Manganese in PDB 5ej5: Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
Enzymatic activity of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
All present enzymatic activity of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H:
2.2.1.9;
Protein crystallography data
The structure of Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H, PDB code: 5ej5
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)
|
33.76 /
2.30
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.760,
90.800,
170.100,
75.79,
83.29,
64.34
|
|
R / Rfree (%)
|
18.3 /
23.4
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
(pdb code 5ej5). 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 Soaked with 2-Ketoglutarate For 1.5 H, PDB code: 5ej5:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 5ej5
Go back to
Manganese Binding Sites List in 5ej5
Manganese binding site 1 out
of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
 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 1.5 H within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn602
b:34.7
occ:1.00
|
OD1
|
A:ASN469
|
2.1
|
22.0
|
1.0
|
|
O
|
A:GLY471
|
2.1
|
21.3
|
1.0
|
|
OD1
|
A:ASP442
|
2.1
|
21.9
|
1.0
|
|
O1B
|
A:TD6601
|
2.2
|
23.5
|
1.0
|
|
O2A
|
A:TD6601
|
2.2
|
22.6
|
1.0
|
|
O
|
A:HOH748
|
2.4
|
14.3
|
1.0
|
|
CG
|
A:ASN469
|
3.0
|
20.1
|
1.0
|
|
CG
|
A:ASP442
|
3.2
|
25.5
|
1.0
|
|
C
|
A:GLY471
|
3.2
|
21.5
|
1.0
|
|
PA
|
A:TD6601
|
3.2
|
25.1
|
1.0
|
|
PB
|
A:TD6601
|
3.3
|
19.6
|
1.0
|
|
O3A
|
A:TD6601
|
3.3
|
16.9
|
1.0
|
|
ND2
|
A:ASN469
|
3.4
|
19.1
|
1.0
|
|
OD2
|
A:ASP442
|
3.7
|
26.8
|
1.0
|
|
N
|
A:ASP442
|
3.8
|
22.7
|
1.0
|
|
N
|
A:GLY471
|
4.0
|
25.4
|
1.0
|
|
CA
|
A:GLY472
|
4.1
|
16.9
|
1.0
|
|
N
|
A:GLY472
|
4.1
|
20.1
|
1.0
|
|
N
|
A:GLN473
|
4.1
|
22.3
|
1.0
|
|
O3B
|
A:TD6601
|
4.1
|
22.1
|
1.0
|
|
O7
|
A:TD6601
|
4.1
|
29.9
|
1.0
|
|
CA
|
A:GLY471
|
4.2
|
20.4
|
1.0
|
|
N
|
A:ASN469
|
4.3
|
21.5
|
1.0
|
|
O2B
|
A:TD6601
|
4.3
|
16.8
|
1.0
|
|
O
|
A:HOH719
|
4.4
|
18.6
|
1.0
|
|
O
|
A:VAL467
|
4.4
|
19.5
|
1.0
|
|
CB
|
A:ASP442
|
4.4
|
17.5
|
1.0
|
|
O1A
|
A:TD6601
|
4.4
|
16.9
|
1.0
|
|
CB
|
A:ASN469
|
4.4
|
17.2
|
1.0
|
|
CA
