Manganese 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:
Manganese Binding Sites:
The binding sites of Manganese 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 Manganese atom.
In total 8 binding sites of Manganese where determined in the
Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min, PDB code: 5ej8:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 5ej8
Go back to
Manganese Binding Sites List in 5ej8
Manganese binding site 1 out
of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn 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:Mn602
b:11.1
occ:0.55
|
MG
|
A:MG603
|
0.3
|
6.7
|
0.5
|
|
O
|
A:GLY471
|
2.0
|
11.7
|
1.0
|
|
O3B
|
A:TD6601
|
2.1
|
9.1
|
1.0
|
|
OD1
|
A:ASN469
|
2.1
|
9.2
|
1.0
|
|
O1A
|
A:TD6601
|
2.1
|
9.0
|
1.0
|
|
OD1
|
A:ASP442
|
2.2
|
9.6
|
1.0
|
|
O
|
A:HOH901
|
2.2
|
9.7
|
1.0
|
|
HD21
|
A:ASN469
|
3.1
|
12.1
|
1.0
|
|
CG
|
A:ASN469
|
3.1
|
9.8
|
1.0
|
|
H
|
A:ASP442
|
3.2
|
10.6
|
1.0
|
|
C
|
A:GLY471
|
3.2
|
11.5
|
1.0
|
|
CG
|
A:ASP442
|
3.2
|
9.1
|
1.0
|
|
H
|
A:GLN473
|
3.3
|
11.1
|
1.0
|
|
PB
|
A:TD6601
|
3.3
|
9.5
|
1.0
|
|
PA
|
A:TD6601
|
3.3
|
8.8
|
1.0
|
|
HA2
|
A:GLY472
|
3.4
|
10.4
|
1.0
|
|
O3A
|
A:TD6601
|
3.4
|
8.6
|
1.0
|
|
ND2
|
A:ASN469
|
3.4
|
10.1
|
1.0
|
|
H
|
A:ASN469
|
3.5
|
12.1
|
1.0
|
|
H
|
A:GLY471
|
3.5
|
13.5
|
1.0
|
|
OD2
|
A:ASP442
|
3.7
|
10.4
|
1.0
|
|
H
|
A:LEU443
|
3.8
|
9.8
|
1.0
|
|
HG2
|
A:GLN473
|
3.8
|
12.9
|
1.0
|
|
N
|
A:ASP442
|
4.0
|
8.8
|
1.0
|
|
N
|
A:GLY471
|
4.0
|
11.3
|
1.0
|
|
N
|
A:GLN473
|
4.1
|
9.3
|
1.0
|
|
N
|
A:GLY472
|
4.1
|
8.4
|
1.0
|
|
CA
|
A:GLY472
|
4.1
|
8.6
|
1.0
|
|
HA3
|
A:GLY441
|
4.1
|
12.6
|
1.0
|
|
O7
|
A:TD6601
|
4.1
|
9.3
|
1.0
|
|
HG
|
A:LEU443
|
4.2
|
12.0
|
1.0
|
|
CA
|
A:GLY471
|
4.2
|
11.0
|
1.0
|
|
O
|
A:HOH796
|
4.2
|
12.0
|
1.0
|
|
O1B
|
A:TD6601
|
4.3
|
10.5
|
1.0
|
|
HD22
|
A:ASN469
|
4.3
|
12.1
|
1.0
|
|
O2B
|
A:TD6601
|
4.3
|
10.5
|
1.0
|
|
N
|
A:ASN469
|
4.3
|
10.1
|
1.0
|
|
CB
|
A:ASN469
|
4.4
|
11.7
|
1.0
|
|
O
|
A:VAL467
|
4.4
|
10.3
|
1.0
|
|
CB
|
A:ASP442
|
4.4
|
8.0
|
1.0
|
|
O2A
|
A:TD6601
|
4.5
|
9.8
|
1.0
|
|
HB2
|
A:GLN473
|
4.5
|
12.7
|
1.0
|
|
H
|
A:ASN470
|
4.5
|
12.5
|
1.0
|
|
C
|
A:ASN469
|
4.6
|
10.4
|
1.0
|
|
N
|
A:ASN470
|
4.6
|
10.4
|
1.0
|
|
N
|
A:LEU443
|
4.6
|
8.1
|
1.0
|
|
HA2
|
A:GLY441
|
4.6
|
12.6
|
1.0
|
|
CG
|
A:GLN473
|
4.6
|
10.7
|
1.0
|
|
C
|
A:GLY472
|
4.6
|
8.8
|
1.0
|
|
CA
|
A:ASN469
|
4.6
|
11.1
|
1.0
|
|
CA
|
A:ASP442
|
4.7
|
8.2
|
1.0
|
|
HB3
|
A:ASP442
|
4.7
|
9.7
|
1.0
|
|
HA2
|
A:GLY471
|
4.7
|
13.2
|
1.0
|
|
CA
|
A:GLY441
|
4.7
|
10.5
|
