Manganese in PDB 5ej7: Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
Enzymatic activity of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
All present enzymatic activity of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S:
2.2.1.9;
Protein crystallography data
The structure of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S, PDB code: 5ej7
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)
|
32.45 /
1.56
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.600,
90.611,
167.570,
76.08,
83.45,
63.44
|
|
R / Rfree (%)
|
14.6 /
18.3
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
(pdb code 5ej7). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the
Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S, PDB code: 5ej7:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Manganese binding site 1 out
of 9 in 5ej7
Go back to
Manganese Binding Sites List in 5ej7
Manganese binding site 1 out
of 9 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
 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 Soaked with 2-Ketoglutarate For 21 S within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn602
b:12.6
occ:1.00
|
O3B
|
A:TD6601
|
2.1
|
6.0
|
1.0
|
|
OD1
|
A:ASN469
|
2.1
|
6.5
|
1.0
|
|
O1A
|
A:TD6601
|
2.1
|
6.1
|
1.0
|
|
OD1
|
A:ASP442
|
2.1
|
7.5
|
1.0
|
|
O
|
A:GLY471
|
2.1
|
7.8
|
1.0
|
|
O
|
A:HOH803
|
2.2
|
8.6
|
1.0
|
|
CG
|
A:ASN469
|
3.1
|
7.7
|
1.0
|
|
CG
|
A:ASP442
|
3.2
|
12.8
|
1.0
|
|
PA
|
A:TD6601
|
3.3
|
7.5
|
1.0
|
|
C
|
A:GLY471
|
3.3
|
7.4
|
1.0
|
|
PB
|
A:TD6601
|
3.3
|
7.3
|
1.0
|
|
ND2
|
A:ASN469
|
3.5
|
9.4
|
1.0
|
|
O3A
|
A:TD6601
|
3.5
|
6.7
|
1.0
|
|
OD2
|
A:ASP442
|
3.6
|
9.4
|
1.0
|
|
N
|
A:ASP442
|
3.9
|
6.4
|
1.0
|
|
N
|
A:GLY471
|
4.0
|
7.4
|
1.0
|
|
CA
|
A:GLY472
|
4.2
|
6.5
|
1.0
|
|
N
|
A:GLN473
|
4.2
|
7.4
|
1.0
|
|
N
|
A:GLY472
|
4.2
|
6.6
|
1.0
|
|
O7
|
A:TD6601
|
4.2
|
7.3
|
1.0
|
|
N
|
A:ASN469
|
4.2
|
6.5
|
1.0
|
|
O
|
A:HOH820
|
4.3
|
11.5
|
1.0
|
|
CA
|
A:GLY471
|
4.3
|
8.9
|
1.0
|
|
O
|
A:VAL467
|
4.3
|
10.3
|
1.0
|
|
O2B
|
A:TD6601
|
4.3
|
8.6
|
1.0
|
|
O1B
|
A:TD6601
|
4.3
|
8.4
|
1.0
|
|
CB
|
A:ASP442
|
4.4
|
8.7
|
1.0
|
|
CB
|
A:ASN469
|
4.4
|
7.3
|
1.0
|
|
O2A
|
A:TD6601
|
4.4
|
7.1
|
1.0
|
|
N
|
A:LEU443
|
4.5
|
5.7
|
1.0
|
|
C
|