|
A:GLY441
|
4.5
|
19.5
|
1.0
|
|
N
|
A:LEU443
|
4.5
|
16.9
|
1.0
|
|
CA
|
A:ASP442
|
4.6
|
21.5
|
1.0
|
|
C
|
A:GLY441
|
4.6
|
22.8
|
1.0
|
|
C
|
A:GLY472
|
4.6
|
23.4
|
1.0
|
|
C
|
A:ASN469
|
4.7
|
23.7
|
1.0
|
|
N
|
A:ASN470
|
4.7
|
19.9
|
1.0
|
|
CA
|
A:ASN469
|
4.7
|
22.4
|
1.0
|
|
CG
|
A:GLN473
|
4.8
|
23.2
|
1.0
|
|
C
|
A:ASN470
|
5.0
|
28.0
|
1.0
|
|
Manganese binding site 2 out
of 8 in 5ej5
Go back to
Manganese Binding Sites List in 5ej5
Manganese binding site 2 out
of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
 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 1.5 H within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn602
b:31.8
occ:1.00
|
OD1
|
B:ASP442
|
2.1
|
18.9
|
1.0
|
|
O
|
B:GLY471
|
2.1
|
19.6
|
1.0
|
|
OD1
|
B:ASN469
|
2.1
|
21.7
|
1.0
|
|
O
|
B:HOH749
|
2.3
|
16.6
|
1.0
|
|
O2A
|
B:TD6601
|
2.4
|
20.5
|
1.0
|
|
O1B
|
B:TD6601
|
2.4
|
22.4
|
1.0
|
|
CG
|
B:ASP442
|
3.1
|
18.4
|
1.0
|
|
CG
|
B:ASN469
|
3.1
|
25.2
|
1.0
|
|
C
|
B:GLY471
|
3.3
|
19.9
|
1.0
|
|
PA
|
B:TD6601
|
3.3
|
20.5
|
1.0
|
|
O3A
|
B:TD6601
|
3.3
|
28.5
|
1.0
|
|
PB
|
B:TD6601
|
3.4
|
17.8
|
1.0
|
|
ND2
|
B:ASN469
|
3.5
|
23.8
|
1.0
|
|
OD2
|
B:ASP442
|
3.6
|
23.3
|
1.0
|
|
N
|
B:ASP442
|
3.8
|
19.2
|
1.0
|
|
N
|
B:GLY471
|
4.0
|
19.6
|
1.0
|
|
O7
|
B:TD6601
|
4.1
|
29.5
|
1.0
|
|
N
|
B:GLY472
|
4.2
|
17.3
|
1.0
|
|
N
|
B:ASN469
|
4.2
|
18.9
|
1.0
|
|
O
|
B:VAL467
|
4.2
|
20.7
|
1.0
|
|
CA
|
B:GLY472
|
4.2
|
18.7
|
1.0
|
|
O
|
B:HOH828
|
4.3
|
37.0
|
1.0
|
|
CA
|
B:GLY471
|
4.3
|
19.0
|
1.0
|
|
CB
|
B:ASP442
|
4.3
|
17.6
|
1.0
|
|
O2B
|
B:TD6601
|
4.3
|
26.7
|
1.0
|
|
N
|
B:GLN473
|
4.4
|
21.5
|
1.0
|
|
CB
|
B:ASN469
|
4.4
|
22.2
|
1.0
|
|
N
|
B:LEU443
|
4.5
|
18.7
|
1.0
|
|
CA
|
B:GLY441
|
4.5
|
18.7
|
1.0
|
|
CA
|
B:ASP442
|
4.6
|
17.0
|
1.0
|
|
O1A
|
B:TD6601
|
4.6
|
18.4
|
1.0
|
|
N
|
B:ASN470
|
4.6
|
17.8
|
1.0
|
|
C
|
B:GLY441
|
4.6
|
18.4
|
1.0
|
|
C
|
B:ASN469
|
4.6
|
27.6
|
1.0
|
|
O3B
|
B:TD6601
|
4.6
|
18.4
|
1.0
|
|
CA
|
B:ASN469
|
4.6
|
25.5
|
1.0
|
|
CG
|
B:GLN473
|
4.8
|
24.0
|
1.0
|
|
C
|
B:GLY472
|
4.9
|
25.2
|
1.0
|
|
CG
|
B:LEU443
|
4.9
|
16.9
|
1.0
|
|
C
|
B:ASN470
|
4.9
|
23.6
|
1.0
|
