Magnesium in PDB 5z2u: Thdp-MN2+ Complex of R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
Enzymatic activity of Thdp-MN2+ Complex of R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
All present enzymatic activity of Thdp-MN2+ Complex of R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min:
2.2.1.9;
Protein crystallography data
The structure of Thdp-MN2+ Complex of R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min, PDB code: 5z2u
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)
|
37.28 /
2.35
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.670,
90.700,
169.070,
83.26,
75.96,
64.17
|
|
R / Rfree (%)
|
16.4 /
20.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Thdp-MN2+ Complex of R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min
(pdb code 5z2u). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Thdp-MN2+ Complex of R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min, PDB code: 5z2u:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 5z2u
Go back to
Magnesium Binding Sites List in 5z2u
Magnesium binding site 1 out
of 8 in the Thdp-MN2+ Complex of R395A 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 R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:1.9
occ:1.00
|
OD1
|
A:ASP442
|
1.8
|
12.0
|
1.0
|
|
O
|
A:GLY471
|
2.0
|
14.7
|
1.0
|
|
OD1
|
A:ASN469
|
2.1
|
16.0
|
1.0
|
|
O2A
|
A:TD6601
|
2.1
|
11.9
|
1.0
|
|
O3B
|
A:TD6601
|
2.1
|
11.4
|
1.0
|
|
O
|
A:HOH818
|
2.2
|
12.6
|
1.0
|
|
CG
|
A:ASP442
|
2.9
|
14.1
|
1.0
|
|
CG
|
A:ASN469
|
3.1
|
12.3
|
1.0
|
|
C
|
A:GLY471
|
3.2
|
12.8
|
1.0
|
|
PA
|
A:TD6601
|
3.3
|
9.8
|
1.0
|
|
PB
|
A:TD6601
|
3.3
|
11.8
|
1.0
|
|
ND2
|
A:ASN469
|
3.4
|
12.9
|
1.0
|
|
OD2
|
A:ASP442
|
3.4
|
12.6
|
1.0
|
|
O3A
|
A:TD6601
|
3.4
|
8.2
|
1.0
|
|
N
|
A:ASP442
|
3.7
|
15.5
|
1.0
|
|
N
|
A:GLY471
|
4.0
|
15.3
|
1.0
|
|
N
|
A:GLY472
|
4.1
|
13.2
|
1.0
|
|
CB
|
A:ASP442
|
4.1
|
11.8
|
1.0
|
|
CA
|
A:GLY472
|
4.1
|
13.0
|
1.0
|
|
O7
|
A:TD6601
|
4.2
|
15.0
|
1.0
|
|
CA
|
A:GLY471
|
4.2
|
13.6
|
1.0
|
|
O
|
A:VAL467
|
4.2
|
13.5
|
1.0
|
|
O1B
|
A:TD6601
|
4.3
|
12.6
|
1.0
|
|
N
|
A:ASN469
|
4.3
|
11.1
|
1.0
|
|
N
|
A:GLN473
|
4.3
|
14.7
|
1.0
|
|
O2B
|
A:TD6601
|
4.3
|
15.9
|
1.0
|
|
N
|
A:LEU443
|
4.4
|
11.9
|
1.0
|
|
O
|
A:HOH791
|
4.4
|
14.8
|
1.0
|
|
O1A
|
A:TD6601
|
4.4
|
11.9
|
1.0
|
|
CB
|
A:ASN469
|
4.4
|
11.5
|
1.0
|
|
CA
|
A:ASP442
|
4.4
|
15.5
|
1.0
|
|
CA
|
A:GLY441
|
4.5
|
10.1
|
1.0
|
|
C
|
A:GLY441
|
4.5
|
12.1
|
1.0
|
|
CA
|
A:ASN469
|
4.7
|
13.4
|
1.0
|
|
N
|
A:ASN470
|
4.7
|
14.4
|
1.0
|
|
C
|
A:ASN469
|
4.7
|
14.6
|
1.0
|
|
C
|
A:GLY472