A:ASN469
|
4.6
|
9.7
|
1.0
|
|
N
|
A:ASN470
|
4.6
|
8.5
|
1.0
|
|
CA
|
A:ASP442
|
4.6
|
6.8
|
1.0
|
|
CA
|
A:GLY441
|
4.6
|
5.5
|
1.0
|
|
CA
|
A:ASN469
|
4.6
|
7.8
|
1.0
|
|
C
|
A:GLY441
|
4.7
|
10.0
|
1.0
|
|
CG
|
A:GLN473
|
4.7
|
9.1
|
1.0
|
|
C
|
A:GLY472
|
4.7
|
7.0
|
1.0
|
|
C
|
A:ASN470
|
5.0
|
10.6
|
1.0
|
|
Manganese binding site 2 out
of 9 in 5ej7
Go back to
Manganese Binding Sites List in 5ej7
Manganese binding site 2 out
of 9 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
 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 Soaked with 2-Ketoglutarate For 21 S within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn602
b:13.5
occ:1.00
|
OD1
|
B:ASP442
|
2.1
|
9.0
|
1.0
|
|
O
|
B:GLY471
|
2.1
|
9.1
|
1.0
|
|
OD1
|
B:ASN469
|
2.1
|
8.0
|
1.0
|
|
O1A
|
B:TD6601
|
2.1
|
7.7
|
1.0
|
|
O3B
|
B:TD6601
|
2.2
|
8.6
|
1.0
|
|
O
|
B:HOH887
|
2.2
|
8.3
|
1.0
|
|
CG
|
B:ASN469
|
3.1
|
8.1
|
1.0
|
|
CG
|
B:ASP442
|
3.1
|
11.4
|
1.0
|
|
PA
|
B:TD6601
|
3.3
|
8.1
|
1.0
|
|
C
|
B:GLY471
|
3.3
|
10.3
|
1.0
|
|
PB
|
B:TD6601
|
3.3
|
8.8
|
1.0
|
|
O3A
|
B:TD6601
|
3.4
|
8.3
|
1.0
|
|
ND2
|
B:ASN469
|
3.5
|
8.2
|
1.0
|
|
OD2
|
B:ASP442
|
3.6
|
9.7
|
1.0
|
|
N
|
B:ASP442
|
3.9
|
8.7
|
1.0
|
|
N
|
B:GLY471
|
4.1
|
8.0
|
1.0
|
|
CA
|
B:GLY472
|
4.2
|
11.0
|
1.0
|
|
N
|
B:GLY472
|
4.2
|
8.4
|
1.0
|
|
O7
|
B:TD6601
|
4.2
|
8.4
|
1.0
|
|
N
|
B:GLN473
|
4.2
|
10.4
|
1.0
|
|
O
|
B:HOH884
|
4.2
|
11.4
|
1.0
|
|
N
|
B:ASN469
|
4.2
|
9.4
|
1.0
|
|
CA
|
B:GLY471
|
4.3
|
8.8
|
1.0
|
|
O2B
|
B:TD6601
|
4.3
|
10.6
|
1.0
|
|
O1B
|
B:TD6601
|
4.3
|
10.2
|
1.0
|
|
O
|
B:VAL467
|
4.4
|
8.0
|
1.0
|
|
CB
|
B:ASP442
|
4.4
|
8.9
|
1.0
|
|
O2A
|
B:TD6601
|
4.4
|
7.8
|
1.0
|
|
CB
|
B:ASN469
|
4.4
|
9.1
|
1.0
|
|
N
|
B:LEU443
|
4.5
|
7.2
|
1.0
|
|
C
|
B:ASN469
|
4.6
|
9.9
|
1.0
|
|
N
|
B:ASN470
|
4.6
|
8.2
|
1.0
|
|
CA
|
B:ASP442
|
4.6
|
6.8
|
1.0
|
|
CA
|
B:GLY441
|
4.6
|
8.7
|
1.0
|
|
CA
|
B:ASN469
|
4.6
|
8.5
|
1.0
|
|
C
|
B:GLY441
|
4.7
|
9.6
|
1.0
|
|
C
|
B:GLY472
|
4.7
|
10.4
|
1.0
|
|
CG
|
B:GLN473
|
4.8
|
11.4
|
1.0
|
|
C
|
B:ASN470
|
5.0
|
9.9
|
1.0
|
|
O
|
B:ASN469
|
5.0
|
10.7
|
1.0
|
|
Manganese binding site 3 out
of 9 in 5ej7
Go back to
Manganese Binding Sites List in 5ej7
Manganese binding site 3 out