1.0
|
|
HA
|
A:ASN468
|
4.8
|
12.0
|
1.0
|
|
HG3
|
A:GLN473
|
4.8
|
12.9
|
1.0
|
|
C
|
A:GLY441
|
4.8
|
9.1
|
1.0
|
|
HA3
|
A:GLY472
|
4.9
|
10.4
|
1.0
|
|
H
|
A:GLY472
|
4.9
|
10.1
|
1.0
|
|
HB2
|
A:ASN469
|
4.9
|
14.0
|
1.0
|
|
HB3
|
A:ASN469
|
4.9
|
14.0
|
1.0
|
|
HA3
|
A:GLY471
|
4.9
|
13.2
|
1.0
|
|
CB
|
A:GLN473
|
4.9
|
10.5
|
1.0
|
|
C
|
A:ASN470
|
5.0
|
10.6
|
1.0
|
|
O
|
A:ASN469
|
5.0
|
10.8
|
1.0
|
|
Manganese binding site 2 out
of 8 in 5ej8
Go back to
Manganese Binding Sites List in 5ej8
Manganese binding site 2 out
of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn 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
|
B:Mn603
b:16.3
occ:0.64
|
MG
|
B:MG604
|
0.0
|
2.0
|
0.4
|
|
O
|
B:GLY471
|
2.0
|
10.9
|
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
|
|
OD1
|
B:ASP442
|
2.1
|
10.5
|
1.0
|
|
O
|
B:HOH794
|
2.2
|
10.7
|
1.0
|
|
CG
|
B:ASN469
|
3.1
|
10.0
|
1.0
|
|
HD21
|
B:ASN469
|
3.1
|
12.1
|
1.0
|
|
H
|
B:ASP442
|
3.2
|
12.4
|
1.0
|
|
CG
|
B:ASP442
|
3.2
|
10.3
|
1.0
|
|
C
|
B:GLY471
|
3.2
|
10.0
|
1.0
|
|
PA
|
B:TD6602
|
3.3
|
9.5
|
1.0
|
|
PB
|
B:TD6602
|
3.3
|
9.8
|
1.0
|
|
H
|
B:GLN473
|
3.3
|
12.5
|
1.0
|
|
O3A
|
B:TD6602
|
3.4
|
11.4
|
1.0
|
|
HA2
|
B:GLY472
|
3.4
|
12.7
|
1.0
|
|
ND2
|
B:ASN469
|
3.5
|
10.1
|
1.0
|
|
H
|
B:ASN469
|
3.5
|
11.8
|
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
|
4.1
|
12.2
|
1.0
|
|
N
|
B:GLY472
|
4.1
|
10.1
|
1.0
|
|
HG
|
B:LEU443
|
4.1
|
13.9
|
1.0
|
|
N
|
B:GLN473
|
4.1
|
10.4
|
1.0
|
|
O7
|
B:TD6602
|
4.1
|
9.9
|
1.0
|
|
CA
|
B:GLY472
|
4.1
|
10.6
|
1.0
|
|
CA
|
B:GLY471
|
4.2
|
10.3
|
1.0
|
|
O
|
B:HOH802
|
4.3
|
12.0
|
1.0
|
|
N
|
B:ASN469
|
4.3
|
9.8
|
1.0
|
|
O3B
|
B:TD6602
|
4.3
|
10.1
|
1.0
|
|
HD22
|
B:ASN469
|
4.3
|
12.1
|
1.0
|
|
O
|
B:VAL467
|
4.3
|
10.9
|
1.0
|
|
O2B
|
B:TD6602
|
4.3
|
10.3
|
1.0
|
|
CB
|
B:ASP442
|
4.4
|
10.7
|
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
|
|
HB2
|
B:GLN473
|
4.6
|
13.4
|
1.0
|
|
HA2
|
B:GLY441
|
4.6
|
12.2
|
1.0
|
|
N
|
B:ASN470
|
4.6
|
10.9
|
1.0
|
|
CA
|
B:ASN469
|
4.6
|
10.8
|
1.0
|
|
CA
|
B:ASP442
|
4.6
|
10.8
|
1.0
|
|
HB3
|
B:ASP442
|
4.6
|
12.8
|
1.0
|
|
CA
|
B:GLY441
|
4.7
|
10.2
|
1.0
|
|
C
|
B:GLY472
|
4.7
|
10.6
|
1.0
|
|
HA2
|
B:GLY471
|
4.7
|
12.4
|
1.0
|
|
HA
|
B:ASN468
|
4.7
|
13.0
|
1.0
|
|
C
|
B:GLY441
|
4.7
|
8.8
|
1.0
|
|
CG
|
B:GLN473
|
4.7
|
12.6
|
1.0
|
|
HB3
|
B:ASN469
|
4.9
|
12.5
|
1.0
|
|
HG3
|
B:GLN473
|
4.9
|
15.1
|
1.0
|
|
H
|
B:GLY472
|
4.9
|
12.1
|
1.0
|
|
HA3
|
B:GLY472
|
5.0
|
12.7
|
1.0
|
|
HA3
|
B:GLY471
|
5.0
|
12.4
|
1.0
|
|
HB2
|
B:ASN469
|
5.0
|
