Manganese in PDB 5ejm: Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
Enzymatic activity of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
All present enzymatic activity of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min:
2.2.1.9;
Protein crystallography data
The structure of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min, PDB code: 5ejm
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)
|
31.48 /
1.72
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.660,
90.670,
169.370,
76.07,
83.29,
64.32
|
|
R / Rfree (%)
|
16.4 /
19.2
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
(pdb code 5ejm). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min, PDB code: 5ejm:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 5ejm
Go back to
Manganese Binding Sites List in 5ejm
Manganese binding site 1 out
of 8 in the Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn602
b:22.6
occ:1.00
|
O1A
|
A:TD5601
|
2.1
|
16.6
|
1.0
|
|
OD1
|
A:ASN469
|
2.1
|
17.0
|
1.0
|
|
O
|
A:GLY471
|
2.1
|
15.0
|
1.0
|
|
O3B
|
A:TD5601
|
2.2
|
11.8
|
1.0
|
|
OD1
|
A:ASP442
|
2.2
|
15.8
|
1.0
|
|
O
|
A:HOH833
|
2.3
|
14.6
|
1.0
|
|
CG
|
A:ASN469
|
3.1
|
17.1
|
1.0
|
|
CG
|
A:ASP442
|
3.2
|
19.0
|
1.0
|
|
PA
|
A:TD5601
|
3.3
|
14.6
|
1.0
|
|
C
|
A:GLY471
|
3.3
|
15.0
|
1.0
|
|
PB
|
A:TD5601
|
3.3
|
15.3
|
1.0
|
|
O3A
|
A:TD5601
|
3.4
|
14.0
|
1.0
|
|
ND2
|
A:ASN469
|
3.5
|
16.4
|
1.0
|
|
OD2
|
A:ASP442
|
3.7
|
18.4
|
1.0
|
|
N
|
A:ASP442
|
3.9
|
11.2
|
1.0
|
|
N
|
A:GLY471
|
4.1
|
14.5
|
1.0
|
|
N
|
A:GLN473
|
4.1
|
16.1
|
1.0
|
|
CA
|
A:GLY472
|
4.2
|
14.9
|
1.0
|
|
N
|
A:GLY472
|
4.2
|
13.0
|
1.0
|
|
O7
|
A:TD5601
|
4.2
|
16.6
|
1.0
|
|
O
|
A:HOH851
|
4.2
|
16.6
|
1.0
|
|
N
|
A:ASN469
|
4.3
|
13.7
|
1.0
|
|
O2B
|
A:TD5601
|
4.3
|
18.1
|
1.0
|
|
CA
|
A:GLY471
|
4.3
|
16.9
|
1.0
|
|
O
|
A:VAL467
|
4.3
|
14.5
|
1.0
|
|
O2A
|
A:TD5601
|
4.4
|
13.8
|
1.0
|
|
O1B
|
A:TD5601
|
4.4
|
16.6
|
1.0
|
|
CB
|
A:ASN469
|
4.4
|
14.6
|
1.0
|
|
CB
|
A:ASP442
|
4.4
|
16.2
|
1.0
|
|
N
|
A:LEU443
|
4.6
|
15.3
|
1.0
|
|
C
|
A:ASN469
|
4.6
|
15.8
|
1.0
|
