ3
|
A:LYS70
|
3.1
|
65.1
|
1.0
|
|
CG
|
A:ASP311
|
3.3
|
14.4
|
0.6
|
|
OD1
|
A:ASP311
|
3.5
|
16.1
|
0.6
|
|
O
|
A:HOH857
|
3.5
|
15.7
|
1.0
|
|
O
|
A:HOH727
|
3.7
|
23.9
|
1.0
|
|
O
|
A:HOH1253
|
3.9
|
37.0
|
1.0
|
|
O
|
A:HOH1242
|
3.9
|
21.7
|
1.0
|
|
O
|
A:HOH708
|
3.9
|
37.0
|
1.0
|
|
O
|
A:HOH707
|
4.0
|
31.9
|
1.0
|
|
O
|
A:HOH740
|
4.2
|
19.8
|
1.0
|
|
OE1
|
A:GLU233
|
4.4
|
12.6
|
1.0
|
|
HB2
|
A:ASP311
|
4.4
|
15.3
|
0.5
|
|
HB3
|
A:SER230
|
4.5
|
13.1
|
1.0
|
|
CE
|
A:LYS70
|
4.5
|
43.3
|
1.0
|
|
CB
|
A:ASP311
|
4.6
|
13.4
|
0.6
|
|
OE2
|
A:GLU233
|
4.7
|
18.5
|
1.0
|
|
HB3
|
A:ASP311
|
4.7
|
15.3
|
0.5
|
|
H
|
A:SER230
|
4.7
|
10.8
|
1.0
|
|
HE3
|
A:LYS70
|
4.7
|
52.0
|
1.0
|
|
HA
|
A:MET229
|
4.7
|
10.3
|
1.0
|
|
HB3
|
A:ASP311
|
4.8
|
16.0
|
0.6
|
|
HE2
|
A:LYS70
|
4.8
|
52.0
|
1.0
|
|
HB2
|
A:ASP311
|
4.9
|
16.0
|
0.6
|
|
CD
|
A:GLU233
|
5.0
|
14.1
|
1.0
|
|
Magnesium binding site 3 out
of 15 in 5ej8
Go back to
Magnesium Binding Sites List in 5ej8
Magnesium binding site 3 out
of 15 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:2.0
occ:0.36
|
MN
|
B:MN603
|
0.0
|
16.3
|
0.6
|
|
O
|
B:GLY471
|
2.1
|
10.9
|
1.0
|
|
OD1
|
B:ASP442
|
2.1
|
10.5
|
1.0
|
|
O1A
|
B:TD6602
|
2.1
|
11.0
|
1.0
|
|
OD1
|
B:ASN469
|
2.1
|
10.7
|
1.0
|
|
O1B
|
B:TD6602
|
2.1
|
9.7
|
1.0
|
|
O
|
B:HOH794
|
2.2
|
10.7
|
1.0
|
|
CG
|
B:ASN469
|
3.1
|
10.0
|
1.0
|
|
H
|
B:ASP442
|
3.1
|
12.4
|
1.0
|
|
HD21
|
B:ASN469
|
3.1
|
12.1
|
1.0
|
|
CG
|
B:ASP442
|
3.1
|
10.3
|
1.0
|
|
C
|
B:GLY471
|
3.3
|
10.0
|
1.0
|
|
PA
|
B:TD6602
|
3.3
|
9.5
|
1.0
|
|
PB
|
B:TD6602
|
3.4
|
9.8
|
1.0
|
|
H
|
B:GLN473
|
3.4
|
12.5
|
1.0
|
|
O3A
|
B:TD6602
|
3.4
|
11.4
|
1.0
|
|
H
|
B:ASN469
|
3.4
|
11.8
|
1.0
|
|
ND2
|
B:ASN469
|
3.5
|
10.1
|
1.0
|
|
HA2
|
B:GLY472
|
3.5
|
12.7
|
1.0
|
|
H
|
B:GLY471
|
3.5
|
12.3
|
1.0
|
|
OD2
|
B:ASP442
|
3.6
|
10.8
|
1.0
|
|
H
|
B:LEU443
|
3.7
|
10.7
|
1.0
|
|
N
|
B:ASP442
|
3.9
|
10.3
|
1.0
|
|
HG2
|
B:GLN473
|
3.9
|
15.1
|
1.0
|
|
N
|
B:GLY471
|
4.0
|
10.2
|
1.0
|
|
HA3
|
B:GLY441
|
4.0
|
12.2
|