12.5
|
1.0
|
|
C
|
B:ASN470
|
5.0
|
10.8
|
1.0
|
|
Manganese binding site 3 out
of 8 in 5ej8
Go back to
Manganese Binding Sites List in 5ej8
Manganese binding site 3 out
of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn 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
|
C:Mn603
b:15.7
occ:0.41
|
MG
|
C:MG604
|
0.1
|
5.2
|
0.6
|
|
O1A
|
C:TD6602
|
2.0
|
10.3
|
1.0
|
|
O1B
|
C:TD6602
|
2.1
|
10.8
|
1.0
|
|
OD1
|
C:ASP442
|
2.1
|
11.2
|
1.0
|
|
O
|
C:HOH859
|
2.1
|
11.8
|
1.0
|
|
O
|
C:GLY471
|
2.1
|
11.6
|
1.0
|
|
OD1
|
C:ASN469
|
2.1
|
11.8
|
1.0
|
|
H
|
C:ASP442
|
3.0
|
12.5
|
1.0
|
|
CG
|
C:ASN469
|
3.1
|
11.9
|
1.0
|
|
HD21
|
C:ASN469
|
3.1
|
14.7
|
1.0
|
|
CG
|
C:ASP442
|
3.1
|
11.3
|
1.0
|
|
PA
|
C:TD6602
|
3.3
|
9.6
|
1.0
|
|
PB
|
C:TD6602
|
3.3
|
10.5
|
1.0
|
|
C
|
C:GLY471
|
3.3
|
11.8
|
1.0
|
|
O3A
|
C:TD6602
|
3.4
|
10.3
|
1.0
|
|
H
|
C:GLN473
|
3.4
|
12.5
|
1.0
|
|
H
|
C:ASN469
|
3.5
|
15.3
|
1.0
|
|
HA2
|
C:GLY472
|
3.5
|
13.9
|
1.0
|
|
ND2
|
C:ASN469
|
3.5
|
12.2
|
1.0
|
|
H
|
C:GLY471
|
3.6
|
13.4
|
1.0
|
|
OD2
|
C:ASP442
|
3.6
|
12.2
|
1.0
|
|
H
|
C:LEU443
|
3.7
|
11.7
|
1.0
|
|
N
|
C:ASP442
|
3.8
|
10.4
|
1.0
|
|
HG2
|
C:GLN473
|
3.9
|
16.4
|
1.0
|
|
HA3
|
C:GLY441
|
4.0
|
12.3
|
1.0
|
|
N
|
C:GLY471
|
4.1
|
11.2
|
1.0
|
|
O7
|
C:TD6602
|
4.1
|
10.4
|
1.0
|
|
HG
|
C:LEU443
|
4.1
|
13.8
|
1.0
|
|
N
|
C:GLN473
|
4.2
|
10.4
|
1.0
|
|
N
|
C:GLY472
|
4.2
|
11.2
|
1.0
|
|
CA
|
C:GLY472
|
4.2
|
11.6
|
1.0
|
|
O
|
C:HOH800
|
4.2
|
13.9
|
1.0
|
|
N
|
C:ASN469
|
4.3
|
12.7
|
1.0
|
|
CA
|
C:GLY471
|
4.3
|
10.9
|
1.0
|
|
O
|
C:VAL467
|
4.3
|
12.0
|
1.0
|
|
O3B
|
C:TD6602
|
4.3
|
11.0
|
1.0
|
|
CB
|
C:ASP442
|
4.3
|
10.9
|
1.0
|
|
HD22
|
C:ASN469
|
4.3
|
14.7
|
1.0
|
|
O2B
|
C:TD6602
|
4.3
|
11.4
|
1.0
|
|
O2A
|
C:TD6602
|
4.4
|
10.1
|
1.0
|
|
CB
|
C:ASN469
|
4.4
|
12.5
|
1.0
|
|
HA2
|
C:GLY441
|
4.5
|
12.3
|
1.0
|
|
N
|
C:LEU443
|
4.5
|
9.7
|
1.0
|
|
H
|
C:ASN470
|
4.5
|
14.1
|
1.0
|
|
CA
|
C:ASP442
|
4.5
|
10.7
|
1.0
|
|
CA
|
C:GLY441
|
4.5
|
10.3
|
1.0
|
|
HB2
|
C:GLN473
|
4.6
|
13.6
|
1.0
|
|
HB3
|
C:ASP442
|
4.6
|
13.1
|
1.0
|
|
C
|
C:ASN469
|
4.6
|
11.9
|
1.0
|
|
C
|
C:GLY441
|
4.6
|
9.8
|
1.0
|
|
N
|
C:ASN470
|
4.6
|
11.8
|
1.0
|
|
CA
|
C:ASN469
|
4.7
|
13.2
|
1.0
|
|
HA
|
C:ASN468
|
4.7
|
16.2
|
1.0
|
|
CG
|
C:GLN473
|
4.7
|
13.7
|
1.0
|
|
HA2
|
C:GLY471
|
4.7
|
13.1
|
1.0
|
|
C
|
C:GLY472
|
4.7
|
11.6
|
1.0
|
|
HG3
|
C:GLN473
|
4.9
|
16.4
|
1.0
|
|
HB3
|
C:ASN469
|
4.9
|
15.0
|
1.0
|
|
HB2
|
C:LEU443
|
5.0
|
12.5
|
1.0
|
|
HB2
|
C:ASN469
|
5.0
|
15.0
|
1.0
|
|
HA3
|
C:GLY472
|
5.0
|
13.9
|
1.0
|
