Magnesium in PDB 5z2r: Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
Enzymatic activity of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
All present enzymatic activity of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min:
2.2.1.9;
Protein crystallography data
The structure of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min, PDB code: 5z2r
was solved by
M.M.Qin,
Z.H.Guo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
38.63 /
2.30
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.630,
90.750,
172.370,
82.91,
75.71,
64.20
|
|
R / Rfree (%)
|
17 /
20.1
|
Other elements in 5z2r:
The structure of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
(pdb code 5z2r). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min, PDB code: 5z2r:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 5z2r
Go back to
Magnesium Binding Sites List in 5z2r
Magnesium binding site 1 out
of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:7.1
occ:1.00
|
O
|
A:HOH747
|
1.9
|
35.8
|
1.0
|
|
O
|
A:GLY471
|
2.0
|
25.9
|
1.0
|
|
O3B
|
A:TD6601
|
2.0
|
13.1
|
1.0
|
|
O2A
|
A:TD6601
|
2.0
|
18.7
|
1.0
|
|
OD1
|
A:ASP442
|
2.1
|
25.1
|
1.0
|
|
OD1
|
A:ASN469
|
2.1
|
22.1
|
1.0
|
|
CG
|
A:ASN469
|
3.0
|
22.0
|
1.0
|
|
CG
|
A:ASP442
|
3.1
|
23.3
|
1.0
|
|
C
|
A:GLY471
|
3.2
|
23.6
|
1.0
|
|
PA
|
A:TD6601
|
3.2
|
17.4
|
1.0
|
|
PB
|
A:TD6601
|
3.2
|
15.0
|
1.0
|
|
O3A
|
A:TD6601
|
3.4
|
13.4
|
1.0
|
|
ND2
|
A:ASN469
|
3.4
|
21.9
|
1.0
|
|
OD2
|
A:ASP442
|
3.6
|
23.5
|
1.0
|
|
N
|
A:ASP442
|
3.9
|
19.6
|
1.0
|
|
N
|
A:GLY471
|
4.0
|
24.0
|
1.0
|
|
N
|
A:GLY472
|
4.0
|
22.8
|
1.0
|
|
N
|
A:GLN473
|
4.1
|
21.7
|
1.0
|
|
CA
|
A:GLY472
|
4.1
|
22.1
|
1.0
|
|
CA
|
A:GLY471
|
4.1
|
23.2
|
1.0
|
|
O7
|
A:TD6601
|
4.2
|
18.8
|
1.0
|
|
O1B
|
A:TD6601
|
4.2
|
14.9
|
1.0
|
|
O
|
A:HOH717
|
4.2
|
15.2
|
1.0
|
|
O2B
|
A:TD6601
|
4.3
|
13.1
|
1.0
|
|
O1A
|
A:TD6601
|
4.3
|
12.1
|
1.0
|
|
N
|
A:ASN469
|
4.3
|
22.3
|
1.0
|
|
CB
|
A:ASP442
|
4.3
|
21.9
|
1.0
|
|
CB
|
A:ASN469
|
4.4
|
22.3
|
1.0
|
|
O
|
A:VAL467
|
4.4
|
20.2
|
1.0
|
|
N
|
A:LEU443
|
4.5
|
19.3
|
1.0
|
|
CA
|
A:ASP442
|
4.6
|
21.0
|
1.0
|
|
C
|
A:ASN469