|
CA
|
A:GLY441
|
4.6
|
12.4
|
1.0
|
|
N
|
A:ASN470
|
4.6
|
15.4
|
1.0
|
|
CA
|
A:ASN469
|
4.7
|
14.0
|
1.0
|
|
CA
|
A:ASP442
|
4.7
|
11.3
|
1.0
|
|
C
|
A:GLY441
|
4.7
|
12.7
|
1.0
|
|
C
|
A:GLY472
|
4.7
|
15.7
|
1.0
|
|
CG
|
A:GLN473
|
4.7
|
18.5
|
1.0
|
|
CB
|
A:GLN473
|
5.0
|
16.7
|
1.0
|
|
Manganese binding site 2 out
of 8 in 5ejm
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Manganese Binding Sites List in 5ejm
Manganese binding site 2 out
of 8 in the Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn602
b:22.1
occ:1.00
|
OD1
|
B:ASP442
|
2.1
|
15.2
|
1.0
|
|
OD1
|
B:ASN469
|
2.1
|
19.6
|
1.0
|
|
O3B
|
B:TD5601
|
2.1
|
14.6
|
1.0
|
|
O1A
|
B:TD5601
|
2.2
|
14.8
|
1.0
|
|
O
|
B:HOH747
|
2.2
|
11.9
|
1.0
|
|
O
|
B:GLY471
|
2.2
|
17.2
|
1.0
|
|
CG
|
B:ASN469
|
3.1
|
17.9
|
1.0
|
|
CG
|
B:ASP442
|
3.1
|
15.7
|
1.0
|
|
PB
|
B:TD5601
|
3.3
|
15.8
|
1.0
|
|
PA
|
B:TD5601
|
3.3
|
14.4
|
1.0
|
|
C
|
B:GLY471
|
3.4
|
18.4
|
1.0
|
|
ND2
|
B:ASN469
|
3.4
|
17.2
|
1.0
|
|
O3A
|
B:TD5601
|
3.5
|
12.8
|
1.0
|
|
OD2
|
B:ASP442
|
3.7
|
16.8
|
1.0
|
|
N
|
B:ASP442
|
3.8
|
18.6
|
1.0
|
|
N
|
B:GLY471
|
4.1
|
15.3
|
1.0
|
|
N
|
B:GLN473
|
4.2
|
15.4
|
1.0
|
|
O7
|
B:TD5601
|
4.2
|
16.8
|
1.0
|
|
N
|
B:ASN469
|
4.2
|
14.9
|
1.0
|
|
CA
|
B:GLY472
|
4.2
|
16.6
|
1.0
|
|
N
|
B:GLY472
|
4.3
|
13.7
|
1.0
|
|
O
|
B:VAL467
|
4.3
|
14.2
|
1.0
|
|
O2B
|
B:TD5601
|
4.3
|
16.5
|
1.0
|
|
O
|
B:HOH743
|
4.3
|
15.9
|
1.0
|
|
CB
|
B:ASP442
|
4.3
|
16.9
|
1.0
|
|
CA
|
B:GLY471
|
4.3
|
17.9
|
1.0
|
|
O1B
|
B:TD5601
|
4.4
|
14.6
|
1.0
|
|
CB
|
B:ASN469
|
4.4
|
15.2
|
1.0
|
|
O2A
|
B:TD5601
|
4.4
|
11.7
|
1.0
|
|
N
|
B:LEU443
|
4.6
|
13.3
|
1.0
|
|
CA
|
B:GLY441
|
4.6
|
13.7
|
1.0
|
|
CA
|
B:ASP442
|
4.6
|
16.2
|
1.0
|
|
C
|
B:ASN469
|
4.6
|
15.0
|
1.0
|
|
N
|
B:ASN470
|
4.6
|
14.0
|
1.0
|
|
C
|
B:GLY441
|
4.7
|
15.9
|
1.0
|
|
CA
|
B:ASN469
|
4.7
|
15.3
|
1.0
|
|
CG
|
B:GLN473
|
4.7
|
15.4
|
1.0
|
|
C
|
B:GLY472
|
4.8
|
17.1
|
1.0
|
|
CB
|
B:GLN473
|
5.0
|
16.1
|
1.0
|
|
C
|
B:ASN470
|
5.0
|
15.8
|
1.0
|
|
Manganese binding site 3 out
of 8 in 5ejm