|
Manganese binding site 4 out
of 8 in 5ej8
Go back to
Manganese Binding Sites List in 5ej8
Manganese binding site 4 out
of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn 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
|
D:Mn603
b:16.1
occ:0.47
|
MG
|
D:MG604
|
0.1
|
7.4
|
0.5
|
|
O1A
|
D:TD6602
|
2.1
|
10.9
|
1.0
|
|
O
|
D:GLY471
|
2.1
|
12.0
|
1.0
|
|
OD1
|
D:ASN469
|
2.1
|
12.7
|
1.0
|
|
OD1
|
D:ASP442
|
2.1
|
13.2
|
1.0
|
|
O1B
|
D:TD6602
|
2.1
|
12.4
|
1.0
|
|
O
|
D:HOH870
|
2.2
|
12.3
|
1.0
|
|
H
|
D:ASP442
|
3.1
|
14.2
|
1.0
|
|
HD21
|
D:ASN469
|
3.1
|
15.3
|
1.0
|
|
CG
|
D:ASN469
|
3.1
|
12.8
|
1.0
|
|
CG
|
D:ASP442
|
3.1
|
13.5
|
1.0
|
|
PA
|
D:TD6602
|
3.2
|
11.8
|
1.0
|
|
C
|
D:GLY471
|
3.3
|
12.1
|
1.0
|
|
PB
|
D:TD6602
|
3.3
|
12.7
|
1.0
|
|
H
|
D:GLN473
|
3.4
|
15.1
|
1.0
|
|
O3A
|
D:TD6602
|
3.4
|
12.4
|
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
|
|
H
|
D:GLY471
|
3.5
|
16.3
|
1.0
|
|
OD2
|
D:ASP442
|
3.6
|
14.1
|
1.0
|
|
H
|
D:LEU443
|
3.7
|
14.9
|
1.0
|
|
N
|
D:ASP442
|
3.8
|
11.8
|
1.0
|
|
HG2
|
D:GLN473
|
3.9
|
16.8
|
1.0
|
|
HA3
|
D:GLY441
|
4.0
|
14.8
|
1.0
|
|
N
|
D:GLY471
|
4.0
|
13.6
|
1.0
|
|
HG
|
D:LEU443
|
4.1
|
15.5
|
1.0
|
|
O7
|
D:TD6602
|
4.1
|
11.2
|
1.0
|
|
N
|
D:GLN473
|
4.2
|
12.6
|
1.0
|
|
N
|
D:GLY472
|
4.2
|
12.8
|
1.0
|
|
CA
|
D:GLY472
|
4.2
|
12.4
|
1.0
|
|
O
|
D:HOH825
|
4.2
|
14.9
|
1.0
|
|
CA
|
D:GLY471
|
4.3
|
12.9
|
1.0
|
|
N
|
D:ASN469
|
4.3
|
13.9
|
1.0
|
|
HD22
|
D:ASN469
|
4.3
|
15.3
|
1.0
|
|
O3B
|
D:TD6602
|
4.3
|
13.2
|
1.0
|
|
O
|
D:VAL467
|
4.3
|
13.2
|
1.0
|
|
O2A
|
D:TD6602
|
4.3
|
11.1
|
1.0
|
|
CB
|
D:ASP442
|
4.4
|
12.2
|
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
|
|
HA2
|
D:GLY441
|
4.5
|
14.8
|
1.0
|
|
N
|
D:LEU443
|
4.5
|
12.5
|
1.0
|
|
HB2
|
D:GLN473
|
4.5
|
16.5
|
1.0
|
|
C
|
D:ASN469
|
4.6
|
12.6
|
1.0
|
|
CA
|
D:ASP442
|
4.6
|
11.6
|
1.0
|
|
CA
|
D:GLY441
|
4.6
|
12.4
|
1.0
|
|
N
|
D:ASN470
|
4.6
|
13.4
|
1.0
|
|
HB3
|
D:ASP442
|
4.6
|
14.6
|
1.0
|
|
CA
|
D:ASN469
|
4.7
|
13.7
|
1.0
|
|
C
|
D:GLY441
|
4.7
|
11.9
|
1.0
|
|
CG
|
D:GLN473
|
4.7
|
14.0
|
1.0
|
|
HA
|
D:ASN468
|
4.7
|
16.5
|
1.0
|
|
HA2
|
D:GLY471
|
4.7
|
15.5
|
1.0
|
|
C
|
D:GLY472
|
4.7
|
12.1
|
1.0
|
|
HG3
|
D:GLN473
|
4.8
|
16.8
|
1.0
|
|
HB3
|
D:ASN469
|
4.9
|
16.5
|
1.0
|
|
HB2
|
D:ASN469
|
5.0
|
16.5
|
1.0
|
|
H
|
D:GLY472
|
5.0
|
15.3
|
1.0
|
|
Manganese binding site 5 out
of 8 in 5ej8
Go back to
Manganese Binding Sites List in 5ej8
Manganese binding site 5 out
of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn 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