1.0
|
|
HG
|
B:LEU443
|
4.1
|
13.9
|
1.0
|
|
N
|
B:GLY472
|
4.1
|
10.1
|
1.0
|
|
O7
|
B:TD6602
|
4.1
|
9.9
|
1.0
|
|
N
|
B:GLN473
|
4.2
|
10.4
|
1.0
|
|
CA
|
B:GLY472
|
4.2
|
10.6
|
1.0
|
|
CA
|
B:GLY471
|
4.2
|
10.3
|
1.0
|
|
N
|
B:ASN469
|
4.2
|
9.8
|
1.0
|
|
O
|
B:HOH802
|
4.3
|
12.0
|
1.0
|
|
O
|
B:VAL467
|
4.3
|
10.9
|
1.0
|
|
HD22
|
B:ASN469
|
4.3
|
12.1
|
1.0
|
|
CB
|
B:ASP442
|
4.3
|
10.7
|
1.0
|
|
O3B
|
B:TD6602
|
4.3
|
10.1
|
1.0
|
|
O2B
|
B:TD6602
|
4.4
|
10.3
|
1.0
|
|
CB
|
B:ASN469
|
4.4
|
10.4
|
1.0
|
|
O2A
|
B:TD6602
|
4.4
|
12.5
|
1.0
|
|
H
|
B:ASN470
|
4.5
|
13.1
|
1.0
|
|
N
|
B:LEU443
|
4.5
|
8.9
|
1.0
|
|
C
|
B:ASN469
|
4.6
|
11.1
|
1.0
|
|
HA2
|
B:GLY441
|
4.6
|
12.2
|
1.0
|
|
N
|
B:ASN470
|
4.6
|
10.9
|
1.0
|
|
CA
|
B:ASP442
|
4.6
|
10.8
|
1.0
|
|
HB3
|
B:ASP442
|
4.6
|
12.8
|
1.0
|
|
CA
|
B:ASN469
|
4.6
|
10.8
|
1.0
|
|
HB2
|
B:GLN473
|
4.6
|
13.4
|
1.0
|
|
CA
|
B:GLY441
|
4.6
|
10.2
|
1.0
|
|
HA
|
B:ASN468
|
4.7
|
13.0
|
1.0
|
|
C
|
B:GLY441
|
4.7
|
8.8
|
1.0
|
|
HA2
|
B:GLY471
|
4.7
|
12.4
|
1.0
|
|
C
|
B:GLY472
|
4.7
|
10.6
|
1.0
|
|
CG
|
B:GLN473
|
4.8
|
12.6
|
1.0
|
|
HB3
|
B:ASN469
|
4.9
|
12.5
|
1.0
|
|
HG3
|
B:GLN473
|
5.0
|
15.1
|
1.0
|
|
HB2
|
B:ASN469
|
5.0
|
12.5
|
1.0
|
|
H
|
B:GLY472
|
5.0
|
12.1
|
1.0
|
|
C
|
B:ASN470
|
5.0
|
10.8
|
1.0
|
|
HA3
|
B:GLY471
|
5.0
|
12.4
|
1.0
|
|
HA3
|
B:GLY472
|
5.0
|
12.7
|
1.0
|
|
Magnesium binding site 4 out
of 15 in 5ej8
Go back to
Magnesium Binding Sites List in 5ej8
Magnesium binding site 4 out
of 15 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg607
b:26.2
occ:1.00
|
O
|
B:HOH875
|
1.9
|
33.3
|
1.0
|
|
O
|
B:HOH953
|
1.9
|
31.0
|
1.0
|
|
O
|
B:HOH895
|
2.0
|
24.6
|
1.0
|
|
O
|
B:HOH1130
|
2.0
|
27.4
|
1.0
|
|
O
|
B:HOH1322
|
2.0
|
33.1
|
1.0
|
|
OD2
|
B:ASP311
|
2.3
|
17.7
|
0.6
|
|
CG
|
B:ASP311
|
3.3
|
16.4
|
0.6
|
|
O
|
B:HOH843
|
3.6
|
16.4
|
1.0
|
|
OD1
|
B:ASP311
|
3.6
|
16.4
|
0.6
|
|
O
|
B:HOH713
|
3.8
|
26.9
|
1.0
|
|
O
|
B:HOH1356
|
3.9
|
47.4
|
1.0
|
|
O
|
B:HOH1252
|
4.0
|
22.8
|
1.0
|
|
O
|
B:HOH755
|