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Manganese Binding Sites List in 5ejm
Manganese binding site 3 out
of 8 in the Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn602
b:28.0
occ:1.00
|
OD1
|
C:ASN469
|
2.1
|
22.3
|
1.0
|
|
OD1
|
C:ASP442
|
2.1
|
22.5
|
1.0
|
|
O3B
|
C:TD5601
|
2.2
|
20.5
|
1.0
|
|
O
|
C:GLY471
|
2.2
|
21.5
|
1.0
|
|
O
|
C:HOH734
|
2.2
|
18.9
|
1.0
|
|
O1A
|
C:TD5601
|
2.2
|
19.8
|
1.0
|
|
CG
|
C:ASN469
|
3.0
|
22.8
|
1.0
|
|
CG
|
C:ASP442
|
3.2
|
24.6
|
1.0
|
|
PA
|
C:TD5601
|
3.3
|
21.4
|
1.0
|
|
PB
|
C:TD5601
|
3.4
|
24.1
|
1.0
|
|
C
|
C:GLY471
|
3.4
|
23.4
|
1.0
|
|
ND2
|
C:ASN469
|
3.4
|
24.1
|
1.0
|
|
O3A
|
C:TD5601
|
3.5
|
19.5
|
1.0
|
|
OD2
|
C:ASP442
|
3.7
|
20.9
|
1.0
|
|
N
|
C:ASP442
|
3.8
|
21.4
|
1.0
|
|
N
|
C:GLY471
|
4.1
|
21.9
|
1.0
|
|
N
|
C:GLN473
|
4.2
|
22.2
|
1.0
|
|
O
|
C:HOH824
|
4.2
|
21.5
|
1.0
|
|
O
|
C:VAL467
|
4.2
|
21.6
|
1.0
|
|
N
|
C:ASN469
|
4.2
|
22.8
|
1.0
|
|
CA
|
C:GLY472
|
4.2
|
21.2
|
1.0
|
|
N
|
C:GLY472
|
4.2
|
21.4
|
1.0
|
|
O7
|
C:TD5601
|
4.3
|
18.6
|
1.0
|
|
O2B
|
C:TD5601
|
4.3
|
24.8
|
1.0
|
|
CA
|
C:GLY471
|
4.3
|
23.8
|
1.0
|
|
CB
|
C:ASP442
|
4.4
|
20.6
|
1.0
|
|
CB
|
C:ASN469
|
4.4
|
27.0
|
1.0
|
|
O1B
|
C:TD5601
|
4.4
|
21.9
|
1.0
|
|
O2A
|
C:TD5601
|
4.4
|
19.1
|
1.0
|
|
CA
|
C:GLY441
|
4.5
|
20.3
|
1.0
|
|
N
|
C:LEU443
|
4.6
|
20.3
|
1.0
|
|
CA
|
C:ASP442
|
4.6
|
20.5
|
1.0
|
|
C
|
C:ASN469
|
4.6
|
24.7
|
1.0
|
|
C
|
C:GLY441
|
4.6
|
23.9
|
1.0
|
|
N
|
C:ASN470
|
4.6
|
23.8
|
1.0
|
|
CA
|
C:ASN469
|
4.6
|
23.4
|
1.0
|
|
CG
|
C:GLN473
|
4.7
|
23.6
|
1.0
|
|
C
|
C:GLY472
|
4.7
|
21.9
|
1.0
|
|
CB
|
C:GLN473
|
5.0
|
23.4
|
1.0
|
|
Manganese binding site 4 out
of 8 in 5ejm
Go back to
Manganese Binding Sites List in 5ejm
Manganese binding site 4 out
of 8 in the Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn602
b:23.4
occ:1.00
|
O1A
|
D:TD5601
|
2.1
|
19.8
|
1.0
|
|
OD1
|
D:ASP442
|
2.1
|
16.6
|
1.0
|
|
O
|
D:GLY471
|
2.1
|
18.4
|
1.0
|
|
OD1
|
D:ASN469
|
2.1
|
18.0
|
1.0
|
|
O3B
|
D:TD5601
|
2.2
|
17.2
|
1.0
|
|
O
|
D:HOH787
|
2.3
|
14.5
|
1.0
|
|
CG
|
D:ASN469
|
3.1