|
4.6
|
22.9
|
1.0
|
|
C
|
A:GLY472
|
4.7
|
21.8
|
1.0
|
|
CA
|
A:ASN469
|
4.7
|
22.6
|
1.0
|
|
CA
|
A:GLY441
|
4.7
|
18.6
|
1.0
|
|
CG
|
A:GLN473
|
4.7
|
23.9
|
1.0
|
|
N
|
A:ASN470
|
4.7
|
23.0
|
1.0
|
|
C
|
A:GLY441
|
4.7
|
18.9
|
1.0
|
|
C
|
A:ASN470
|
5.0
|
24.0
|
1.0
|
|
CB
|
A:GLN473
|
5.0
|
23.4
|
1.0
|
|
O
|
A:ASN469
|
5.0
|
23.2
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 5z2r
Go back to
Magnesium Binding Sites List in 5z2r
Magnesium binding site 2 out
of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:1.6
occ:1.00
|
O
|
B:HOH724
|
1.8
|
15.7
|
1.0
|
|
O
|
B:GLY471
|
2.0
|
18.8
|
1.0
|
|
OD1
|
B:ASP442
|
2.0
|
19.5
|
1.0
|
|
O2A
|
B:TD6601
|
2.0
|
20.2
|
1.0
|
|
OD1
|
B:ASN469
|
2.1
|
20.8
|
1.0
|
|
O3B
|
B:TD6601
|
2.1
|
21.0
|
1.0
|
|
CG
|
B:ASP442
|
3.1
|
20.2
|
1.0
|
|
CG
|
B:ASN469
|
3.1
|
21.4
|
1.0
|
|
C
|
B:GLY471
|
3.2
|
20.3
|
1.0
|
|
PA
|
B:TD6601
|
3.2
|
18.9
|
1.0
|
|
PB
|
B:TD6601
|
3.3
|
20.5
|
1.0
|
|
O3A
|
B:TD6601
|
3.3
|
18.4
|
1.0
|
|
ND2
|
B:ASN469
|
3.6
|
20.4
|
1.0
|
|
OD2
|
B:ASP442
|
3.6
|
13.8
|
1.0
|
|
N
|
B:ASP442
|
3.9
|
20.6
|
1.0
|
|
N
|
B:GLY471
|
4.0
|
24.0
|
1.0
|
|
N
|
B:GLY472
|
4.1
|
20.9
|
1.0
|
|
CA
|
B:GLY471
|
4.1
|
21.4
|
1.0
|
|
CA
|
B:GLY472
|
4.1
|
20.8
|
1.0
|
|
O7
|
B:TD6601
|
4.2
|
20.7
|
1.0
|
|
N
|
B:GLN473
|
4.2
|
23.0
|
1.0
|
|
O1B
|
B:TD6601
|
4.3
|
20.5
|
1.0
|
|
O2B
|
B:TD6601
|
4.3
|
18.3
|
1.0
|
|
O1A
|
B:TD6601
|
4.3
|
16.8
|
1.0
|
|
N
|
B:ASN469
|
4.3
|
23.7
|
1.0
|
|
CB
|
B:ASP442
|
4.4
|
18.2
|
1.0
|
|
O
|
B:VAL467
|
4.4
|
23.0
|
1.0
|
|
O
|
B:HOH824
|
4.5
|
25.4
|
1.0
|
|
CB
|
B:ASN469
|
4.5
|
22.4
|
1.0
|
|
N
|
B:LEU443
|
4.5
|
16.9
|
1.0
|
|
CA
|
B:GLY441
|
4.6
|
18.0
|
1.0
|
|
CA
|
B:ASP442
|
4.7
|
18.1
|
1.0
|
|
C
|
B:ASN469
|
4.7
|
25.8
|
1.0
|
|
N
|
B:ASN470
|
4.7
|
25.4
|
1.0
|
|
CA
|
B:ASN469
|
4.7
|
24.0
|
1.0
|
|
C
|
B:GLY441
|
4.7
|
20.4
|
1.0
|
|
C
|
B:GLY472
|
4.8
|
22.0
|
1.0
|
|
CG
|
B:GLN473
|
4.8
|
24.7
|
1.0
|
|
C
|
B:ASN470
|
4.9
|
26.9
|
1.0
|
|
CG
|
B:LEU443
|
5.0
|
18.7
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 5z2r
Go back to
Magnesium Binding Sites List in 5z2r
Magnesium binding site 3 out