of 9 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
 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 Soaked with 2-Ketoglutarate For 21 S within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn602
b:15.5
occ:1.00
|
OD1
|
C:ASP442
|
2.1
|
9.9
|
1.0
|
|
O
|
C:GLY471
|
2.1
|
11.0
|
1.0
|
|
OD1
|
C:ASN469
|
2.1
|
8.8
|
1.0
|
|
O1A
|
C:TD6601
|
2.1
|
7.5
|
1.0
|
|
O
|
C:HOH6206
|
2.1
|
8.9
|
1.0
|
|
O3B
|
C:TD6601
|
2.2
|
8.4
|
1.0
|
|
CG
|
C:ASN469
|
3.1
|
10.2
|
1.0
|
|
CG
|
C:ASP442
|
3.1
|
10.0
|
1.0
|
|
C
|
C:GLY471
|
3.3
|
10.8
|
1.0
|
|
PA
|
C:TD6601
|
3.3
|
8.1
|
1.0
|
|
PB
|
C:TD6601
|
3.3
|
8.4
|
1.0
|
|
O3A
|
C:TD6601
|
3.4
|
7.4
|
1.0
|
|
ND2
|
C:ASN469
|
3.5
|
11.7
|
1.0
|
|
OD2
|
C:ASP442
|
3.6
|
10.8
|
1.0
|
|
N
|
C:ASP442
|
3.8
|
7.5
|
1.0
|
|
N
|
C:GLY471
|
4.0
|
11.0
|
1.0
|
|
O7
|
C:TD6601
|
4.1
|
7.9
|
1.0
|
|
N
|
C:GLY472
|
4.1
|
8.2
|
1.0
|
|
CA
|
C:GLY472
|
4.2
|
9.8
|
1.0
|
|
N
|
C:GLN473
|
4.2
|
11.3
|
1.0
|
|
CA
|
C:GLY471
|
4.2
|
9.2
|
1.0
|
|
N
|
C:ASN469
|
4.2
|
10.9
|
1.0
|
|
O
|
C:HOH6263
|
4.3
|
13.2
|
1.0
|
|
O
|
C:VAL467
|
4.3
|
8.3
|
1.0
|
|
CB
|
C:ASP442
|
4.3
|
11.8
|
1.0
|
|
O2B
|
C:TD6601
|
4.3
|
9.1
|
1.0
|
|
O1B
|
C:TD6601
|
4.3
|
9.8
|
1.0
|
|
O2A
|
C:TD6601
|
4.4
|
8.6
|
1.0
|
|
CB
|
C:ASN469
|
4.4
|
10.2
|
1.0
|
|
N
|
C:LEU443
|
4.5
|
8.1
|
1.0
|
|
CA
|
C:ASP442
|
4.6
|
10.3
|
1.0
|
|
C
|
C:ASN469
|
4.6
|
8.8
|
1.0
|
|
CA
|
C:GLY441
|
4.6
|
8.7
|
1.0
|
|
N
|
C:ASN470
|
4.6
|
10.0
|
1.0
|
|
CA
|
C:ASN469
|
4.6
|
12.3
|
1.0
|
|
C
|
C:GLY441
|
4.7
|
7.7
|
1.0
|
|
C
|
C:GLY472
|
4.7
|
10.7
|
1.0
|
|
CG
|
C:GLN473
|
4.7
|
9.6
|
1.0
|
|
C
|
C:ASN470
|
5.0
|
15.2
|
1.0
|
|
Manganese binding site 4 out
of 9 in 5ej7
Go back to
Manganese Binding Sites List in 5ej7
Manganese binding site 4 out
of 9 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
 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 Soaked with 2-Ketoglutarate For 21 S within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn602
b:18.1
occ:1.00
|
OD1
|
D:ASN469
|
2.1
|
12.5
|
1.0
|
|
OD1
|
D:ASP442
|
2.1
|
12.5
|
1.0
|
|
O3B
|
D:TD6601
|
2.1
|
10.4
|
1.0
|
|
O1A
|
D:TD6601
|
2.1
|
9.7
|
1.0
|
|
O
|
D:GLY471
|
2.1
|
11.9
|
1.0
|
|
O
|
D:HOH864
|
2.2
|
11.2
|
1.0
|
|
CG
|
D:ASN469
|
3.1
|
12.9
|
1.0
|
|
CG
|
D:ASP442
|
3.1