|
18.4
|
1.0
|
|
CG
|
D:ASP442
|
3.2
|
19.1
|
1.0
|
|
PA
|
D:TD5601
|
3.2
|
16.7
|
1.0
|
|
C
|
D:GLY471
|
3.3
|
18.4
|
1.0
|
|
PB
|
D:TD5601
|
3.4
|
19.2
|
1.0
|
|
O3A
|
D:TD5601
|
3.4
|
15.1
|
1.0
|
|
ND2
|
D:ASN469
|
3.5
|
17.5
|
1.0
|
|
OD2
|
D:ASP442
|
3.6
|
20.1
|
1.0
|
|
N
|
D:ASP442
|
3.8
|
18.5
|
1.0
|
|
N
|
D:GLY471
|
4.1
|
17.0
|
1.0
|
|
O7
|
D:TD5601
|
4.2
|
18.0
|
1.0
|
|
N
|
D:GLY472
|
4.2
|
15.3
|
1.0
|
|
CA
|
D:GLY472
|
4.2
|
17.3
|
1.0
|
|
N
|
D:GLN473
|
4.2
|
17.2
|
1.0
|
|
N
|
D:ASN469
|
4.3
|
18.2
|
1.0
|
|
O
|
D:VAL467
|
4.3
|
16.1
|
1.0
|
|
CA
|
D:GLY471
|
4.3
|
16.9
|
1.0
|
|
O2B
|
D:TD5601
|
4.3
|
19.6
|
1.0
|
|
O
|
D:HOH899
|
4.3
|
19.3
|
1.0
|
|
CB
|
D:ASP442
|
4.4
|
18.2
|
1.0
|
|
O2A
|
D:TD5601
|
4.4
|
13.5
|
1.0
|
|
O1B
|
D:TD5601
|
4.4
|
18.8
|
1.0
|
|
CB
|
D:ASN469
|
4.4
|
17.4
|
1.0
|
|
N
|
D:LEU443
|
4.5
|
16.9
|
1.0
|
|
CA
|
D:GLY441
|
4.6
|
18.6
|
1.0
|
|
CA
|
D:ASP442
|
4.6
|
17.1
|
1.0
|
|
C
|
D:ASN469
|
4.6
|
16.5
|
1.0
|
|
N
|
D:ASN470
|
4.6
|
19.7
|
1.0
|
|
C
|
D:GLY441
|
4.6
|
19.9
|
1.0
|
|
CA
|
D:ASN469
|
4.7
|
16.4
|
1.0
|
|
CG
|
D:GLN473
|
4.7
|
18.9
|
1.0
|
|
C
|
D:GLY472
|
4.8
|
18.4
|
1.0
|
|
Manganese binding site 5 out
of 8 in 5ejm
Go back to
Manganese Binding Sites List in 5ejm
Manganese binding site 5 out
of 8 in the Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn602
b:21.1
occ:1.00
|
OD1
|
E:ASN469
|
2.1
|
14.3
|
1.0
|
|
O
|
E:GLY471
|
2.1
|
15.4
|
1.0
|
|
O1A
|
E:TD5601
|
2.1
|
16.1
|
1.0
|
|
OD1
|
E:ASP442
|
2.1
|
14.2
|
1.0
|
|
O3B
|
E:TD5601
|
2.2
|
14.9
|
1.0
|
|
O
|
E:HOH818
|
2.3
|
11.2
|
1.0
|
|
CG
|
E:ASN469
|
3.0
|
14.3
|
1.0
|
|
CG
|
E:ASP442
|
3.2
|
17.1
|
1.0
|
|
PA
|
E:TD5601
|
3.3
|
16.2
|
1.0
|
|
C
|
E:GLY471
|
3.3
|
15.8
|
1.0
|
|
PB
|
E:TD5601
|
3.3
|
16.5
|
1.0
|
|
O3A
|
E:TD5601
|
3.4
|
13.8
|
1.0
|
|
ND2
|
E:ASN469
|
3.4
|
14.8
|
1.0
|
|
OD2
|
E:ASP442
|
3.7
|
18.4
|
1.0
|
|
N
|
E:ASP442
|
3.9
|
11.5
|
1.0
|
|
N
|
E:GLY471
|
4.0
|
15.7
|
1.0
|
|
N
|
E:GLY472
|
4.2
|
15.0
|
1.0
|
|
O7
|
E:TD5601
|
4.2
|
17.7
|
1.0
|
|
CA
|
E:GLY472
|
4.2
|
15.9
|
1.0
|
|
N
|
E:GLN473