of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg602
b:1.0
occ:1.00
|
O
|
C:GLY471
|
1.9
|
17.9
|
1.0
|
|
OD1
|
C:ASP442
|
2.0
|
17.4
|
1.0
|
|
OD1
|
C:ASN469
|
2.1
|
19.1
|
1.0
|
|
O2A
|
C:TD6601
|
2.1
|
17.4
|
1.0
|
|
O3B
|
C:TD6601
|
2.1
|
17.1
|
1.0
|
|
O
|
C:HOH2955
|
2.5
|
28.1
|
1.0
|
|
CG
|
C:ASP442
|
3.0
|
16.1
|
1.0
|
|
C
|
C:GLY471
|
3.1
|
17.0
|
1.0
|
|
CG
|
C:ASN469
|
3.2
|
20.2
|
1.0
|
|
PA
|
C:TD6601
|
3.2
|
17.1
|
1.0
|
|
PB
|
C:TD6601
|
3.2
|
16.7
|
1.0
|
|
O3A
|
C:TD6601
|
3.3
|
16.9
|
1.0
|
|
OD2
|
C:ASP442
|
3.5
|
16.3
|
1.0
|
|
ND2
|
C:ASN469
|
3.6
|
20.5
|
1.0
|
|
N
|
C:ASP442
|
3.9
|
14.1
|
1.0
|
|
N
|
C:GLY472
|
3.9
|
17.2
|
1.0
|
|
CA
|
C:GLY472
|
4.0
|
17.4
|
1.0
|
|
N
|
C:GLY471
|
4.0
|
18.7
|
1.0
|
|
N
|
C:GLN473
|
4.0
|
20.8
|
1.0
|
|
O7
|
C:TD6601
|
4.1
|
20.5
|
1.0
|
|
CA
|
C:GLY471
|
4.1
|
16.9
|
1.0
|
|
O2B
|
C:TD6601
|
4.2
|
15.6
|
1.0
|
|
O
|
C:HOH2811
|
4.2
|
21.0
|
1.0
|
|
CB
|
C:ASP442
|
4.3
|
15.6
|
1.0
|
|
O1B
|
C:TD6601
|
4.3
|
12.6
|
1.0
|
|
N
|
C:ASN469
|
4.3
|
18.5
|
1.0
|
|
O1A
|
C:TD6601
|
4.4
|
14.3
|
1.0
|
|
O
|
C:VAL467
|
4.4
|
15.3
|
1.0
|
|
CB
|
C:ASN469
|
4.5
|
19.4
|
1.0
|
|
N
|
C:LEU443
|
4.5
|
14.0
|
1.0
|
|
C
|
C:GLY472
|
4.6
|
19.3
|
1.0
|
|
CA
|
C:ASP442
|
4.6
|
14.0
|
1.0
|
|
C
|
C:ASN469
|
4.7
|
17.6
|
1.0
|
|
CA
|
C:GLY441
|
4.7
|
12.4
|
1.0
|
|
CG
|
C:GLN473
|
4.7
|
22.7
|
1.0
|
|
CA
|
C:ASN469
|
4.7
|
18.6
|
1.0
|
|
C
|
C:GLY441
|
4.7
|
12.6
|
1.0
|
|
N
|
C:ASN470
|
4.8
|
18.2
|
1.0
|
|
CG
|
C:LEU443
|
5.0
|
13.6
|
1.0
|
|
C
|
C:ASN470
|
5.0
|
20.2
|
1.0
|
|
CB
|
C:GLN473
|
5.0
|
22.4
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 5z2r
Go back to
Magnesium Binding Sites List in 5z2r
Magnesium binding site 4 out
of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg602
b:1.0
occ:1.00
|
OD1
|
D:ASN469
|
2.0
|
17.9
|
1.0
|
|
OD1
|
D:ASP442
|
2.0
|
18.7
|
1.0
|
|
O
|
D:GLY471
|
2.0
|
20.1
|
1.0
|
|
O2A
|
D:TD6601
|
2.1
|
17.4
|
1.0
|
|
O3B
|
D:TD6601
|
2.1
|
18.5
|
1.0
|
|
O
|
D:HOH750
|
2.5
|
13.6
|
1.0
|
|
CG
|
D:ASN469
|
3.0
|
16.8
|
1.0
|
|
CG
|
D:ASP442
|
3.1
|
15.3
|
1.0
|
|
C
|
D:GLY471
|
3.2
|
18.2
|
1.0
|
|
PA
|