|
13.7
|
1.0
|
|
PA
|
D:TD6601
|
3.3
|
10.6
|
1.0
|
|
PB
|
D:TD6601
|
3.3
|
10.7
|
1.0
|
|
C
|
D:GLY471
|
3.3
|
12.3
|
1.0
|
|
O3A
|
D:TD6601
|
3.5
|
10.6
|
1.0
|
|
ND2
|
D:ASN469
|
3.5
|
12.9
|
1.0
|
|
OD2
|
D:ASP442
|
3.6
|
13.3
|
1.0
|
|
N
|
D:ASP442
|
3.8
|
11.0
|
1.0
|
|
N
|
D:GLY471
|
4.1
|
12.3
|
1.0
|
|
O7
|
D:TD6601
|
4.2
|
10.4
|
1.0
|
|
N
|
D:GLN473
|
4.2
|
12.4
|
1.0
|
|
N
|
D:GLY472
|
4.2
|
11.8
|
1.0
|
|
CA
|
D:GLY472
|
4.2
|
11.7
|
1.0
|
|
O
|
D:HOH792
|
4.2
|
15.3
|
1.0
|
|
N
|
D:ASN469
|
4.2
|
15.4
|
1.0
|
|
O
|
D:VAL467
|
4.2
|
13.2
|
1.0
|
|
O2B
|
D:TD6601
|
4.3
|
11.4
|
1.0
|
|
CA
|
D:GLY471
|
4.3
|
13.2
|
1.0
|
|
O1B
|
D:TD6601
|
4.3
|
11.4
|
1.0
|
|
CB
|
D:ASP442
|
4.3
|
12.1
|
1.0
|
|
CB
|
D:ASN469
|
4.4
|
13.4
|
1.0
|
|
O2A
|
D:TD6601
|
4.4
|
10.3
|
1.0
|
|
N
|
D:LEU443
|
4.5
|
10.5
|
1.0
|
|
C
|
D:ASN469
|
4.6
|
14.0
|
1.0
|
|
CA
|
D:GLY441
|
4.6
|
11.7
|
1.0
|
|
CA
|
D:ASP442
|
4.6
|
10.9
|
1.0
|
|
N
|
D:ASN470
|
4.6
|
12.9
|
1.0
|
|
CA
|
D:ASN469
|
4.6
|
14.0
|
1.0
|
|
C
|
D:GLY441
|
4.6
|
13.5
|
1.0
|
|
CG
|
D:GLN473
|
4.7
|
15.2
|
1.0
|
|
C
|
D:GLY472
|
4.8
|
12.7
|
1.0
|
|
O
|
D:ASN469
|
5.0
|
13.5
|
1.0
|
|
Manganese binding site 5 out
of 9 in 5ej7
Go back to
Manganese Binding Sites List in 5ej7
Manganese binding site 5 out
of 9 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
 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 Soaked with 2-Ketoglutarate For 21 S within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn602
b:13.4
occ:1.00
|
OD1
|
E:ASN469
|
2.1
|
7.4
|
1.0
|
|
O
|
E:GLY471
|
2.1
|
7.1
|
1.0
|
|
O1A
|
E:TD6601
|
2.1
|
6.3
|
1.0
|
|
OD1
|
E:ASP442
|
2.1
|
7.2
|
1.0
|
|
O3B
|
E:TD6601
|
2.2
|
7.2
|
1.0
|
|
O
|
E:HOH843
|
2.2
|
7.9
|
1.0
|
|
CG
|
E:ASN469
|
3.1
|
7.1
|
1.0
|
|
CG
|
E:ASP442
|
3.1
|
9.5
|
1.0
|
|
PA
|
E:TD6601
|
3.3
|
7.1
|
1.0
|
|
C
|
E:GLY471
|
3.3
|
8.3
|
1.0
|
|
PB
|
E:TD6601
|
3.4
|
7.3
|
1.0
|
|
O3A
|
E:TD6601
|
3.4
|
6.8
|
1.0
|
|
ND2
|
E:ASN469
|
3.5
|
7.7
|
1.0
|
|
OD2
|
E:ASP442
|
3.6
|
9.8
|
1.0
|
|
N
|
E:ASP442
|
3.9
|
6.8
|
1.0
|
|
N
|
E:GLY471
|
4.0
|
9.2
|
1.0
|
|
CA
|
E:GLY472
|
4.1
|
6.9
|
1.0
|
|
N
|
E:GLY472
|
4.1
|
7.8
|
1.0
|
|
N
|
E:GLN473
|
4.1
|
7.0
|
1.0
|
|
O7
|
E:TD6601
|
4.2
|
8.6
|
1.0
|
|
N
|
E:ASN469
|
4.2
|
7.3
|