4.2
|
19.5
|
1.0
|
|
O
|
B:HOH741
|
4.2
|
34.3
|
1.0
|
|
OE1
|
B:GLU233
|
4.3
|
12.7
|
1.0
|
|
HB2
|
B:ASP311
|
4.3
|
17.8
|
0.4
|
|
HB3
|
B:SER230
|
4.5
|
13.7
|
1.0
|
|
OE2
|
B:GLU233
|
4.5
|
16.7
|
1.0
|
|
O
|
B:HOH1141
|
4.5
|
26.8
|
1.0
|
|
HB3
|
B:ASP311
|
4.6
|
17.8
|
0.4
|
|
CB
|
B:ASP311
|
4.6
|
15.8
|
0.6
|
|
H
|
B:SER230
|
4.7
|
11.9
|
1.0
|
|
HA
|
B:MET229
|
4.7
|
12.3
|
1.0
|
|
HB3
|
B:ASP311
|
4.7
|
19.0
|
0.6
|
|
CD
|
B:GLU233
|
4.9
|
13.7
|
1.0
|
|
CB
|
B:ASP311
|
4.9
|
14.8
|
0.4
|
|
HB2
|
B:ASP311
|
4.9
|
19.0
|
0.6
|
|
HD22
|
B:ASN329
|
5.0
|
23.1
|
1.0
|
|
Magnesium binding site 5 out
of 15 in 5ej8
Go back to
Magnesium Binding Sites List in 5ej8
Magnesium binding site 5 out
of 15 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg604
b:5.2
occ:0.59
|
MN
|
C:MN603
|
0.1
|
15.7
|
0.4
|
|
OD1
|
C:ASN469
|
2.1
|
11.8
|
1.0
|
|
O1B
|
C:TD6602
|
2.1
|
10.8
|
1.0
|
|
O
|
C:GLY471
|
2.1
|
11.6
|
1.0
|
|
O1A
|
C:TD6602
|
2.1
|
10.3
|
1.0
|
|
OD1
|
C:ASP442
|
2.1
|
11.2
|
1.0
|
|
O
|
C:HOH859
|
2.1
|
11.8
|
1.0
|
|
CG
|
C:ASN469
|
3.0
|
11.9
|
1.0
|
|
HD21
|
C:ASN469
|
3.1
|
14.7
|
1.0
|
|
H
|
C:ASP442
|
3.1
|
12.5
|
1.0
|
|
CG
|
C:ASP442
|
3.2
|
11.3
|
1.0
|
|
C
|
C:GLY471
|
3.3
|
11.8
|
1.0
|
|
H
|
C:GLN473
|
3.3
|
12.5
|
1.0
|
|
PB
|
C:TD6602
|
3.3
|
10.5
|
1.0
|
|
PA
|
C:TD6602
|
3.3
|
9.6
|
1.0
|
|
ND2
|
C:ASN469
|
3.4
|
12.2
|
1.0
|
|
O3A
|
C:TD6602
|
3.4
|
10.3
|
1.0
|
|
H
|
C:ASN469
|
3.4
|
15.3
|
1.0
|
|
HA2
|
C:GLY472
|
3.5
|
13.9
|
1.0
|
|
H
|
C:GLY471
|
3.5
|
13.4
|
1.0
|
|
OD2
|
C:ASP442
|
3.7
|
12.2
|
1.0
|
|
H
|
C:LEU443
|
3.8
|
11.7
|
1.0
|
|
HG2
|
C:GLN473
|
3.8
|
16.4
|
1.0
|
|
N
|
C:ASP442
|
3.9
|
10.4
|
1.0
|
|
HA3
|
C:GLY441
|
4.0
|
12.3
|
1.0
|
|
N
|
C:GLY471
|
4.0
|
11.2
|
1.0
|
|
N
|
C:GLN473
|
4.1
|
10.4
|
1.0
|
|
N
|
C:GLY472
|
4.2
|
11.2
|
1.0
|
|
HG
|
C:LEU443
|
4.2
|
13.8
|
1.0
|
|
O7
|
C:TD6602
|
4.2
|
10.4
|
1.0
|
|
CA
|
C:GLY472
|
4.2
|
11.6
|
1.0
|
|
O
|
C:HOH800
|
4.2
|
13.9
|
1.0
|
|
N
|
C:ASN469
|
4.2
|
12.7
|
1.0
|
|
CA
|
C:GLY471
|
4.3
|
10.9
|
1.0