D:TD6601
|
3.2
|
17.8
|
1.0
|
|
PB
|
D:TD6601
|
3.3
|
18.7
|
1.0
|
|
ND2
|
D:ASN469
|
3.4
|
16.4
|
1.0
|
|
O3A
|
D:TD6601
|
3.4
|
17.4
|
1.0
|
|
OD2
|
D:ASP442
|
3.6
|
13.6
|
1.0
|
|
N
|
D:ASP442
|
3.9
|
14.8
|
1.0
|
|
N
|
D:GLY471
|
4.0
|
17.9
|
1.0
|
|
O
|
D:HOH859
|
4.0
|
35.3
|
1.0
|
|
N
|
D:GLY472
|
4.1
|
18.4
|
1.0
|
|
N
|
D:GLN473
|
4.1
|
21.2
|
1.0
|
|
CA
|
D:GLY472
|
4.1
|
18.1
|
1.0
|
|
CA
|
D:GLY471
|
4.2
|
17.7
|
1.0
|
|
O7
|
D:TD6601
|
4.2
|
20.4
|
1.0
|
|
O2B
|
D:TD6601
|
4.2
|
17.0
|
1.0
|
|
N
|
D:ASN469
|
4.2
|
19.0
|
1.0
|
|
CB
|
D:ASN469
|
4.3
|
17.4
|
1.0
|
|
CB
|
D:ASP442
|
4.3
|
15.0
|
1.0
|
|
O
|
D:VAL467
|
4.4
|
19.1
|
1.0
|
|
O1A
|
D:TD6601
|
4.4
|
14.1
|
1.0
|
|
O1B
|
D:TD6601
|
4.4
|
17.8
|
1.0
|
|
N
|
D:LEU443
|
4.5
|
16.3
|
1.0
|
|
C
|
D:ASN469
|
4.6
|
19.4
|
1.0
|
|
CA
|
D:ASN469
|
4.6
|
18.4
|
1.0
|
|
N
|
D:ASN470
|
4.6
|
19.1
|
1.0
|
|
CG
|
D:GLN473
|
4.7
|
22.6
|
1.0
|
|
CA
|
D:ASP442
|
4.7
|
15.1
|
1.0
|
|
CA
|
D:GLY441
|
4.7
|
14.9
|
1.0
|
|
C
|
D:GLY472
|
4.7
|
19.1
|
1.0
|
|
C
|
D:GLY441
|
4.8
|
15.3
|
1.0
|
|
CG
|
D:LEU443
|
4.8
|
19.5
|
1.0
|
|
C
|
D:ASN470
|
5.0
|
19.3
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 5z2r
Go back to
Magnesium Binding Sites List in 5z2r
Magnesium binding site 5 out
of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg601
b:1.0
occ:1.00
|
O
|
E:GLY471
|
1.9
|
18.6
|
1.0
|
|
O13
|
E:TDP607
|
2.0
|
13.9
|
1.0
|
|
OD1
|
E:ASP442
|
2.0
|
15.4
|
1.0
|
|
O22
|
E:TDP607
|
2.0
|
16.9
|
1.0
|
|
O
|
E:HOH732
|
2.0
|
14.4
|
1.0
|
|
OD1
|
E:ASN469
|
2.1
|
18.2
|
1.0
|
|
CG
|
E:ASP442
|
3.1
|
15.7
|
1.0
|
|
CG
|
E:ASN469
|
3.1
|
17.8
|
1.0
|
|
C
|
E:GLY471
|
3.1
|
18.6
|
1.0
|
|
P1
|
E:TDP607
|
3.3
|
14.9
|
1.0
|
|
P2
|
E:TDP607
|
3.3
|
16.6
|
1.0
|
|
ND2
|
E:ASN469
|
3.5
|
16.3
|
1.0
|
|
O11
|
E:TDP607
|
3.6
|
15.2
|
1.0
|
|
OD2
|
E:ASP442
|
3.6
|
17.5
|
1.0
|
|
N
|
E:ASP442
|
3.9
|
12.6
|
1.0
|
|
N
|
E:GLY471
|
3.9
|
19.1
|
1.0
|
|
N
|
E:GLY472
|
4.0
|
18.4
|
1.0
|
|
O
|
E:HOH757
|
4.0
|
13.6
|
1.0
|
|
CA
|
E:GLY472
|
4.1
|
19.2
|
1.0
|
|
CA
|
E:GLY471
|
4.1
|
18.9
|
1.0
|
|
N
|
E:GLN473
|
4.1
|
21.2
|
1.0
|
|
O5G
|
E:TDP607
|
4.1
|
16.9