|
4.8
|
15.2
|
1.0
|
|
CG
|
A:GLN473
|
4.9
|
15.1
|
1.0
|
|
C
|
A:ASP442
|
4.9
|
10.3
|
1.0
|
|
CG
|
A:LEU443
|
5.0
|
11.3
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 5z2u
Go back to
Magnesium Binding Sites List in 5z2u
Magnesium binding site 2 out
of 8 in the Thdp-MN2+ Complex of R395A 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 R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:22.9
occ:1.00
|
O
|
B:HOH728
|
2.0
|
11.5
|
1.0
|
|
OD1
|
B:ASP442
|
2.0
|
12.1
|
1.0
|
|
ND2
|
B:ASN469
|
2.0
|
13.2
|
1.0
|
|
O
|
B:GLY471
|
2.0
|
14.4
|
1.0
|
|
O2A
|
B:TD6601
|
2.3
|
12.1
|
1.0
|
|
O3B
|
B:TD6601
|
2.4
|
10.9
|
1.0
|
|
CG
|
B:ASN469
|
2.7
|
11.3
|
1.0
|
|
OD1
|
B:ASN469
|
2.7
|
20.4
|
1.0
|
|
CG
|
B:ASP442
|
3.1
|
11.8
|
1.0
|
|
O3A
|
B:TD6601
|
3.2
|
9.4
|
1.0
|
|
PA
|
B:TD6601
|
3.3
|
12.7
|
1.0
|
|
C
|
B:GLY471
|
3.3
|
12.9
|
1.0
|
|
PB
|
B:TD6601
|
3.3
|
12.1
|
1.0
|
|
OD2
|
B:ASP442
|
3.6
|
11.4
|
1.0
|
|
N
|
B:ASP442
|
3.8
|
10.7
|
1.0
|
|
O1B
|
B:TD6601
|
3.9
|
11.8
|
1.0
|
|
N
|
B:GLY471
|
4.0
|
12.5
|
1.0
|
|
CB
|
B:ASN469
|
4.1
|
14.7
|
1.0
|
|
N
|
B:GLY472
|
4.2
|
10.1
|
1.0
|
|
CA
|
B:GLY472
|
4.2
|
11.5
|
1.0
|
|
N
|
B:GLN473
|
4.2
|
11.6
|
1.0
|
|
O1A
|
B:TD6601
|
4.2
|
9.0
|
1.0
|
|
O7
|
B:TD6601
|
4.2
|
14.8
|
1.0
|
|
CA
|
B:GLY471
|
4.3
|
13.7
|
1.0
|
|
N
|
B:ASN469
|
4.3
|
15.5
|
1.0
|
|
O
|
B:HOH720
|
4.3
|
16.1
|
1.0
|
|
CB
|
B:ASP442
|
4.3
|
9.9
|
1.0
|
|
O
|
B:VAL467
|
4.3
|
14.3
|
1.0
|
|
O2B
|
B:TD6601
|
4.3
|
8.7
|
1.0
|
|
CA
|
B:GLY441
|
4.5
|
8.9
|
1.0
|
|
CA
|
B:ASN469
|
4.5
|
13.7
|
1.0
|
|
C
|
B:ASN469
|
4.6
|
12.7
|
1.0
|
|
N
|
B:LEU443
|
4.6
|
9.6
|
1.0
|
|
CA
|
B:ASP442
|
4.6
|
11.1
|
1.0
|
|
C
|
B:GLY441
|
4.6
|
11.8
|
1.0
|
|
N
|
B:ASN470
|
4.7
|
12.0
|
1.0
|
|
C
|
B:GLY472
|
4.7
|
12.0
|
1.0
|
|
CG
|
B:GLN473
|
4.8
|
13.2
|
1.0
|
|
O
|
B:ASN469
|
4.9
|
14.0
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 5z2u
Go back to
Magnesium Binding Sites List in 5z2u
Magnesium binding site 3 out
of 8 in the Thdp-MN2+ Complex of R395A 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 R395A 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
|
12.7
|
1.0
|
|
OD1
|
C:ASP442
|
1.9
|
13.3
|
1.0
|
|
OD1
|
C:ASN469
|
2.1
|
9.8
|
1.0
|
|
O
|
C:HOH766
|
2.1
|
11.2
|
1.0
|
|
O3B
|
C:TD6601
|
2.1
|
10.4
|
1.0
|
|
O2A
|
C:TD6601
|
2.2
|
13.1
|
1.0
|
|
CG
|
C:ASP442
|
3.0
|
12.1
|
1.0
|
|
C
|
C:GLY471
|
3.0
|
10.6
|
1.0
|
|
CG
|
C:ASN469
|
3.2
|
9.8
|
1.0
|
|
PA
|
C:TD6601
|
3.4
|
12.9
|
1.0
|
|
PB
|
C:TD6601
|
3.4
|
13.2
|
1.0
|
|
OD2
|
C:ASP442
|
3.5
|
12.3
|
1.0
|
|
O3A
|
C:TD6601
|
3.6
|
11.8
|
1.0