|
|
HD22
|
C:ASN469
|
4.3
|
14.7
|
1.0
|
|
O3B
|
C:TD6602
|
4.3
|
11.0
|
1.0
|
|
O2B
|
C:TD6602
|
4.3
|
11.4
|
1.0
|
|
O
|
C:VAL467
|
4.3
|
12.0
|
1.0
|
|
CB
|
C:ASN469
|
4.3
|
12.5
|
1.0
|
|
CB
|
C:ASP442
|
4.4
|
10.9
|
1.0
|
|
O2A
|
C:TD6602
|
4.5
|
10.1
|
1.0
|
|
HB2
|
C:GLN473
|
4.5
|
13.6
|
1.0
|
|
H
|
C:ASN470
|
4.5
|
14.1
|
1.0
|
|
HA2
|
C:GLY441
|
4.5
|
12.3
|
1.0
|
|
C
|
C:ASN469
|
4.5
|
11.9
|
1.0
|
|
N
|
C:ASN470
|
4.6
|
11.8
|
1.0
|
|
N
|
C:LEU443
|
4.6
|
9.7
|
1.0
|
|
CA
|
C:ASN469
|
4.6
|
13.2
|
1.0
|
|
CA
|
C:ASP442
|
4.6
|
10.7
|
1.0
|
|
HB3
|
C:ASP442
|
4.6
|
13.1
|
1.0
|
|
CG
|
C:GLN473
|
4.6
|
13.7
|
1.0
|
|
CA
|
C:GLY441
|
4.6
|
10.3
|
1.0
|
|
C
|
C:GLY472
|
4.7
|
11.6
|
1.0
|
|
C
|
C:GLY441
|
4.7
|
9.8
|
1.0
|
|
HA
|
C:ASN468
|
4.7
|
16.2
|
1.0
|
|
HA2
|
C:GLY471
|
4.7
|
13.1
|
1.0
|
|
HG3
|
C:GLN473
|
4.8
|
16.4
|
1.0
|
|
HB3
|
C:ASN469
|
4.9
|
15.0
|
1.0
|
|
HB2
|
C:ASN469
|
4.9
|
15.0
|
1.0
|
|
CB
|
C:GLN473
|
4.9
|
11.4
|
1.0
|
|
C
|
C:ASN470
|
5.0
|
12.1
|
1.0
|
|
H
|
C:GLY472
|
5.0
|
13.5
|
1.0
|
|
HA3
|
C:GLY472
|
5.0
|
13.9
|
1.0
|
|
HA3
|
C:GLY471
|
5.0
|
13.1
|
1.0
|
|
O
|
C:ASN469
|
5.0
|
13.8
|
1.0
|
|
Magnesium binding site 6 out
of 15 in 5ej8
Go back to
Magnesium Binding Sites List in 5ej8
Magnesium binding site 6 out
of 15 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg608
b:16.0
occ:1.00
|
HO2
|
C:EDO607
|
1.4
|
23.3
|
1.0
|
|
O
|
C:HOH790
|
2.0
|
15.7
|
1.0
|
|
O2
|
C:EDO607
|
2.0
|
19.4
|
1.0
|
|
OD2
|
C:ASP311
|
2.1
|
15.2
|
1.0
|
|
O
|
C:HOH1104
|
2.1
|
19.5
|
1.0
|
|
O
|
C:HOH1087
|
2.2
|
19.4
|
1.0
|
|
CG
|
C:ASP311
|
3.1
|
14.5
|
1.0
|
|
C2
|
C:EDO607
|
3.2
|
20.9
|
1.0
|
|
H21
|
C:EDO607
|
3.2
|
25.1
|
1.0
|
|
OD1
|
C:ASP311
|
3.4
|
14.7
|
1.0
|
|
H22
|
C:EDO607
|
3.7
|
25.1
|
1.0
|
|
O
|
C:HOH880
|
3.7
|
15.2
|
1.0
|
|
O
|
C:HOH935
|
4.0
|
20.9
|
1.0
|
|
O
|
C:HOH761
|
4.0
|
15.2
|
1.0
|
|
O
|
C:HOH889
|
4.0
|
23.2
|
1.0
|
|
O
|
C:HOH1387
|
4.1
|
45.8
|
1.0
|
|
O
|
C:HOH1379
|
4.1
|
32.0
|
1.0
|
|
OE1
|
C:GLU233
|
4.2
|
12.6
|
1.0
|
|
O1
|
C:EDO607