|
Manganese binding site 3 out
of 8 in 5ej5
Go back to
Manganese Binding Sites List in 5ej5
Manganese binding site 3 out
of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
 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 1.5 H within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn602
b:39.2
occ:1.00
|
OD1
|
C:ASN469
|
2.0
|
24.1
|
1.0
|
|
O
|
C:GLY471
|
2.1
|
26.2
|
1.0
|
|
OD1
|
C:ASP442
|
2.2
|
23.4
|
1.0
|
|
O1B
|
C:TD6601
|
2.2
|
16.3
|
1.0
|
|
O2A
|
C:TD6601
|
2.4
|
17.2
|
1.0
|
|
O
|
C:HOH791
|
2.5
|
21.5
|
1.0
|
|
CG
|
C:ASN469
|
2.9
|
25.0
|
1.0
|
|
CG
|
C:ASP442
|
3.2
|
24.3
|
1.0
|
|
C
|
C:GLY471
|
3.2
|
21.3
|
1.0
|
|
ND2
|
C:ASN469
|
3.3
|
27.1
|
1.0
|
|
PB
|
C:TD6601
|
3.3
|
17.9
|
1.0
|
|
O3A
|
C:TD6601
|
3.3
|
13.6
|
1.0
|
|
PA
|
C:TD6601
|
3.3
|
16.6
|
1.0
|
|
OD2
|
C:ASP442
|
3.6
|
22.4
|
1.0
|
|
CA
|
C:GLY472
|
4.0
|
18.7
|
1.0
|
|
N
|
C:ASP442
|
4.0
|
15.9
|
1.0
|
|
N
|
C:GLY472
|
4.0
|
20.4
|
1.0
|
|
N
|
C:GLN473
|
4.0
|
28.3
|
1.0
|
|
N
|
C:GLY471
|
4.0
|
33.1
|
1.0
|
|
O7
|
C:TD6601
|
4.1
|
27.4
|
1.0
|
|
CA
|
C:GLY471
|
4.2
|
28.2
|
1.0
|
|
O2B
|
C:TD6601
|
4.2
|
21.0
|
1.0
|
|
N
|
C:ASN469
|
4.3
|
28.2
|
1.0
|
|
CB
|
C:ASN469
|
4.3
|
26.8
|
1.0
|
|
O
|
C:HOH767
|
4.3
|
22.3
|
1.0
|
|
O3B
|
C:TD6601
|
4.4
|
17.7
|
1.0
|
|
O
|
C:VAL467
|
4.4
|
24.4
|
1.0
|
|
CB
|
C:ASP442
|
4.5
|
17.3
|
1.0
|
|
C
|
C:GLY472
|
4.6
|
31.0
|
1.0
|
|
CG
|
C:GLN473
|
4.6
|
29.6
|
1.0
|
|
C
|
C:ASN469
|
4.6
|
26.8
|
1.0
|
|
CA
|
C:ASN469
|
4.6
|
26.6
|
1.0
|
|
O1A
|
C:TD6601
|
4.6
|
20.7
|
1.0
|
|
N
|
C:ASN470
|
4.6
|
19.4
|
1.0
|
|
CA
|
C:GLY441
|
4.7
|
20.6
|
1.0
|
|
N
|
C:LEU443
|
4.7
|
16.8
|
1.0
|
|
CA
|
C:ASP442
|
4.8
|
22.3
|
1.0
|
|
C
|
C:GLY441
|
4.8
|
19.3
|
1.0
|
|
CB
|
C:GLN473
|
4.9
|
29.6
|
1.0
|
|
C
|
C:ASN470
|
5.0
|
26.4
|
1.0
|
|
Manganese binding site 4 out
of 8 in 5ej5
Go back to
Manganese Binding Sites List in 5ej5
Manganese binding site 4 out
of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
 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 1.5 H within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn602
b:34.4
occ:1.00
|
OD1
|
D:ASP442
|
2.0
|
26.5
|
1.0
|
|
O