|
4.2
|
17.6
|
1.0
|
|
O
|
E:HOH747
|
4.2
|
17.0
|
1.0
|
|
N
|
E:ASN469
|
4.2
|
13.4
|
1.0
|
|
CA
|
E:GLY471
|
4.3
|
15.7
|
1.0
|
|
O2B
|
E:TD5601
|
4.3
|
15.2
|
1.0
|
|
O
|
E:VAL467
|
4.4
|
14.9
|
1.0
|
|
O1B
|
E:TD5601
|
4.4
|
14.3
|
1.0
|
|
CB
|
E:ASP442
|
4.4
|
13.5
|
1.0
|
|
CB
|
E:ASN469
|
4.4
|
15.8
|
1.0
|
|
O2A
|
E:TD5601
|
4.4
|
13.7
|
1.0
|
|
N
|
E:LEU443
|
4.5
|
14.4
|
1.0
|
|
C
|
E:ASN469
|
4.6
|
14.1
|
1.0
|
|
CA
|
E:GLY441
|
4.6
|
11.2
|
1.0
|
|
CA
|
E:ASP442
|
4.6
|
13.3
|
1.0
|
|
N
|
E:ASN470
|
4.6
|
15.1
|
1.0
|
|
CA
|
E:ASN469
|
4.6
|
14.8
|
1.0
|
|
C
|
E:GLY441
|
4.7
|
14.5
|
1.0
|
|
CG
|
E:GLN473
|
4.7
|
16.7
|
1.0
|
|
C
|
E:GLY472
|
4.8
|
17.5
|
1.0
|
|
C
|
E:ASN470
|
5.0
|
16.5
|
1.0
|
|
Manganese binding site 6 out
of 8 in 5ejm
Go back to
Manganese Binding Sites List in 5ejm
Manganese binding site 6 out
of 8 in the Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn602
b:20.4
occ:1.00
|
OD1
|
F:ASP442
|
2.0
|
15.8
|
1.0
|
|
OD1
|
F:ASN469
|
2.1
|
15.2
|
1.0
|
|
O
|
F:GLY471
|
2.1
|
16.0
|
1.0
|
|
O3B
|
F:TD5601
|
2.1
|
15.3
|
1.0
|
|
O1A
|
F:TD5601
|
2.2
|
12.6
|
1.0
|
|
O
|
F:HOH746
|
2.3
|
15.9
|
1.0
|
|
CG
|
F:ASP442
|
3.1
|
14.6
|
1.0
|
|
CG
|
F:ASN469
|
3.1
|
16.8
|
1.0
|
|
C
|
F:GLY471
|
3.3
|
16.3
|
1.0
|
|
PB
|
F:TD5601
|
3.3
|
15.6
|
1.0
|
|
PA
|
F:TD5601
|
3.3
|
15.7
|
1.0
|
|
O3A
|
F:TD5601
|
3.5
|
15.4
|
1.0
|
|
ND2
|
F:ASN469
|
3.5
|
16.7
|
1.0
|
|
OD2
|
F:ASP442
|
3.5
|
15.7
|
1.0
|
|
N
|
F:ASP442
|
3.8
|
15.8
|
1.0
|
|
N
|
F:GLY471
|
4.1
|
16.0
|
1.0
|
|
N
|
F:GLN473
|
4.2
|
16.5
|
1.0
|
|
O7
|
F:TD5601
|
4.2
|
18.1
|
1.0
|
|
N
|
F:GLY472
|
4.2
|
14.3
|
1.0
|
|
CA
|
F:GLY472
|
4.2
|
15.7
|
1.0
|
|
N
|
F:ASN469
|
4.2
|
16.2
|
1.0
|
|
O
|
F:VAL467
|
4.2
|
16.3
|
1.0
|
|
O2B
|
F:TD5601
|
4.3
|
15.7
|
1.0
|
|
CB
|
F:ASP442
|
4.3
|
16.9
|
1.0
|
|
CA
|
F:GLY471
|
4.3
|
16.8
|
1.0
|
|
O
|
F:HOH734
|
4.3
|
17.6
|
1.0
|
|
O1B
|
F:TD5601
|
4.4
|
16.3
|
1.0
|
|
CB
|
F:ASN469
|
4.4
|
16.0
|
1.0
|
|
O2A
|
F:TD5601
|
4.4
|
14.1
|
1.0
|
|
N
|
F:LEU443
|
4.5
|
13.2
|
1.0
|
|
CA
|
F:ASP442
|
4.6
|
15.2
|
1.0
|
|
C