|
E:Mn602
b:11.6
occ:0.47
|
MG
|
E:MG603
|
0.2
|
8.8
|
0.5
|
|
O
|
E:GLY471
|
2.0
|
10.9
|
1.0
|
|
O1A
|
E:TD6601
|
2.1
|
8.1
|
1.0
|
|
OD1
|
E:ASN469
|
2.1
|
10.1
|
1.0
|
|
O1B
|
E:TD6601
|
2.1
|
9.4
|
1.0
|
|
OD1
|
E:ASP442
|
2.2
|
10.7
|
1.0
|
|
O
|
E:HOH783
|
2.2
|
9.6
|
1.0
|
|
HD21
|
E:ASN469
|
3.1
|
13.1
|
1.0
|
|
CG
|
E:ASN469
|
3.1
|
9.1
|
1.0
|
|
H
|
E:ASP442
|
3.2
|
10.9
|
1.0
|
|
CG
|
E:ASP442
|
3.2
|
9.5
|
1.0
|
|
C
|
E:GLY471
|
3.2
|
10.5
|
1.0
|
|
PA
|
E:TD6601
|
3.3
|
8.8
|
1.0
|
|
PB
|
E:TD6601
|
3.3
|
9.8
|
1.0
|
|
H
|
E:GLN473
|
3.3
|
12.8
|
1.0
|
|
O3A
|
E:TD6601
|
3.4
|
9.5
|
1.0
|
|
HA2
|
E:GLY472
|
3.4
|
11.9
|
1.0
|
|
ND2
|
E:ASN469
|
3.4
|
10.9
|
1.0
|
|
H
|
E:ASN469
|
3.5
|
13.4
|
1.0
|
|
H
|
E:GLY471
|
3.5
|
12.7
|
1.0
|
|
OD2
|
E:ASP442
|
3.6
|
11.8
|
1.0
|
|
H
|
E:LEU443
|
3.7
|
11.9
|
1.0
|
|
HG2
|
E:GLN473
|
3.8
|
15.5
|
1.0
|
|
N
|
E:ASP442
|
3.9
|
9.1
|
1.0
|
|
N
|
E:GLY471
|
4.0
|
10.6
|
1.0
|
|
HA3
|
E:GLY441
|
4.1
|
12.2
|
1.0
|
|
N
|
E:GLY472
|
4.1
|
9.3
|
1.0
|
|
CA
|
E:GLY472
|
4.1
|
9.9
|
1.0
|
|
O7
|
E:TD6601
|
4.1
|
8.2
|
1.0
|
|
N
|
E:GLN473
|
4.1
|
10.7
|
1.0
|
|
HG
|
E:LEU443
|
4.1
|
11.5
|
1.0
|
|
CA
|
E:GLY471
|
4.2
|
10.3
|
1.0
|
|
O3B
|
E:TD6601
|
4.3
|
9.8
|
1.0
|
|
O
|
E:HOH876
|
4.3
|
12.9
|
1.0
|
|
HD22
|
E:ASN469
|
4.3
|
13.1
|
1.0
|
|
N
|
E:ASN469
|
4.3
|
11.2
|
1.0
|
|
O2B
|
E:TD6601
|
4.4
|
11.2
|
1.0
|
|
O
|
E:VAL467
|
4.4
|
10.9
|
1.0
|
|
CB
|
E:ASP442
|
4.4
|
10.7
|
1.0
|
|
CB
|
E:ASN469
|
4.4
|
10.3
|
1.0
|
|
O2A
|
E:TD6601
|
4.4
|
9.4
|
1.0
|
|
HB2
|
E:GLN473
|
4.5
|
13.1
|
1.0
|
|
H
|
E:ASN470
|
4.5
|
13.1
|
1.0
|
|
N
|
E:LEU443
|
4.6
|
9.9
|
1.0
|
|
C
|
E:ASN469
|
4.6
|
9.8
|
1.0
|
|
HA2
|
E:GLY441
|
4.6
|
12.2
|
1.0
|
|
N
|
E:ASN470
|
4.6
|
10.9
|
1.0
|
|
CA
|
E:ASN469
|
4.6
|
10.6
|
1.0
|
|
CA
|
E:ASP442
|
4.7
|
9.7
|
1.0
|
|
HB3
|
E:ASP442
|
4.7
|
12.9
|
1.0
|
|
CA
|
E:GLY441
|
4.7
|
10.2
|
1.0
|
|
HA2
|
E:GLY471
|
4.7
|
12.4
|
1.0
|
|
CG
|
E:GLN473
|
4.7
|
12.9
|
1.0
|
|
C
|
E:GLY472
|
4.7
|
9.3
|
1.0
|
|
HA
|
E:ASN468
|
4.7
|
13.0
|
1.0
|
|
C
|
E:GLY441
|
4.8
|
9.9
|
1.0
|
|
HG3
|
E:GLN473
|
4.8
|
15.5
|
1.0
|
|
HA3
|
E:GLY472
|
4.9
|
11.9
|
1.0
|
|
HB3
|
E:ASN469
|
4.9
|
12.4
|
1.0
|
|
H
|
E:GLY472
|
4.9
|
11.2
|
1.0
|
|
HB2
|
E:ASN469
|
4.9
|
12.4
|
1.0
|
|
HA3
|
E:GLY471
|
4.9
|
12.4
|
1.0
|
|
C
|
E:ASN470
|
5.0
|
11.3
|
1.0
|
|
CB
|
E:GLN473
|
5.0
|
10.9
|
1.0
|
|
HB2
|
E:LEU443
|
5.0
|
10.8
|
1.0
|
|
Manganese binding site 6 out
of 8 in 5ej8
Go back to
Manganese Binding Sites List in 5ej8
Manganese binding site 6 out