|
D:GLY471
|
2.2
|
24.7
|
1.0
|
|
O1B
|
D:TD6601
|
2.2
|
22.2
|
1.0
|
|
OD1
|
D:ASN469
|
2.2
|
29.6
|
1.0
|
|
O
|
D:HOH710
|
2.3
|
24.5
|
1.0
|
|
O2A
|
D:TD6601
|
2.3
|
24.8
|
1.0
|
|
CG
|
D:ASP442
|
3.0
|
26.3
|
1.0
|
|
CG
|
D:ASN469
|
3.3
|
30.4
|
1.0
|
|
C
|
D:GLY471
|
3.4
|
16.5
|
1.0
|
|
PA
|
D:TD6601
|
3.4
|
24.1
|
1.0
|
|
PB
|
D:TD6601
|
3.4
|
20.5
|
1.0
|
|
OD2
|
D:ASP442
|
3.5
|
25.8
|
1.0
|
|
O3A
|
D:TD6601
|
3.6
|
19.1
|
1.0
|
|
ND2
|
D:ASN469
|
3.7
|
33.2
|
1.0
|
|
N
|
D:ASP442
|
3.8
|
21.8
|
1.0
|
|
N
|
D:GLY471
|
3.9
|
30.0
|
1.0
|
|
N
|
D:ASN469
|
4.1
|
27.7
|
1.0
|
|
O
|
D:HOH820
|
4.1
|
31.6
|
1.0
|
|
O
|
D:VAL467
|
4.1
|
24.7
|
1.0
|
|
CA
|
D:GLY471
|
4.2
|
26.1
|
1.0
|
|
O7
|
D:TD6601
|
4.2
|
23.1
|
1.0
|
|
CB
|
D:ASP442
|
4.3
|
17.6
|
1.0
|
|
N
|
D:GLY472
|
4.3
|
15.9
|
1.0
|
|
CA
|
D:GLY472
|
4.3
|
19.4
|
1.0
|
|
N
|
D:GLN473
|
4.4
|
26.3
|
1.0
|
|
O3B
|
D:TD6601
|
4.4
|
21.3
|
1.0
|
|
N
|
D:ASN470
|
4.4
|
26.7
|
1.0
|
|
CB
|
D:ASN469
|
4.5
|
33.3
|
1.0
|
|
C
|
D:ASN469
|
4.5
|
27.1
|
1.0
|
|
N
|
D:LEU443
|
4.5
|
17.5
|
1.0
|
|
O2B
|
D:TD6601
|
4.5
|
18.6
|
1.0
|
|
CA
|
D:ASP442
|
4.5
|
24.2
|
1.0
|
|
CA
|
D:ASN469
|
4.6
|
25.8
|
1.0
|
|
CA
|
D:GLY441
|
4.6
|
20.3
|
1.0
|
|
O1A
|
D:TD6601
|
4.6
|
21.0
|
1.0
|
|
C
|
D:GLY441
|
4.6
|
28.3
|
1.0
|
|
C
|
D:ASN470
|
4.8
|
27.9
|
1.0
|
|
CG
|
D:GLN473
|
4.8
|
31.4
|
1.0
|
|
C
|
D:GLY472
|
4.9
|
32.4
|
1.0
|
|
O
|
D:ASN469
|
5.0
|
26.0
|
1.0
|
|
Manganese binding site 5 out
of 8 in 5ej5
Go back to
Manganese Binding Sites List in 5ej5
Manganese binding site 5 out
of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
 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 1.5 H within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn602
b:30.4
occ:1.00
|
O
|
E:HOH745
|
1.9
|
15.0
|
1.0
|
|
O
|
E:GLY471
|
2.0
|
25.2
|
1.0
|
|
OD1
|
E:ASP442
|
2.1
|
22.7
|
1.0
|
|
O2A
|
E:TD6601
|
2.2
|
20.8
|
1.0
|
|
OD1
|
E:ASN469
|
2.2
|
15.5
|
1.0
|
|
O1B
|
E:TD6601
|
2.3
|
20.6
|
1.0
|
|
CG
|
E:ASP442
|
3.1
|
20.4
|
1.0
|
|
C
|
E:GLY471
|
3.2
|
20.8
|
1.0
|
|
CG
|
E:ASN469
|
3.3
|
20.7
|
1.0
|
|
PA
|
E:TD6601
|
3.3
|
21.5
|
1.0
|
|
PB
|
E:TD6601
|
3.4
|
23.2
|
1.0