|
4.3
|
16.7
|
1.0
|
|
C1
|
C:EDO607
|
4.3
|
19.8
|
1.0
|
|
OE2
|
C:GLU233
|
4.4
|
14.7
|
1.0
|
|
HB3
|
C:SER230
|
4.4
|
14.3
|
1.0
|
|
CB
|
C:ASP311
|
4.5
|
12.3
|
1.0
|
|
HA
|
C:MET229
|
4.6
|
11.2
|
1.0
|
|
H
|
C:SER230
|
4.6
|
11.6
|
1.0
|
|
HB3
|
C:ASP311
|
4.6
|
14.7
|
1.0
|
|
CD
|
C:GLU233
|
4.7
|
12.3
|
1.0
|
|
HB2
|
C:ASP311
|
4.8
|
14.7
|
1.0
|
|
H11
|
C:EDO607
|
4.8
|
23.7
|
1.0
|
|
O
|
C:HOH1221
|
4.9
|
49.5
|
1.0
|
|
Magnesium binding site 7 out
of 15 in 5ej8
Go back to
Magnesium Binding Sites List in 5ej8
Magnesium binding site 7 out
of 15 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg604
b:7.4
occ:0.53
|
MN
|
D:MN603
|
0.1
|
16.1
|
0.5
|
|
O
|
D:GLY471
|
2.0
|
12.0
|
1.0
|
|
OD1
|
D:ASN469
|
2.1
|
12.7
|
1.0
|
|
O1A
|
D:TD6602
|
2.1
|
10.9
|
1.0
|
|
OD1
|
D:ASP442
|
2.1
|
13.2
|
1.0
|
|
O1B
|
D:TD6602
|
2.2
|
12.4
|
1.0
|
|
O
|
D:HOH870
|
2.2
|
12.3
|
1.0
|
|
CG
|
D:ASN469
|
3.1
|
12.8
|
1.0
|
|
HD21
|
D:ASN469
|
3.1
|
15.3
|
1.0
|
|
H
|
D:ASP442
|
3.1
|
14.2
|
1.0
|
|
CG
|
D:ASP442
|
3.1
|
13.5
|
1.0
|
|
C
|
D:GLY471
|
3.2
|
12.1
|
1.0
|
|
PA
|
D:TD6602
|
3.3
|
11.8
|
1.0
|
|
H
|
D:GLN473
|
3.3
|
15.1
|
1.0
|
|
PB
|
D:TD6602
|
3.4
|
12.7
|
1.0
|
|
O3A
|
D:TD6602
|
3.4
|
12.4
|
1.0
|
|
H
|
D:GLY471
|
3.5
|
16.3
|
1.0
|
|
ND2
|
D:ASN469
|
3.5
|
12.8
|
1.0
|
|
H
|
D:ASN469
|
3.5
|
16.7
|
1.0
|
|
HA2
|
D:GLY472
|
3.5
|
14.9
|
1.0
|
|
OD2
|
D:ASP442
|
3.6
|
14.1
|
1.0
|
|
H
|
D:LEU443
|
3.7
|
14.9
|
1.0
|
|
HG2
|
D:GLN473
|
3.8
|
16.8
|
1.0
|
|
N
|
D:ASP442
|
3.9
|
11.8
|
1.0
|
|
N
|
D:GLY471
|
4.0
|
13.6
|
1.0
|
|
HG
|
D:LEU443
|
4.1
|
15.5
|
1.0
|
|
HA3
|
D:GLY441
|
4.1
|
14.8
|
1.0
|
|
N
|
D:GLY472
|
4.1
|
12.8
|
1.0
|
|
N
|
D:GLN473
|
4.1
|
12.6
|
1.0
|
|
O7
|
D:TD6602
|
4.2
|
11.2
|
1.0
|
|
CA
|
D:GLY472
|
4.2
|
12.4
|
1.0
|
|
CA
|
D:GLY471
|
4.2
|
12.9
|
1.0
|
|
N
|
D:ASN469
|
4.3
|
13.9
|
1.0
|
|
O
|
D:HOH825
|
4.3
|
14.9
|
1.0
|
|
HD22
|
D:ASN469
|
4.3
|
15.3
|
1.0
|
|
O3B
|
D:TD6602
|
4.3
|
13.2
|
1.0
|
|
CB
|
D:ASP442
|
4.4
|
12.2
|
1.0
|
|
O
|
D:VAL467
|
4.4
|
13.2