of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn 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
|
F:Mn603
b:11.1
occ:0.51
|
MG
|
F:MG604
|
0.1
|
10.4
|
0.5
|
|
O
|
F:GLY471
|
2.1
|
9.6
|
1.0
|
|
O1A
|
F:TD6602
|
2.1
|
10.1
|
1.0
|
|
OD1
|
F:ASP442
|
2.1
|
11.1
|
1.0
|
|
OD1
|
F:ASN469
|
2.1
|
11.4
|
1.0
|
|
O1B
|
F:TD6602
|
2.2
|
9.6
|
1.0
|
|
O
|
F:HOH820
|
2.2
|
24.7
|
1.0
|
|
CG
|
F:ASN469
|
3.1
|
9.1
|
1.0
|
|
H
|
F:ASP442
|
3.1
|
9.7
|
1.0
|
|
CG
|
F:ASP442
|
3.1
|
10.3
|
1.0
|
|
HD21
|
F:ASN469
|
3.2
|
13.6
|
1.0
|
|
C
|
F:GLY471
|
3.3
|
8.6
|
1.0
|
|
PA
|
F:TD6602
|
3.3
|
9.2
|
1.0
|
|
PB
|
F:TD6602
|
3.4
|
9.5
|
1.0
|
|
O3A
|
F:TD6602
|
3.4
|
8.3
|
1.0
|
|
H
|
F:GLN473
|
3.4
|
12.0
|
1.0
|
|
H
|
F:ASN469
|
3.5
|
13.1
|
1.0
|
|
HA2
|
F:GLY472
|
3.5
|
11.4
|
1.0
|
|
ND2
|
F:ASN469
|
3.5
|
11.3
|
1.0
|
|
H
|
F:GLY471
|
3.5
|
12.8
|
1.0
|
|
OD2
|
F:ASP442
|
3.6
|
11.1
|
1.0
|
|
H
|
F:LEU443
|
3.7
|
10.9
|
1.0
|
|
N
|
F:ASP442
|
3.9
|
8.0
|
1.0
|
|
HG2
|
F:GLN473
|
3.9
|
15.6
|
1.0
|
|
HA3
|
F:GLY441
|
4.0
|
10.4
|
1.0
|
|
N
|
F:GLY471
|
4.0
|
10.7
|
1.0
|
|
HG
|
F:LEU443
|
4.1
|
12.8
|
1.0
|
|
O7
|
F:TD6602
|
4.1
|
9.3
|
1.0
|
|
N
|
F:GLY472
|
4.1
|
10.4
|
1.0
|
|
N
|
F:GLN473
|
4.2
|
10.0
|
1.0
|
|
CA
|
F:GLY472
|
4.2
|
9.5
|
1.0
|
|
O
|
F:HOH757
|
4.2
|
11.3
|
1.0
|
|
CA
|
F:GLY471
|
4.2
|
11.0
|
1.0
|
|
N
|
F:ASN469
|
4.3
|
10.9
|
1.0
|
|
O
|
F:VAL467
|
4.3
|
11.6
|
1.0
|
|
CB
|
F:ASP442
|
4.3
|
9.4
|
1.0
|
|
O2B
|
F:TD6602
|
4.3
|
10.3
|
1.0
|
|
HD22
|
F:ASN469
|
4.3
|
13.6
|
1.0
|
|
O3B
|
F:TD6602
|
4.4
|
10.4
|
1.0
|
|
O2A
|
F:TD6602
|
4.4
|
8.9
|
1.0
|
|
CB
|
F:ASN469
|
4.4
|
10.6
|
1.0
|
|
H
|
F:ASN470
|
4.5
|
11.7
|
1.0
|
|
N
|
F:LEU443
|
4.5
|
9.1
|
1.0
|
|
HA2
|
F:GLY441
|
4.5
|
10.4
|
1.0
|
|
C
|
F:ASN469
|
4.6
|
10.3
|
1.0
|
|
CA
|
F:ASP442
|
4.6
|
9.5
|
1.0
|
|
N
|
F:ASN470
|
4.6
|
9.8
|
1.0
|
|
HB3
|
F:ASP442
|
4.6
|
11.2
|
1.0
|
|
HB2
|
F:GLN473
|
4.6
|
14.7
|
1.0
|
|
CA
|
F:GLY441
|
4.6
|
8.6
|
1.0
|
|
CA
|
F:ASN469
|
4.6
|
9.8
|
1.0
|
|
HA2
|
F:GLY471
|
4.7
|
13.2
|
1.0
|
|
HA
|
F:ASN468
|
4.7
|
11.2
|
1.0
|
|
C
|
F:GLY441
|
4.7
|
8.7
|
1.0
|
|
C
|
F:GLY472
|
4.7
|
10.1
|
1.0
|
|
CG
|
F:GLN473
|
4.8
|
13.0
|
1.0
|
|
HB3
|
F:ASN469
|
4.9
|
12.7
|
1.0
|
|
H
|
F:GLY472
|
5.0
|
12.5
|
1.0
|
|
HB2
|
F:ASN469
|
5.0
|
12.7
|
1.0
|
|
HA3
|
F:GLY472
|
5.0
|
11.4
|
1.0
|
|
HA3
|
F:GLY471
|
5.0
|
13.2
|
1.0
|
|
HG3
|
F:GLN473
|
5.0
|
15.6
|
1.0
|
|
HB2
|
F:LEU443
|
5.0
|
11.2
|
1.0
|
|
C
|
F:ASN470
|
5.0
|
10.9
|
1.0
|
|
Manganese binding site 7 out
of 8 in 5ej8
Go back to
Manganese Binding Sites List in 5ej8