|
|
O3A
|
E:TD6601
|
3.5
|
19.8
|
1.0
|
|
OD2
|
E:ASP442
|
3.6
|
21.3
|
1.0
|
|
ND2
|
E:ASN469
|
3.8
|
20.0
|
1.0
|
|
N
|
E:ASP442
|
3.8
|
18.2
|
1.0
|
|
N
|
E:GLY471
|
4.0
|
19.3
|
1.0
|
|
O
|
E:HOH835
|
4.0
|
20.5
|
1.0
|
|
N
|
E:GLN473
|
4.1
|
19.2
|
1.0
|
|
N
|
E:GLY472
|
4.1
|
19.3
|
1.0
|
|
CA
|
E:GLY472
|
4.1
|
21.9
|
1.0
|
|
O7
|
E:TD6601
|
4.2
|
25.7
|
1.0
|
|
CA
|
E:GLY471
|
4.2
|
20.5
|
1.0
|
|
N
|
E:ASN469
|
4.2
|
24.8
|
1.0
|
|
O
|
E:VAL467
|
4.3
|
24.3
|
1.0
|
|
CB
|
E:ASP442
|
4.3
|
18.4
|
1.0
|
|
O3B
|
E:TD6601
|
4.4
|
19.8
|
1.0
|
|
O2B
|
E:TD6601
|
4.4
|
22.6
|
1.0
|
|
O1A
|
E:TD6601
|
4.5
|
14.0
|
1.0
|
|
N
|
E:LEU443
|
4.5
|
19.7
|
1.0
|
|
CB
|
E:ASN469
|
4.6
|
21.2
|
1.0
|
|
CA
|
E:GLY441
|
4.6
|
20.8
|
1.0
|
|
N
|
E:ASN470
|
4.6
|
23.0
|
1.0
|
|
C
|
E:ASN469
|
4.6
|
20.4
|
1.0
|
|
CA
|
E:ASP442
|
4.6
|
21.2
|
1.0
|
|
C
|
E:GLY472
|
4.6
|
20.1
|
1.0
|
|
C
|
E:GLY441
|
4.6
|
22.3
|
1.0
|
|
CA
|
E:ASN469
|
4.7
|
20.4
|
1.0
|
|
CG
|
E:GLN473
|
4.7
|
23.3
|
1.0
|
|
C
|
E:ASN470
|
4.9
|
21.7
|
1.0
|
|
CB
|
E:GLN473
|
5.0
|
17.1
|
1.0
|
|
Manganese binding site 6 out
of 8 in 5ej5
Go back to
Manganese Binding Sites List in 5ej5
Manganese binding site 6 out
of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
 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 1.5 H within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn602
b:34.1
occ:1.00
|
O
|
F:GLY471
|
2.1
|
22.5
|
1.0
|
|
OD1
|
F:ASP442
|
2.1
|
14.8
|
1.0
|
|
OD1
|
F:ASN469
|
2.2
|
24.2
|
1.0
|
|
O1B
|
F:TD6601
|
2.3
|
23.4
|
1.0
|
|
O2A
|
F:TD6601
|
2.3
|
20.9
|
1.0
|
|
O
|
F:HOH720
|
2.6
|
19.4
|
1.0
|
|
CG
|
F:ASN469
|
3.1
|
24.6
|
1.0
|
|
CG
|
F:ASP442
|
3.3
|
16.2
|
1.0
|
|
C
|
F:GLY471
|
3.3
|
21.8
|
1.0
|
|
PA
|
F:TD6601
|
3.3
|
22.1
|
1.0
|
|
O3A
|
F:TD6601
|
3.3
|
26.2
|
1.0
|
|
PB
|
F:TD6601
|
3.3
|
22.4
|
1.0
|
|
ND2
|
F:ASN469
|
3.4
|
16.8
|
1.0
|
|
OD2
|
F:ASP442
|
3.8
|
15.9
|
1.0
|
|
N
|
F:ASP442
|
3.9
|
22.0
|
1.0
|
|
N
|
F:GLY471
|
3.9
|
17.3
|
1.0
|
|
O7
|
F:TD6601
|
4.1
|
29.4
|
1.0
|
|
CA
|
F:GLY471
|
4.2
|
19.4
|
1.0
|
|
N
|
F:GLN473
|
4.2
|
20.4
|
1.0
|
|
O
|
F:HOH778
|
4.2
|
16.9
|
1.0
|
|
N
|
F:GLY472
|
4.2
|