|
F:ASN469
|
4.6
|
16.3
|
1.0
|
|
N
|
F:ASN470
|
4.6
|
16.0
|
1.0
|
|
CA
|
F:GLY441
|
4.6
|
16.2
|
1.0
|
|
CA
|
F:ASN469
|
4.6
|
16.1
|
1.0
|
|
C
|
F:GLY441
|
4.7
|
16.8
|
1.0
|
|
C
|
F:GLY472
|
4.7
|
15.3
|
1.0
|
|
CG
|
F:GLN473
|
4.7
|
18.3
|
1.0
|
|
CB
|
F:GLN473
|
5.0
|
17.9
|
1.0
|
|
C
|
F:ASN470
|
5.0
|
16.1
|
1.0
|
|
Manganese binding site 7 out
of 8 in 5ejm
Go back to
Manganese Binding Sites List in 5ejm
Manganese binding site 7 out
of 8 in the Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn602
b:23.5
occ:1.00
|
OD1
|
G:ASN469
|
2.1
|
17.7
|
1.0
|
|
O
|
G:GLY471
|
2.1
|
14.8
|
1.0
|
|
O1A
|
G:TD5601
|
2.1
|
15.5
|
1.0
|
|
OD1
|
G:ASP442
|
2.1
|
16.5
|
1.0
|
|
O3B
|
G:TD5601
|
2.1
|
15.5
|
1.0
|
|
O
|
G:HOH806
|
2.3
|
15.0
|
1.0
|
|
CG
|
G:ASN469
|
3.1
|
16.8
|
1.0
|
|
CG
|
G:ASP442
|
3.2
|
19.2
|
1.0
|
|
C
|
G:GLY471
|
3.3
|
17.2
|
1.0
|
|
PB
|
G:TD5601
|
3.3
|
19.8
|
1.0
|
|
PA
|
G:TD5601
|
3.3
|
17.1
|
1.0
|
|
O3A
|
G:TD5601
|
3.5
|
21.0
|
1.0
|
|
ND2
|
G:ASN469
|
3.5
|
16.2
|
1.0
|
|
OD2
|
G:ASP442
|
3.6
|
18.5
|
1.0
|
|
N
|
G:ASP442
|
3.9
|
18.3
|
1.0
|
|
N
|
G:GLY471
|
4.0
|
18.9
|
1.0
|
|
N
|
G:GLY472
|
4.1
|
16.2
|
1.0
|
|
CA
|
G:GLY472
|
4.2
|
14.4
|
1.0
|
|
N
|
G:GLN473
|
4.2
|
16.5
|
1.0
|
|
O7
|
G:TD5601
|
4.2
|
17.3
|
1.0
|
|
N
|
G:ASN469
|
4.2
|
15.8
|
1.0
|
|
CA
|
G:GLY471
|
4.3
|
19.6
|
1.0
|
|
O2B
|
G:TD5601
|
4.3
|
19.4
|
1.0
|
|
O
|
G:HOH780
|
4.3
|
17.3
|
1.0
|
|
O
|
G:VAL467
|
4.3
|
16.9
|
1.0
|
|
O1B
|
G:TD5601
|
4.3
|
20.7
|
1.0
|
|
CB
|
G:ASP442
|
4.4
|
18.2
|
1.0
|
|
CB
|
G:ASN469
|
4.4
|
16.6
|
1.0
|
|
O2A
|
G:TD5601
|
4.4
|
14.2
|
1.0
|
|
N
|
G:LEU443
|
4.6
|
18.6
|
1.0
|
|
C
|
G:ASN469
|
4.6
|
19.1
|
1.0
|
|
N
|
G:ASN470
|
4.6
|
15.9
|
1.0
|
|
CA
|
G:ASP442
|
4.6
|
18.8
|
1.0
|
|
CA
|
G:ASN469
|
4.6
|
17.2
|
1.0
|
|
CA
|
G:GLY441
|
4.7
|
15.0
|
1.0
|
|
C
|
G:GLY441
|
4.7
|
18.2
|
1.0
|
|
CG
|
G:GLN473
|
4.7
|
21.2
|
1.0
|
|
C
|
G:GLY472
|
4.7
|
16.4
|
1.0
|
|
C
|
G:ASN470
|
5.0
|
19.1
|
1.0
|
|
Manganese binding site 8 out
of 8 in 5ejm
Go back to
Manganese Binding Sites List in 5ejm
Manganese binding site 8 out