|
1.0
|
|
O21
|
E:TDP607
|
4.2
|
16.5
|
1.0
|
|
N
|
E:ASN469
|
4.2
|
16.9
|
1.0
|
|
CB
|
E:ASP442
|
4.3
|
13.3
|
1.0
|
|
O23
|
E:TDP607
|
4.3
|
15.2
|
1.0
|
|
O
|
E:VAL467
|
4.3
|
16.1
|
1.0
|
|
O12
|
E:TDP607
|
4.4
|
12.9
|
1.0
|
|
CB
|
E:ASN469
|
4.4
|
18.2
|
1.0
|
|
N
|
E:LEU443
|
4.5
|
10.3
|
1.0
|
|
C
|
E:ASN469
|
4.6
|
17.3
|
1.0
|
|
CA
|
E:ASP442
|
4.6
|
12.3
|
1.0
|
|
N
|
E:ASN470
|
4.6
|
17.6
|
1.0
|
|
CA
|
E:ASN469
|
4.7
|
17.1
|
1.0
|
|
C
|
E:GLY472
|
4.7
|
20.1
|
1.0
|
|
CG
|
E:GLN473
|
4.7
|
20.5
|
1.0
|
|
CA
|
E:GLY441
|
4.7
|
12.6
|
1.0
|
|
C
|
E:GLY441
|
4.7
|
12.5
|
1.0
|
|
C
|
E:ASN470
|
4.9
|
19.4
|
1.0
|
|
CG
|
E:LEU443
|
4.9
|
9.1
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 5z2r
Go back to
Magnesium Binding Sites List in 5z2r
Magnesium binding site 6 out
of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg602
b:1.0
occ:1.00
|
OD1
|
F:ASP442
|
1.9
|
15.7
|
1.0
|
|
O3B
|
F:TD6601
|
2.0
|
18.1
|
1.0
|
|
O
|
F:GLY471
|
2.1
|
18.2
|
1.0
|
|
OD1
|
F:ASN469
|
2.1
|
13.5
|
1.0
|
|
O
|
F:HOH727
|
2.1
|
18.4
|
1.0
|
|
O2A
|
F:TD6601
|
2.1
|
20.4
|
1.0
|
|
CG
|
F:ASP442
|
3.0
|
15.3
|
1.0
|
|
CG
|
F:ASN469
|
3.1
|
13.0
|
1.0
|
|
PA
|
F:TD6601
|
3.2
|
20.2
|
1.0
|
|
C
|
F:GLY471
|
3.2
|
19.2
|
1.0
|
|
PB
|
F:TD6601
|
3.3
|
18.2
|
1.0
|
|
O3A
|
F:TD6601
|
3.4
|
18.4
|
1.0
|
|
ND2
|
F:ASN469
|
3.4
|
11.8
|
1.0
|
|
OD2
|
F:ASP442
|
3.5
|
14.1
|
1.0
|
|
N
|
F:ASP442
|
3.9
|
16.8
|
1.0
|
|
N
|
F:GLY471
|
4.0
|
18.9
|
1.0
|
|
N
|
F:GLY472
|
4.1
|
19.9
|
1.0
|
|
O7
|
F:TD6601
|
4.2
|
22.9
|
1.0
|
|
N
|
F:GLN473
|
4.2
|
20.0
|
1.0
|
|
CA
|
F:GLY472
|
4.2
|
18.5
|
1.0
|
|
CA
|
F:GLY471
|
4.2
|
18.9
|
1.0
|
|
O1B
|
F:TD6601
|
4.3
|
19.4
|
1.0
|
|
N
|
F:ASN469
|
4.3
|
17.6
|
1.0
|
|
CB
|
F:ASP442
|
4.3
|
14.9
|
1.0
|
|
O2B
|
F:TD6601
|
4.3
|
16.2
|
1.0
|
|
CB
|
F:ASN469
|
4.4
|
15.7
|
1.0
|
|
O
|
F:VAL467
|
4.4
|
18.8
|
1.0
|
|
O1A
|
F:TD6601
|
4.4
|
19.1
|
1.0
|
|
O
|
F:HOH845
|
4.5
|
14.1
|
1.0
|
|
N
|
F:LEU443
|
4.6
|
13.4
|
1.0
|
|
C
|
F:ASN469
|
4.6
|
16.6
|
1.0
|
|
CA
|
F:ASP442
|
4.6
|
15.3
|
1.0
|
|
CA
|
F:ASN469
|
4.6
|
16.8
|
1.0
|
|
N
|
F:ASN470
|
4.7
|
18.1
|
1.0
|
|
CG
|
F:GLN473