20.8
|
1.0
|
|
CA
|
F:GLY472
|
4.2
|
23.0
|
1.0
|
|
N
|
F:ASN469
|
4.3
|
21.9
|
1.0
|
|
O
|
F:VAL467
|
4.3
|
18.5
|
1.0
|
|
O3B
|
F:TD6601
|
4.3
|
29.2
|
1.0
|
|
O2B
|
F:TD6601
|
4.4
|
24.6
|
1.0
|
|
CB
|
F:ASN469
|
4.4
|
19.3
|
1.0
|
|
CB
|
F:ASP442
|
4.5
|
18.4
|
1.0
|
|
O1A
|
F:TD6601
|
4.6
|
15.6
|
1.0
|
|
CA
|
F:GLY441
|
4.6
|
14.6
|
1.0
|
|
N
|
F:LEU443
|
4.6
|
20.8
|
1.0
|
|
C
|
F:ASN469
|
4.6
|
18.5
|
1.0
|
|
CG
|
F:GLN473
|
4.7
|
12.3
|
1.0
|
|
N
|
F:ASN470
|
4.7
|
17.7
|
1.0
|
|
CA
|
F:ASN469
|
4.7
|
24.0
|
1.0
|
|
C
|
F:GLY441
|
4.7
|
20.1
|
1.0
|
|
CA
|
F:ASP442
|
4.7
|
23.3
|
1.0
|
|
C
|
F:GLY472
|
4.8
|
19.9
|
1.0
|
|
C
|
F:ASN470
|
4.9
|
19.1
|
1.0
|
|
CG
|
F:LEU443
|
5.0
|
19.9
|
1.0
|
|
CB
|
F:GLN473
|
5.0
|
19.1
|
1.0
|
|
Manganese binding site 7 out
of 8 in 5ej5
Go back to
Manganese Binding Sites List in 5ej5
Manganese binding site 7 out
of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
 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 1.5 H within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn602
b:34.8
occ:1.00
|
O2A
|
G:TD6601
|
2.0
|
26.4
|
1.0
|
|
O1B
|
G:TD6601
|
2.1
|
24.8
|
1.0
|
|
O
|
G:HOH794
|
2.1
|
23.7
|
1.0
|
|
OD1
|
G:ASN469
|
2.1
|
22.7
|
1.0
|
|
OD1
|
G:ASP442
|
2.3
|
24.8
|
1.0
|
|
O
|
G:GLY471
|
2.4
|
27.1
|
1.0
|
|
CG
|
G:ASN469
|
3.1
|
31.5
|
1.0
|
|
PA
|
G:TD6601
|
3.2
|
27.0
|
1.0
|
|
PB
|
G:TD6601
|
3.2
|
26.0
|
1.0
|
|
O3A
|
G:TD6601
|
3.3
|
21.8
|
1.0
|
|
CG
|
G:ASP442
|
3.4
|
25.8
|
1.0
|
|
ND2
|
G:ASN469
|
3.6
|
32.0
|
1.0
|
|
C
|
G:GLY471
|
3.6
|
26.6
|
1.0
|
|
N
|
G:ASP442
|
3.8
|
30.2
|
1.0
|
|
OD2
|
G:ASP442
|
4.0
|
25.3
|
1.0
|
|
N
|
G:GLN473
|
4.1
|
25.1
|
1.0
|
|
O
|
G:HOH755
|
4.1
|
28.0
|
1.0
|
|
O7
|
G:TD6601
|
4.1
|
28.1
|
1.0
|
|
CA
|
G:GLY472
|
4.2
|
23.7
|
1.0
|
|
O3B
|
G:TD6601
|
4.2
|
34.6
|
1.0
|
|
O
|
G:VAL467
|
4.2
|
24.9
|
1.0
|
|
N
|
G:ASN469
|
4.2
|
31.5
|
1.0
|
|
O1A
|
G:TD6601
|
4.3
|
21.6
|
1.0
|
|
O2B
|
G:TD6601
|
4.3
|
25.1
|
1.0
|
|
N
|
G:GLY472
|
4.3
|
31.0
|
1.0
|
|
CA
|
G:GLY441
|
4.4
|
23.7
|
1.0
|
|
N
|
G:GLY471
|
4.4
|
40.5
|
1.0
|
|
CB
|
G:ASN469
|
4.5
|
21.1
|
1.0
|
|
CB
|
G:ASP442
|
4.5
|
21.1
|
1.0
|
|
C
|
G:GLY441