1.0
|
|
O
|
E:VAL467
|
4.3
|
9.3
|
1.0
|
|
CA
|
E:GLY471
|
4.3
|
11.6
|
1.0
|
|
O
|
E:HOH787
|
4.3
|
14.2
|
1.0
|
|
O2B
|
E:TD6601
|
4.3
|
8.5
|
1.0
|
|
CB
|
E:ASP442
|
4.4
|
8.8
|
1.0
|
|
O1B
|
E:TD6601
|
4.4
|
9.1
|
1.0
|
|
CB
|
E:ASN469
|
4.4
|
9.3
|
1.0
|
|
O2A
|
E:TD6601
|
4.4
|
7.0
|
1.0
|
|
N
|
E:LEU443
|
4.5
|
5.9
|
1.0
|
|
C
|
E:ASN469
|
4.6
|
8.1
|
1.0
|
|
N
|
E:ASN470
|
4.6
|
8.1
|
1.0
|
|
CA
|
E:ASN469
|
4.6
|
7.5
|
1.0
|
|
CA
|
E:GLY441
|
4.6
|
7.4
|
1.0
|
|
CA
|
E:ASP442
|
4.6
|
7.1
|
1.0
|
|
C
|
E:GLY441
|
4.7
|
10.2
|
1.0
|
|
C
|
E:GLY472
|
4.7
|
8.1
|
1.0
|
|
CG
|
E:GLN473
|
4.7
|
9.0
|
1.0
|
|
C
|
E:ASN470
|
5.0
|
11.9
|
1.0
|
|
CG
|
E:LEU443
|
5.0
|
7.9
|
1.0
|
|
Manganese binding site 6 out
of 9 in 5ej7
Go back to
Manganese Binding Sites List in 5ej7
Manganese binding site 6 out
of 9 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
 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 Soaked with 2-Ketoglutarate For 21 S within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn602
b:13.8
occ:1.00
|
OD1
|
F:ASN469
|
2.0
|
8.2
|
1.0
|
|
O
|
F:GLY471
|
2.1
|
9.2
|
1.0
|
|
OD1
|
F:ASP442
|
2.1
|
8.4
|
1.0
|
|
O3B
|
F:TD6601
|
2.1
|
8.2
|
1.0
|
|
O1A
|
F:TD6601
|
2.1
|
8.1
|
1.0
|
|
O
|
F:HOH744
|
2.2
|
8.4
|
1.0
|
|
CG
|
F:ASN469
|
3.0
|
8.4
|
1.0
|
|
CG
|
F:ASP442
|
3.1
|
11.2
|
1.0
|
|
C
|
F:GLY471
|
3.3
|
11.0
|
1.0
|
|
PA
|
F:TD6601
|
3.3
|
7.9
|
1.0
|
|
PB
|
F:TD6601
|
3.3
|
8.5
|
1.0
|
|
ND2
|
F:ASN469
|
3.4
|
8.3
|
1.0
|
|
O3A
|
F:TD6601
|
3.5
|
7.8
|
1.0
|
|
OD2
|
F:ASP442
|
3.6
|
11.9
|
1.0
|
|
N
|
F:ASP442
|
3.9
|
8.8
|
1.0
|
|
N
|
F:GLY471
|
4.0
|
10.4
|
1.0
|
|
N
|
F:GLY472
|
4.1
|
7.9
|
1.0
|
|
CA
|
F:GLY472
|
4.2
|
9.4
|
1.0
|
|
N
|
F:GLN473
|
4.2
|
8.2
|
1.0
|
|
O7
|
F:TD6601
|
4.2
|
8.3
|
1.0
|
|
N
|
F:ASN469
|
4.2
|
9.3
|
1.0
|
|
CA
|
F:GLY471
|
4.3
|
10.0
|
1.0
|
|
O
|
F:HOH830
|
4.3
|
11.8
|
1.0
|
|
O
|
F:VAL467
|
4.3
|
8.2
|
1.0
|
|
O2B
|
F:TD6601
|
4.3
|
9.0
|
1.0
|
|
O1B
|
F:TD6601
|
4.3
|
9.0
|
1.0
|
|
CB
|
F:ASP442
|
4.4
|
8.1
|
1.0
|
|
CB
|
F:ASN469
|
4.4
|
10.0
|
1.0
|
|
O2A
|
F:TD6601
|
4.4
|
8.8
|
1.0
|
|
N
|
F:LEU443
|
4.6
|
8.6
|
1.0
|
|
C
|
F:ASN469
|
4.6
|
8.7
|
1.0
|
|
CA
|
F:GLY441
|
4.6
|
7.9
|
1.0
|
|
N
|
F:ASN470
|
4.6
|
8.4
|
1.0
|
|
CA
|
F:ASP442
|
4.6