|
4.7
|
20.8
|
1.0
|
|
CA
|
F:GLY441
|
4.7
|
16.3
|
1.0
|
|
C
|
F:GLY472
|
4.7
|
18.6
|
1.0
|
|
C
|
F:GLY441
|
4.7
|
16.3
|
1.0
|
|
O
|
F:ASN469
|
5.0
|
16.6
|
1.0
|
|
C
|
F:ASN470
|
5.0
|
19.1
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 5z2r
Go back to
Magnesium Binding Sites List in 5z2r
Magnesium binding site 7 out
of 7 in the Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Thdp-MN2+ Complex of R395K Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg602
b:1.4
occ:1.00
|
OD1
|
H:ASP442
|
2.0
|
17.8
|
1.0
|
|
O
|
H:GLY471
|
2.0
|
21.7
|
1.0
|
|
O2A
|
H:TD6601
|
2.0
|
24.4
|
1.0
|
|
OD1
|
H:ASN469
|
2.0
|
24.9
|
1.0
|
|
O3B
|
H:TD6601
|
2.2
|
24.2
|
1.0
|
|
O
|
H:HOH848
|
2.6
|
28.4
|
1.0
|
|
CG
|
H:ASN469
|
3.1
|
25.2
|
1.0
|
|
CG
|
H:ASP442
|
3.1
|
18.8
|
1.0
|
|
C
|
H:GLY471
|
3.2
|
22.6
|
1.0
|
|
PA
|
H:TD6601
|
3.2
|
24.3
|
1.0
|
|
PB
|
H:TD6601
|
3.3
|
23.1
|
1.0
|
|
O3A
|
H:TD6601
|
3.3
|
23.8
|
1.0
|
|
ND2
|
H:ASN469
|
3.5
|
24.5
|
1.0
|
|
OD2
|
H:ASP442
|
3.6
|
19.1
|
1.0
|
|
N
|
H:ASP442
|
3.8
|
19.6
|
1.0
|
|
N
|
H:GLY471
|
4.0
|
25.0
|
1.0
|
|
N
|
H:GLY472
|
4.1
|
23.3
|
1.0
|
|
CA
|
H:GLY471
|
4.2
|
23.1
|
1.0
|
|
O7
|
H:TD6601
|
4.2
|
27.6
|
1.0
|
|
CA
|
H:GLY472
|
4.2
|
24.0
|
1.0
|
|
N
|
H:GLN473
|
4.2
|
26.1
|
1.0
|
|
O2B
|
H:TD6601
|
4.2
|
20.0
|
1.0
|
|
N
|
H:ASN469
|
4.3
|
24.4
|
1.0
|
|
O
|
H:HOH803
|
4.3
|
29.7
|
1.0
|
|
CB
|
H:ASP442
|
4.3
|
18.6
|
1.0
|
|
O1B
|
H:TD6601
|
4.3
|
24.4
|
1.0
|
|
O1A
|
H:TD6601
|
4.3
|
23.2
|
1.0
|
|
O
|
H:VAL467
|
4.4
|
22.6
|
1.0
|
|
CB
|
H:ASN469
|
4.4
|
25.2
|
1.0
|
|
N
|
H:LEU443
|
4.5
|
16.9
|
1.0
|
|
CA
|
H:ASP442
|
4.6
|
19.1
|
1.0
|
|
CA
|
H:GLY441
|
4.6
|
17.6
|
1.0
|
|
C
|
H:ASN469
|
4.7
|
26.2
|
1.0
|
|
CG
|
H:GLN473
|
4.7
|
30.1
|
1.0
|
|
C
|
H:GLY441
|
4.7
|
18.6
|
1.0
|
|
CA
|
H:ASN469
|
4.7
|
25.2
|
1.0
|
|
N
|
H:ASN470
|
4.7
|
26.6
|
1.0
|
|
C
|
H:GLY472
|
4.8
|
24.7
|
1.0
|
|
C
|
H:ASN470
|
5.0
|
26.9
|
1.0
|
|
CG
|
H:LEU443
|
5.0
|
19.8
|
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. V. 475 3651 2018.
ISSN: ESSN 1470-8728
PubMed: 30341164
DOI: 10.1042/BCJ20180548
Page generated: Mon Sep 30 11:41:37 2024
|