Manganese binding site 7 out
of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn 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
|
G:Mn602
b:14.7
occ:0.45
|
MG
|
G:MG603
|
0.1
|
6.7
|
0.6
|
|
OD1
|
G:ASN469
|
2.1
|
11.6
|
1.0
|
|
O
|
G:GLY471
|
2.1
|
10.9
|
1.0
|
|
OD1
|
G:ASP442
|
2.1
|
11.0
|
1.0
|
|
O1B
|
G:TD6601
|
2.1
|
10.9
|
1.0
|
|
O1A
|
G:TD6601
|
2.1
|
10.5
|
1.0
|
|
O
|
G:HOH818
|
2.2
|
11.6
|
1.0
|
|
CG
|
G:ASN469
|
3.0
|
12.0
|
1.0
|
|
HD21
|
G:ASN469
|
3.1
|
15.0
|
1.0
|
|
H
|
G:ASP442
|
3.1
|
13.0
|
1.0
|
|
CG
|
G:ASP442
|
3.1
|
10.8
|
1.0
|
|
C
|
G:GLY471
|
3.3
|
10.9
|
1.0
|
|
PA
|
G:TD6601
|
3.3
|
10.4
|
1.0
|
|
H
|
G:GLN473
|
3.3
|
14.7
|
1.0
|
|
PB
|
G:TD6601
|
3.3
|
10.9
|
1.0
|
|
O3A
|
G:TD6601
|
3.4
|
10.2
|
1.0
|
|
ND2
|
G:ASN469
|
3.4
|
12.5
|
1.0
|
|
H
|
G:ASN469
|
3.4
|
13.7
|
1.0
|
|
HA2
|
G:GLY472
|
3.5
|
13.3
|
1.0
|
|
H
|
G:GLY471
|
3.6
|
13.7
|
1.0
|
|
OD2
|
G:ASP442
|
3.6
|
13.1
|
1.0
|
|
H
|
G:LEU443
|
3.7
|
11.0
|
1.0
|
|
N
|
G:ASP442
|
3.9
|
10.9
|
1.0
|
|
HG2
|
G:GLN473
|
3.9
|
19.0
|
1.0
|
|
HA3
|
G:GLY441
|
4.0
|
12.3
|
1.0
|
|
N
|
G:GLY471
|
4.1
|
11.4
|
1.0
|
|
N
|
G:GLN473
|
4.1
|
12.2
|
1.0
|
|
N
|
G:GLY472
|
4.2
|
11.2
|
1.0
|
|
O7
|
G:TD6601
|
4.2
|
9.6
|
1.0
|
|
HG
|
G:LEU443
|
4.2
|
13.7
|
1.0
|
|
CA
|
G:GLY472
|
4.2
|
11.1
|
1.0
|
|
N
|
G:ASN469
|
4.2
|
11.4
|
1.0
|
|
CA
|
G:GLY471
|
4.3
|
12.4
|
1.0
|
|
O
|
G:HOH817
|
4.3
|
13.2
|
1.0
|
|
HD22
|
G:ASN469
|
4.3
|
15.0
|
1.0
|
|
O3B
|
G:TD6601
|
4.3
|
11.9
|
1.0
|
|
O2B
|
G:TD6601
|
4.3
|
11.1
|
1.0
|
|
O
|
G:VAL467
|
4.3
|
12.6
|
1.0
|
|
CB
|
G:ASP442
|
4.3
|
9.8
|
1.0
|
|
CB
|
G:ASN469
|
4.4
|
11.4
|
1.0
|
|
O2A
|
G:TD6601
|
4.4
|
10.8
|
1.0
|
|
H
|
G:ASN470
|
4.5
|
14.6
|
1.0
|
|
HA2
|
G:GLY441
|
4.5
|
12.3
|
1.0
|
|
N
|
G:LEU443
|
4.5
|
9.2
|
1.0
|
|
C
|
G:ASN469
|
4.6
|
12.1
|
1.0
|
|
HB2
|
G:GLN473
|
4.6
|
16.1
|
1.0
|
|
CA
|
G:ASP442
|
4.6
|
9.3
|
1.0
|
|
CA
|
G:ASN469
|
4.6
|
11.5
|
1.0
|
|
N
|
G:ASN470
|
4.6
|
12.1
|
1.0
|
|
HB3
|
G:ASP442
|
4.6
|
11.8
|
1.0
|
|
CA
|
G:GLY441
|
4.6
|
10.2
|
1.0
|
|
HA
|
G:ASN468
|
4.7
|
14.2
|
1.0
|
|
CG
|
G:GLN473
|
4.7
|
15.8
|
1.0
|
|
C
|
G:GLY441
|
4.7
|
9.9
|
1.0
|
|
C
|
G:GLY472
|
4.7
|
12.2
|
1.0
|
|
HA2
|
G:GLY471
|
4.7
|
14.9
|
1.0
|
|
HG3
|
G:GLN473
|
4.9
|
19.0
|
1.0
|
|
HB3
|
G:ASN469
|
4.9
|
13.7
|
1.0
|
|
HB2
|
G:ASN469
|
4.9
|
13.7
|
1.0
|
|
H
|
G:GLY472
|
5.0
|
13.4
|
1.0
|
|
HA3
|
G:GLY471
|
5.0
|
14.9
|
1.0
|
|
C
|
G:ASN470
|
5.0
|
12.1
|
1.0
|
|
Manganese binding site 8 out
of 8 in 5ej8
Go back to
Manganese Binding Sites List in 5ej8