|
7.5
|
1.0
|
|
CA
|
F:ASN469
|
4.6
|
8.8
|
1.0
|
|
C
|
F:GLY441
|
4.7
|
12.3
|
1.0
|
|
C
|
F:GLY472
|
4.7
|
10.3
|
1.0
|
|
CG
|
F:GLN473
|
4.8
|
11.7
|
1.0
|
|
C
|
F:ASN470
|
5.0
|
11.1
|
1.0
|
|
Manganese binding site 7 out
of 9 in 5ej7
Go back to
Manganese Binding Sites List in 5ej7
Manganese binding site 7 out
of 9 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
 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 Soaked with 2-Ketoglutarate For 21 S within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn602
b:15.7
occ:1.00
|
O
|
G:GLY471
|
2.1
|
11.5
|
1.0
|
|
O1A
|
G:TD6601
|
2.1
|
9.3
|
1.0
|
|
OD1
|
G:ASN469
|
2.1
|
9.1
|
1.0
|
|
OD1
|
G:ASP442
|
2.1
|
8.9
|
1.0
|
|
O3B
|
G:TD6601
|
2.1
|
9.6
|
1.0
|
|
O
|
G:HOH832
|
2.2
|
9.1
|
1.0
|
|
CG
|
G:ASN469
|
3.1
|
10.9
|
1.0
|
|
CG
|
G:ASP442
|
3.1
|
13.5
|
1.0
|
|
C
|
G:GLY471
|
3.3
|
9.0
|
1.0
|
|
PA
|
G:TD6601
|
3.3
|
9.8
|
1.0
|
|
PB
|
G:TD6601
|
3.3
|
8.6
|
1.0
|
|
O3A
|
G:TD6601
|
3.4
|
8.3
|
1.0
|
|
ND2
|
G:ASN469
|
3.5
|
10.9
|
1.0
|
|
OD2
|
G:ASP442
|
3.6
|
11.4
|
1.0
|
|
N
|
G:ASP442
|
3.8
|
10.4
|
1.0
|
|
N
|
G:GLY471
|
4.0
|
12.3
|
1.0
|
|
N
|
G:GLY472
|
4.1
|
8.9
|
1.0
|
|
N
|
G:GLN473
|
4.1
|
9.5
|
1.0
|
|
CA
|
G:GLY472
|
4.2
|
8.8
|
1.0
|
|
O7
|
G:TD6601
|
4.2
|
8.8
|
1.0
|
|
CA
|
G:GLY471
|
4.2
|
11.1
|
1.0
|
|
N
|
G:ASN469
|
4.3
|
10.1
|
1.0
|
|
O
|
G:VAL467
|
4.3
|
9.8
|
1.0
|
|
O2B
|
G:TD6601
|
4.3
|
8.2
|
1.0
|
|
O1B
|
G:TD6601
|
4.3
|
10.3
|
1.0
|
|
O
|
G:HOH789
|
4.3
|
12.9
|
1.0
|
|
CB
|
G:ASP442
|
4.3
|
9.5
|
1.0
|
|
O2A
|
G:TD6601
|
4.4
|
10.0
|
1.0
|
|
CB
|
G:ASN469
|
4.4
|
9.6
|
1.0
|
|
N
|
G:LEU443
|
4.5
|
9.8
|
1.0
|
|
C
|
G:ASN469
|
4.6
|
13.6
|
1.0
|
|
CA
|
G:ASP442
|
4.6
|
12.3
|
1.0
|
|
N
|
G:ASN470
|
4.6
|
10.1
|
1.0
|
|
CA
|
G:GLY441
|
4.6
|
8.3
|
1.0
|
|
CG
|
G:GLN473
|
4.6
|
11.4
|
1.0
|
|
CA
|
G:ASN469
|
4.7
|
13.7
|
1.0
|
|
C
|
G:GLY441
|
4.7
|
10.9
|
1.0
|
|
C
|
G:GLY472
|
4.7
|
12.5
|
1.0
|
|
C
|
G:ASN470
|
4.9
|
17.0
|
1.0
|
|
O
|
G:ASN469
|
5.0
|
12.1
|
1.0
|
|
CB
|
G:GLN473
|
5.0
|
12.7
|
1.0
|
|
Manganese binding site 8 out
of 9 in 5ej7
Go back to
Manganese Binding Sites List in 5ej7
Manganese binding site 8 out
of 9 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