|
4.6
|
26.9
|
1.0
|
|
N
|
G:LEU443
|
4.6
|
18.5
|
1.0
|
|
CA
|
G:GLY471
|
4.7
|
30.1
|
1.0
|
|
C
|
G:GLY472
|
4.7
|
25.9
|
1.0
|
|
CA
|
G:ASN469
|
4.7
|
22.2
|
1.0
|
|
CA
|
G:ASP442
|
4.7
|
26.8
|
1.0
|
|
C
|
G:ASN469
|
4.8
|
27.9
|
1.0
|
|
CG
|
G:GLN473
|
4.8
|
17.9
|
1.0
|
|
N
|
G:ASN470
|
4.8
|
21.7
|
1.0
|
|
Manganese binding site 8 out
of 8 in 5ej5
Go back to
Manganese Binding Sites List in 5ej5
Manganese binding site 8 out
of 8 in the Ecmend-Thdp-MN2+ Complex Soaked with 2-Ketoglutarate For 1.5 H
 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 1.5 H within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mn602
b:30.6
occ:1.00
|
O1B
|
H:TD6601
|
2.1
|
18.5
|
1.0
|
|
OD1
|
H:ASN469
|
2.1
|
26.0
|
1.0
|
|
O
|
H:GLY471
|
2.1
|
21.2
|
1.0
|
|
O2A
|
H:TD6601
|
2.2
|
16.3
|
1.0
|
|
OD1
|
H:ASP442
|
2.2
|
26.9
|
1.0
|
|
O
|
H:HOH818
|
2.4
|
18.0
|
1.0
|
|
CG
|
H:ASN469
|
3.1
|
27.4
|
1.0
|
|
CG
|
H:ASP442
|
3.1
|
22.6
|
1.0
|
|
C
|
H:GLY471
|
3.2
|
21.5
|
1.0
|
|
PA
|
H:TD6601
|
3.3
|
22.7
|
1.0
|
|
PB
|
H:TD6601
|
3.3
|
23.9
|
1.0
|
|
O3A
|
H:TD6601
|
3.5
|
18.5
|
1.0
|
|
ND2
|
H:ASN469
|
3.5
|
24.8
|
1.0
|
|
OD2
|
H:ASP442
|
3.6
|
26.0
|
1.0
|
|
N
|
H:ASP442
|
3.8
|
30.1
|
1.0
|
|
N
|
H:GLY471
|
4.0
|
28.1
|
1.0
|
|
O7
|
H:TD6601
|
4.0
|
26.5
|
1.0
|
|
CA
|
H:GLY472
|
4.1
|
20.0
|
1.0
|
|
N
|
H:GLY472
|
4.1
|
17.1
|
1.0
|
|
O
|
H:HOH808
|
4.1
|
22.3
|
1.0
|
|
N
|
H:GLN473
|
4.2
|
21.8
|
1.0
|
|
CA
|
H:GLY471
|
4.2
|
23.0
|
1.0
|
|
N
|
H:ASN469
|
4.2
|
20.7
|
1.0
|
|
O3B
|
H:TD6601
|
4.3
|
21.3
|
1.0
|
|
O2B
|
H:TD6601
|
4.3
|
27.3
|
1.0
|
|
O
|
H:VAL467
|
4.3
|
20.7
|
1.0
|
|
CB
|
H:ASP442
|
4.4
|
16.1
|
1.0
|
|
CB
|
H:ASN469
|
4.4
|
22.6
|
1.0
|
|
O1A
|
H:TD6601
|
4.5
|
21.2
|
1.0
|
|
N
|
H:LEU443
|
4.5
|
18.9
|
1.0
|
|
CA
|
H:GLY441
|
4.6
|
13.4
|
1.0
|
|
CA
|
H:ASP442
|
4.6
|
21.8
|
1.0
|
|
C
|
H:ASN469
|
4.6
|
19.0
|
1.0
|
|
N
|
H:ASN470
|
4.6
|
24.6
|
1.0
|
|
CA
|
H:ASN469
|
4.6
|
24.0
|
1.0
|
|
C
|
H:GLY441
|
4.7
|
22.7
|
1.0
|
|
C
|
H:GLY472
|
4.7
|
23.1
|
1.0
|
|
CG
|
H:GLN473
|
4.8
|
20.4
|
1.0
|
|
C
|
H:ASN470
|
5.0
|
27.1
|
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 00:01:08 2024
|