|
1.0
|
|
O2A
|
D:TD6602
|
4.4
|
11.1
|
1.0
|
|
O2B
|
D:TD6602
|
4.4
|
14.0
|
1.0
|
|
CB
|
D:ASN469
|
4.4
|
13.8
|
1.0
|
|
H
|
D:ASN470
|
4.5
|
16.1
|
1.0
|
|
HB2
|
D:GLN473
|
4.5
|
16.5
|
1.0
|
|
C
|
D:ASN469
|
4.5
|
12.6
|
1.0
|
|
N
|
D:LEU443
|
4.5
|
12.5
|
1.0
|
|
N
|
D:ASN470
|
4.6
|
13.4
|
1.0
|
|
HA2
|
D:GLY441
|
4.6
|
14.8
|
1.0
|
|
CA
|
D:ASN469
|
4.6
|
13.7
|
1.0
|
|
CA
|
D:ASP442
|
4.6
|
11.6
|
1.0
|
|
HB3
|
D:ASP442
|
4.6
|
14.6
|
1.0
|
|
CG
|
D:GLN473
|
4.7
|
14.0
|
1.0
|
|
HA2
|
D:GLY471
|
4.7
|
15.5
|
1.0
|
|
CA
|
D:GLY441
|
4.7
|
12.4
|
1.0
|
|
C
|
D:GLY472
|
4.7
|
12.1
|
1.0
|
|
HA
|
D:ASN468
|
4.7
|
16.5
|
1.0
|
|
C
|
D:GLY441
|
4.7
|
11.9
|
1.0
|
|
HG3
|
D:GLN473
|
4.8
|
16.8
|
1.0
|
|
HB3
|
D:ASN469
|
4.9
|
16.5
|
1.0
|
|
C
|
D:ASN470
|
4.9
|
15.0
|
1.0
|
|
HB2
|
D:ASN469
|
4.9
|
16.5
|
1.0
|
|
H
|
D:GLY472
|
4.9
|
15.3
|
1.0
|
|
HA3
|
D:GLY471
|
4.9
|
15.5
|
1.0
|
|
CB
|
D:GLN473
|
5.0
|
13.7
|
1.0
|
|
O
|
D:ASN469
|
5.0
|
14.1
|
1.0
|
|
HA3
|
D:GLY472
|
5.0
|
14.9
|
1.0
|
|
Magnesium binding site 8 out
of 15 in 5ej8
Go back to
Magnesium Binding Sites List in 5ej8
Magnesium binding site 8 out
of 15 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg608
b:23.5
occ:1.00
|
O
|
D:HOH727
|
1.9
|
26.9
|
1.0
|
|
O
|
D:HOH846
|
2.0
|
23.8
|
1.0
|
|
O
|
D:HOH981
|
2.0
|
28.7
|
1.0
|
|
O
|
D:HOH989
|
2.1
|
25.8
|
1.0
|
|
O
|
D:HOH1215
|
2.1
|
27.9
|
1.0
|
|
OD2
|
D:ASP311
|
2.2
|
23.0
|
1.0
|
|
CG
|
D:ASP311
|
3.2
|
20.2
|
1.0
|
|
OD1
|
D:ASP311
|
3.5
|
20.6
|
1.0
|
|
O
|
D:HOH783
|
3.6
|
18.5
|
1.0
|
|
O
|
D:HOH1264
|
3.8
|
51.1
|
1.0
|
|
O
|
D:HOH1145
|
3.9
|
22.6
|
1.0
|
|
O
|
D:HOH919
|
4.0
|
25.8
|
1.0
|
|
O
|
D:HOH773
|
4.0
|
18.5
|
1.0
|
|
O
|
D:HOH1273
|
4.2
|
38.5
|
1.0
|
|
OE1
|
D:GLU233
|
4.2
|
17.0
|
1.0
|
|
HB3
|
D:SER230
|
4.4
|
17.4
|
1.0
|
|
OE2
|
D:GLU233
|
4.4
|
20.2
|
1.0
|
|
CB
|
D:ASP311
|
4.5
|
17.1
|
1.0
|
|
H
|
D:SER230
|
4.6
|
15.4
|
1.0
|
|
HB3
|
D:ASP311
|
4.6
|
20.6
|
1.0
|
|
HA
|
D:MET229
|
4.6
|
14.5
|
1.0
|
|
CD
|
D:GLU233
|
4.8
|
19.1
|
1.0
|
|
HB2
|