 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 Soaked with 2-Ketoglutarate For 21 S within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn605
b:36.5
occ:1.00
|
OE1
|
G:GLU354
|
2.1
|
15.3
|
1.0
|
|
CD
|
G:GLU354
|
3.1
|
20.2
|
1.0
|
|
OE2
|
G:GLU354
|
3.5
|
20.1
|
1.0
|
|
NE2
|
G:GLN358
|
4.1
|
14.5
|
1.0
|
|
O
|
G:HOH1043
|
4.1
|
19.7
|
1.0
|
|
O
|
G:HOH1246
|
4.3
|
31.6
|
1.0
|
|
CG
|
G:GLU354
|
4.4
|
13.9
|
1.0
|
|
Manganese binding site 9 out
of 9 in 5ej7
Go back to
Manganese Binding Sites List in 5ej7
Manganese binding site 9 out
of 9 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 9 of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 21 S within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mn602
b:16.3
occ:1.00
|
O
|
H:GLY471
|
2.1
|
10.8
|
1.0
|
|
OD1
|
H:ASP442
|
2.1
|
10.7
|
1.0
|
|
OD1
|
H:ASN469
|
2.1
|
11.3
|
1.0
|
|
O
|
H:HOH815
|
2.1
|
11.5
|
1.0
|
|
O3B
|
H:TD6601
|
2.1
|
8.5
|
1.0
|
|
O1A
|
H:TD6601
|
2.2
|
9.2
|
1.0
|
|
CG
|
H:ASN469
|
3.1
|
11.6
|
1.0
|
|
CG
|
H:ASP442
|
3.1
|
10.6
|
1.0
|
|
C
|
H:GLY471
|
3.2
|
23.1
|
1.0
|
|
PA
|
H:TD6601
|
3.3
|
10.5
|
1.0
|
|
PB
|
H:TD6601
|
3.4
|
9.9
|
1.0
|
|
O3A
|
H:TD6601
|
3.5
|
9.2
|
1.0
|
|
ND2
|
H:ASN469
|
3.5
|
12.3
|
1.0
|
|
OD2
|
H:ASP442
|
3.6
|
14.5
|
1.0
|
|
N
|
H:ASP442
|
3.8
|
10.0
|
1.0
|
|
N
|
H:GLY471
|
4.0
|
11.4
|
1.0
|
|
O7
|
H:TD6601
|
4.1
|
10.9
|
1.0
|
|
N
|
H:GLY472
|
4.1
|
11.6
|
1.0
|
|
CA
|
H:GLY472
|
4.1
|
10.6
|
1.0
|
|
CA
|
H:GLY471
|
4.2
|
11.1
|
1.0
|
|
O2B
|
H:TD6601
|
4.2
|
11.2
|
1.0
|
|
N
|
H:GLN473
|
4.2
|
11.2
|
1.0
|
|
N
|
H:ASN469
|
4.3
|
11.7
|
1.0
|
|
O
|
H:HOH826
|
4.3
|
14.6
|
1.0
|
|
O
|
H:VAL467
|
4.3
|
13.2
|
1.0
|
|
O1B
|
H:TD6601
|
4.3
|
10.6
|
1.0
|
|
O2A
|
H:TD6601
|
4.3
|
10.2
|
1.0
|
|
CB
|
H:ASP442
|
4.3
|
12.3
|
1.0
|
|
CB
|
H:ASN469
|
4.4
|
13.1
|
1.0
|
|
N
|
H:LEU443
|
4.5
|
9.7
|
1.0
|
|
CA
|
H:ASP442
|
4.6
|
11.3
|
1.0
|
|
C
|
H:ASN469
|
4.6
|
14.3
|
1.0
|
|
N
|
H:ASN470
|
4.6
|
11.8
|
1.0
|
|
CA
|
H:GLY441
|
4.6
|
11.3
|
1.0
|
|
CA
|
H:ASN469
|
4.7
|
15.7
|
1.0
|
|
C
|
H:GLY441
|
4.7
|
12.7
|
1.0
|
|
C
|
H:GLY472
|
4.8
|
11.0
|
1.0
|
|
CG
|
H:GLN473
|
4.8
|
16.1
|
1.0
|
|
C
|
H:ASN470
|
4.9
|
16.6
|
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
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