of 8 in the Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Thdp-MN2+ Complex of R413A Variant of Ecmend Soaked with 2- Ketoglutarate For 35 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mn602
b:23.7
occ:1.00
|
OD1
|
H:ASN469
|
2.0
|
19.7
|
1.0
|
|
OD1
|
H:ASP442
|
2.1
|
18.8
|
1.0
|
|
O
|
H:GLY471
|
2.1
|
19.0
|
1.0
|
|
O3B
|
H:TD5601
|
2.1
|
19.6
|
1.0
|
|
O1A
|
H:TD5601
|
2.2
|
18.8
|
1.0
|
|
O
|
H:HOH759
|
2.2
|
17.9
|
1.0
|
|
CG
|
H:ASN469
|
3.1
|
22.2
|
1.0
|
|
CG
|
H:ASP442
|
3.1
|
24.7
|
1.0
|
|
PB
|
H:TD5601
|
3.3
|
21.1
|
1.0
|
|
C
|
H:GLY471
|
3.3
|
19.0
|
1.0
|
|
PA
|
H:TD5601
|
3.3
|
19.8
|
1.0
|
|
O3A
|
H:TD5601
|
3.5
|
17.2
|
1.0
|
|
ND2
|
H:ASN469
|
3.5
|
20.2
|
1.0
|
|
OD2
|
H:ASP442
|
3.6
|
23.8
|
1.0
|
|
N
|
H:ASP442
|
3.8
|
18.0
|
1.0
|
|
N
|
H:GLY471
|
4.1
|
19.4
|
1.0
|
|
N
|
H:GLN473
|
4.1
|
19.7
|
1.0
|
|
CA
|
H:GLY472
|
4.2
|
23.3
|
1.0
|
|
N
|
H:GLY472
|
4.2
|
18.9
|
1.0
|
|
O7
|
H:TD5601
|
4.2
|
19.5
|
1.0
|
|
N
|
H:ASN469
|
4.2
|
22.9
|
1.0
|
|
O
|
H:HOH866
|
4.3
|
19.4
|
1.0
|
|
O
|
H:VAL467
|
4.3
|
19.0
|
1.0
|
|
O2B
|
H:TD5601
|
4.3
|
18.9
|
1.0
|
|
CA
|
H:GLY471
|
4.3
|
22.1
|
1.0
|
|
O1B
|
H:TD5601
|
4.4
|
20.4
|
1.0
|
|
CB
|
H:ASP442
|
4.4
|
20.5
|
1.0
|
|
CB
|
H:ASN469
|
4.4
|
22.0
|
1.0
|
|
O2A
|
H:TD5601
|
4.4
|
16.2
|
1.0
|
|
C
|
H:ASN469
|
4.6
|
21.2
|
1.0
|
|
N
|
H:LEU443
|
4.6
|
17.4
|
1.0
|
|
CA
|
H:GLY441
|
4.6
|
17.9
|
1.0
|
|
N
|
H:ASN470
|
4.6
|
20.2
|
1.0
|
|
CA
|
H:ASN469
|
4.6
|
22.1
|
1.0
|
|
CA
|
H:ASP442
|
4.6
|
17.9
|
1.0
|
|
C
|
H:GLY441
|
4.7
|
18.7
|
1.0
|
|
C
|
H:GLY472
|
4.7
|
20.6
|
1.0
|
|
CG
|
H:GLN473
|
4.7
|
22.9
|
1.0
|
|
CB
|
H:GLN473
|
5.0
|
23.0
|
1.0
|
|
C
|
H:ASN470
|
5.0
|
19.9
|
1.0
|
|
O
|
H:ASN469
|
5.0
|
23.4
|
1.0
|
|
Reference:
M.M.Qin,
H.G.Song,
X.Dai,
Y.Z.Chen,
Z.H.Guo.
Two Active Site Arginines Are Critical Determinants of Substrate Binding and Catalysis in Mend, A Thiamine-Dependent Enzyme in Menaquinone Biosynthesis. Biochem. J. 2018.
ISSN: ESSN 1470-8728
PubMed: 30341164
DOI: 10.1042/BCJ20180548
Page generated: Sun Oct 6 00:05:36 2024
|