D:ASP311
|
4.8
|
20.6
|
1.0
|
|
Magnesium binding site 9 out
of 15 in 5ej8
Go back to
Magnesium Binding Sites List in 5ej8
Magnesium binding site 9 out
of 15 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg603
b:8.8
occ:0.53
|
MN
|
E:MN602
|
0.2
|
11.6
|
0.5
|
|
O1A
|
E:TD6601
|
2.1
|
8.1
|
1.0
|
|
OD1
|
E:ASP442
|
2.1
|
10.7
|
1.0
|
|
OD1
|
E:ASN469
|
2.1
|
10.1
|
1.0
|
|
O
|
E:HOH783
|
2.1
|
9.6
|
1.0
|
|
O1B
|
E:TD6601
|
2.2
|
9.4
|
1.0
|
|
O
|
E:GLY471
|
2.2
|
10.9
|
1.0
|
|
H
|
E:ASP442
|
3.0
|
10.9
|
1.0
|
|
CG
|
E:ASN469
|
3.1
|
9.1
|
1.0
|
|
HD21
|
E:ASN469
|
3.1
|
13.1
|
1.0
|
|
CG
|
E:ASP442
|
3.1
|
9.5
|
1.0
|
|
PA
|
E:TD6601
|
3.3
|
8.8
|
1.0
|
|
C
|
E:GLY471
|
3.4
|
10.5
|
1.0
|
|
PB
|
E:TD6601
|
3.4
|
9.8
|
1.0
|
|
O3A
|
E:TD6601
|
3.4
|
9.5
|
1.0
|
|
H
|
E:ASN469
|
3.4
|
13.4
|
1.0
|
|
ND2
|
E:ASN469
|
3.5
|
10.9
|
1.0
|
|
H
|
E:GLN473
|
3.5
|
12.8
|
1.0
|
|
HA2
|
E:GLY472
|
3.5
|
11.9
|
1.0
|
|
H
|
E:GLY471
|
3.6
|
12.7
|
1.0
|
|
OD2
|
E:ASP442
|
3.6
|
11.8
|
1.0
|
|
H
|
E:LEU443
|
3.7
|
11.9
|
1.0
|
|
N
|
E:ASP442
|
3.8
|
9.1
|
1.0
|
|
HA3
|
E:GLY441
|
4.0
|
12.2
|
1.0
|
|
HG2
|
E:GLN473
|
4.0
|
15.5
|
1.0
|
|
N
|
E:GLY471
|
4.1
|
10.6
|
1.0
|
|
O7
|
E:TD6601
|
4.2
|
8.2
|
1.0
|
|
HG
|
E:LEU443
|
4.2
|
11.5
|
1.0
|
|
O
|
E:HOH876
|
4.2
|
12.9
|
1.0
|
|
O
|
E:VAL467
|
4.2
|
10.9
|
1.0
|
|
N
|
E:GLY472
|
4.2
|
9.3
|
1.0
|
|
N
|
E:ASN469
|
4.2
|
11.2
|
1.0
|
|
CA
|
E:GLY472
|
4.3
|
9.9
|
1.0
|
|
N
|
E:GLN473
|
4.3
|
10.7
|
1.0
|
|
CB
|
E:ASP442
|
4.3
|
10.7
|
1.0
|
|
HD22
|
E:ASN469
|
4.3
|
13.1
|
1.0
|
|
CA
|
E:GLY471
|
4.3
|
10.3
|
1.0
|
|
O3B
|
E:TD6601
|
4.3
|
9.8
|
1.0
|
|
O2B
|
E:TD6601
|
4.4
|
11.2
|
1.0
|
|
O2A
|
E:TD6601
|
4.4
|
9.4
|
1.0
|
|
CB
|
E:ASN469
|
4.4
|
10.3
|
1.0
|
|
HA2
|
E:GLY441
|
4.4
|
12.2
|
1.0
|
|
N
|
E:LEU443
|
4.5
|
9.9
|
1.0
|
|
H
|
E:ASN470
|
4.5
|
13.1
|
1.0
|
|
CA
|
E:ASP442
|
4.5
|
9.7
|
1.0
|
|
CA
|
E:GLY441
|
4.5
|
10.2
|
1.0
|
|
HB3
|
E:ASP442
|
4.5
|
12.9
|
1.0
|
|
C
|
E:ASN469
|
4.6
|
9.8
|
1.0
|
|
HB2
|
E:GLN473
|
4.6
|
13.1
|
1.0
|
|
N
|