Manganese binding site 8 out
of 8 in the Ecmend-Thdp-MN2+ Complex Structure Soaked with 2-Ketoglutarate For 2 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn 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
|
H:Mn603
b:13.5
occ:0.52
|
MG
|
H:MG604
|
0.2
|
6.8
|
0.5
|
|
O1A
|
H:TD6602
|
2.0
|
10.7
|
1.0
|
|
O1B
|
H:TD6602
|
2.1
|
9.4
|
1.0
|
|
O
|
H:GLY471
|
2.1
|
11.7
|
1.0
|
|
OD1
|
H:ASP442
|
2.1
|
10.2
|
1.0
|
|
OD1
|
H:ASN469
|
2.2
|
11.8
|
1.0
|
|
O
|
H:HOH830
|
2.2
|
10.2
|
1.0
|
|
H
|
H:ASP442
|
3.1
|
12.6
|
1.0
|
|
HD21
|
H:ASN469
|
3.1
|
13.2
|
1.0
|
|
CG
|
H:ASN469
|
3.1
|
11.0
|
1.0
|
|
CG
|
H:ASP442
|
3.2
|
10.0
|
1.0
|
|
PA
|
H:TD6602
|
3.2
|
10.3
|
1.0
|
|
PB
|
H:TD6602
|
3.3
|
10.2
|
1.0
|
|
C
|
H:GLY471
|
3.3
|
11.6
|
1.0
|
|
O3A
|
H:TD6602
|
3.3
|
9.4
|
1.0
|
|
H
|
H:GLN473
|
3.3
|
12.8
|
1.0
|
|
HA2
|
H:GLY472
|
3.4
|
14.0
|
1.0
|
|
ND2
|
H:ASN469
|
3.5
|
11.0
|
1.0
|
|
H
|
H:ASN469
|
3.5
|
14.1
|
1.0
|
|
H
|
H:GLY471
|
3.6
|
14.2
|
1.0
|
|
OD2
|
H:ASP442
|
3.6
|
11.6
|
1.0
|
|
H
|
H:LEU443
|
3.7
|
11.9
|
1.0
|
|
N
|
H:ASP442
|
3.8
|
10.5
|
1.0
|
|
HG2
|
H:GLN473
|
4.0
|
16.1
|
1.0
|
|
HA3
|
H:GLY441
|
4.0
|
11.9
|
1.0
|
|
O7
|
H:TD6602
|
4.1
|
9.6
|
1.0
|
|
N
|
H:GLY471
|
4.1
|
11.8
|
1.0
|
|
HG
|
H:LEU443
|
4.1
|
13.9
|
1.0
|
|
N
|
H:GLN473
|
4.1
|
10.7
|
1.0
|
|
CA
|
H:GLY472
|
4.2
|
11.6
|
1.0
|
|
N
|
H:GLY472
|
4.2
|
10.8
|
1.0
|
|
O3B
|
H:TD6602
|
4.3
|
10.5
|
1.0
|
|
O
|
H:HOH802
|
4.3
|
13.3
|
1.0
|
|
CA
|
H:GLY471
|
4.3
|
11.1
|
1.0
|
|
O2B
|
H:TD6602
|
4.3
|
10.8
|
1.0
|
|
N
|
H:ASN469
|
4.3
|
11.8
|
1.0
|
|
O
|
H:VAL467
|
4.3
|
10.7
|
1.0
|
|
HD22
|
H:ASN469
|
4.4
|
13.2
|
1.0
|
|
CB
|
H:ASP442
|
4.4
|
10.7
|
1.0
|
|
O2A
|
H:TD6602
|
4.4
|
9.6
|
1.0
|
|
N
|
H:LEU443
|
4.5
|
9.9
|
1.0
|
|
CB
|
H:ASN469
|
4.5
|
10.7
|
1.0
|
|
HA2
|
H:GLY441
|
4.5
|
11.9
|
1.0
|
|
H
|
H:ASN470
|
4.5
|
14.3
|
1.0
|
|
HB2
|
H:GLN473
|
4.6
|
15.3
|
1.0
|
|
CA
|
H:GLY441
|
4.6
|
9.9
|
1.0
|
|
CA
|
H:ASP442
|
4.6
|
10.9
|
1.0
|
|
HB3
|
H:ASP442
|
4.6
|
12.9
|
1.0
|
|
C
|
H:GLY441
|
4.7
|
9.4
|
1.0
|
|
N
|
H:ASN470
|
4.7
|
11.9
|
1.0
|
|
C
|
H:ASN469
|
4.7
|
10.8
|
1.0
|
|
C
|
H:GLY472
|
4.7
|
11.2
|
1.0
|
|
CA
|
H:ASN469
|
4.7
|
12.7
|
1.0
|
|
HA
|
H:ASN468
|
4.7
|
13.5
|
1.0
|
|
HA2
|
H:GLY471
|
4.7
|
13.3
|
1.0
|
|
CG
|
H:GLN473
|
4.8
|
13.4
|
1.0
|
|
HA3
|
H:GLY472
|
4.9
|
14.0
|
1.0
|
|
HB2
|
H:LEU443
|
4.9
|
13.3
|
1.0
|
|
HG3
|
H:GLN473
|
5.0
|
16.1
|
1.0
|
|
H
|
H:GLY472
|
5.0
|
13.0
|
1.0
|
|
HB3
|
H:ASN469
|
5.0
|
12.8
|
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 Oct 6 00:02:37 2024
|