E:ASN470
|
4.6
|
10.9
|
1.0
|
|
CA
|
E:ASN469
|
4.6
|
10.6
|
1.0
|
|
C
|
E:GLY441
|
4.6
|
9.9
|
1.0
|
|
HA
|
E:ASN468
|
4.6
|
13.0
|
1.0
|
|
HA2
|
E:GLY471
|
4.8
|
12.4
|
1.0
|
|
CG
|
E:GLN473
|
4.8
|
12.9
|
1.0
|
|
C
|
E:GLY472
|
4.8
|
9.3
|
1.0
|
|
HB3
|
E:ASN469
|
4.9
|
12.4
|
1.0
|
|
HG3
|
E:GLN473
|
4.9
|
15.5
|
1.0
|
|
HB2
|
E:ASN469
|
5.0
|
12.4
|
1.0
|
|
Magnesium binding site 10 out
of 15 in 5ej8
Go back to
Magnesium Binding Sites List in 5ej8
Magnesium binding site 10 out
of 15 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg607
b:29.9
occ:1.00
|
O
|
E:HOH925
|
2.0
|
25.6
|
1.0
|
|
O
|
E:HOH933
|
2.0
|
35.3
|
1.0
|
|
O
|
E:HOH742
|
2.0
|
35.7
|
1.0
|
|
O
|
E:HOH851
|
2.1
|
33.4
|
1.0
|
|
O
|
E:HOH716
|
2.1
|
30.9
|
1.0
|
|
OD2
|
E:ASP311
|
2.2
|
52.3
|
1.0
|
|
CG
|
E:ASP311
|
3.3
|
40.6
|
1.0
|
|
O
|
E:HOH862
|
3.5
|
16.8
|
1.0
|
|
HZ3
|
E:LYS70
|
3.6
|
58.8
|
1.0
|
|
OD1
|
E:ASP311
|
3.6
|
39.7
|
1.0
|
|
O
|
E:HOH847
|
3.8
|
26.2
|
1.0
|
|
O
|
E:HOH709
|
3.9
|
33.7
|
1.0
|
|
O
|
E:HOH702
|
3.9
|
33.8
|
1.0
|
|
O
|
E:HOH1245
|
4.0
|
20.3
|
1.0
|
|
O
|
E:HOH872
|
4.0
|
23.5
|
1.0
|
|
O2
|
E:FMT608
|
4.0
|
35.3
|
1.0
|
|
OE2
|
E:GLU233
|
4.3
|
12.2
|
1.0
|
|
HZ2
|
E:LYS70
|
4.4
|
58.8
|
1.0
|
|
NZ
|
E:LYS70
|
4.4
|
49.0
|
1.0
|
|
O
|
E:HOH1148
|
4.4
|
22.7
|
1.0
|
|
HB3
|
E:SER230
|
4.5
|
14.2
|
1.0
|
|
OE1
|
E:GLU233
|
4.5
|
17.9
|
1.0
|
|
CB
|
E:ASP311
|
4.6
|
27.9
|
1.0
|
|
HD2
|
E:LYS70
|
4.6
|
44.4
|
1.0
|
|
HA
|
E:MET229
|
4.6
|
11.3
|
1.0
|
|
H
|
E:SER230
|
4.6
|
12.8
|
1.0
|
|
HB3
|
E:ASP311
|
4.7
|
33.5
|
1.0
|
|
HZ1
|
E:LYS70
|
4.7
|
58.8
|
1.0
|
|
CD
|
E:GLU233
|
4.9
|
13.7
|
1.0
|
|
HB2
|
E:ASP311
|
4.9
|
33.5
|
1.0
|
|
HD22
|
E:ASN329
|
5.0
|
24.6
|
1.0
|
|
Reference:
H.G.Song,
C.Dong,
M.M.Qin,
Y.Z.Chen,
Y.R.Sun,
J.J.Liu,
W.Chan,
Z.H.Guo.
A Thiamine-Dependent Enzyme Utilizes An Active Tetrahedral Intermediate in Vitamin K Biosynthesis J.Am.Chem.Soc. V. 138 7244 2016.
ISSN: ESSN 1520-5126
PubMed: 27213829
DOI: 10.1021/JACS.6B03437
Page generated: Sun Sep 29 03:50:39 2024
|