|
|
ND2
|
C:ASN469
|
3.7
|
13.2
|
1.0
|
|
N
|
C:GLY471
|
3.8
|
14.0
|
1.0
|
|
N
|
C:ASP442
|
3.9
|
9.8
|
1.0
|
|
N
|
C:GLY472
|
3.9
|
9.7
|
1.0
|
|
CA
|
C:GLY471
|
4.0
|
12.3
|
1.0
|
|
CA
|
C:GLY472
|
4.0
|
9.8
|
1.0
|
|
N
|
C:GLN473
|
4.1
|
11.2
|
1.0
|
|
O7
|
C:TD6601
|
4.2
|
12.3
|
1.0
|
|
CB
|
C:ASP442
|
4.2
|
10.8
|
1.0
|
|
N
|
C:ASN469
|
4.2
|
11.6
|
1.0
|
|
O
|
C:HOH748
|
4.2
|
13.3
|
1.0
|
|
O2B
|
C:TD6601
|
4.3
|
11.9
|
1.0
|
|
O1B
|
C:TD6601
|
4.4
|
11.3
|
1.0
|
|
CB
|
C:ASN469
|
4.4
|
11.8
|
1.0
|
|
O
|
C:VAL467
|
4.5
|
11.2
|
1.0
|
|
N
|
C:LEU443
|
4.5
|
8.6
|
1.0
|
|
N
|
C:ASN470
|
4.5
|
11.9
|
1.0
|
|
C
|
C:ASN469
|
4.5
|
11.6
|
1.0
|
|
O1A
|
C:TD6601
|
4.6
|
9.8
|
1.0
|
|
CA
|
C:ASP442
|
4.6
|
11.1
|
1.0
|
|
C
|
C:GLY472
|
4.6
|
11.7
|
1.0
|
|
CA
|
C:ASN469
|
4.6
|
12.3
|
1.0
|
|
CG
|
C:GLN473
|
4.6
|
12.8
|
1.0
|
|
CA
|
C:GLY441
|
4.7
|
10.5
|
1.0
|
|
C
|
C:GLY441
|
4.8
|
9.6
|
1.0
|
|
C
|
C:ASN470
|
4.8
|
12.8
|
1.0
|
|
CG
|
C:LEU443
|
4.8
|
11.0
|
1.0
|
|
O
|
C:ASN469
|
4.9
|
11.4
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 5z2u
Go back to
Magnesium Binding Sites List in 5z2u
Magnesium binding site 4 out
of 8 in the Thdp-MN2+ Complex of R395A 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 R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg602
b:6.0
occ:1.00
|
O
|
D:GLY471
|
2.0
|
11.2
|
1.0
|
|
O3B
|
D:TD6601
|
2.0
|
11.3
|
1.0
|
|
OD1
|
D:ASP442
|
2.1
|
9.6
|
1.0
|
|
OD1
|
D:ASN469
|
2.1
|
12.0
|
1.0
|
|
O2A
|
D:TD6601
|
2.1
|
11.3
|
1.0
|
|
O
|
D:HOH822
|
2.4
|
10.0
|
1.0
|
|
CG
|
D:ASN469
|
3.1
|
12.9
|
1.0
|
|
CG
|
D:ASP442
|
3.2
|
10.7
|
1.0
|
|
PA
|
D:TD6601
|
3.2
|
10.2
|
1.0
|
|
PB
|
D:TD6601
|
3.2
|
12.1
|
1.0
|
|
C
|
D:GLY471
|
3.2
|
12.1
|
1.0
|
|
O3A
|
D:TD6601
|
3.3
|
12.3
|
1.0
|
|
ND2
|
D:ASN469
|
3.4
|
10.0
|
1.0
|
|
OD2
|
D:ASP442
|
3.8
|
11.1
|
1.0
|
|
N
|
D:ASP442
|
3.9
|
9.7
|
1.0
|
|
N
|
D:GLY471
|
4.1
|
14.1
|
1.0
|
|
N
|
D:GLY472
|
4.1
|
13.1
|
1.0
|
|
CA
|
D:GLY472
|
4.1
|
9.9
|
1.0
|
|
O7
|
D:TD6601
|
4.1
|
16.5
|
1.0
|
|
O
|
D:HOH732
|
4.1
|
12.9
|
1.0
|
|
N
|
D:GLN473
|
4.2
|
11.9
|
1.0
|
|
O1B
|
D:TD6601
|
4.2
|
12.1
|
1.0
|
|
O2B
|
D:TD6601
|
4.2
|
11.6
|
1.0
|
|
CA
|
D:GLY471
|
4.3
|
12.6
|
1.0
|
|
N
|
D:ASN469
|
4.3
|
16.2
|
1.0
|
|
O
|
D:VAL467
|
4.3
|
11.4
|
1.0
|
|
O1A
|
D:TD6601
|
4.4
|
11.8
|
1.0
|
|
CB
|
D:ASP442
|
4.4
|
11.6
|
1.0
|
|
CB
|
D:ASN469
|
4.4
|
11.9
|
1.0
|
|
N
|
D:LEU443
|
4.5
|
10.1
|
1.0
|
|
CA
|
D:GLY441
|
4.6
|
8.7
|
1.0
|
|
CA
|
D:ASP442
|
4.7
|
11.1
|
1.0
|
|
C
|
D:GLY441
|
4.7
|
9.8
|
1.0
|
|
C
|
D:GLY472
|
4.7
|
10.9
|
1.0
|
|
CA
|
D:ASN469
|
4.7
|
13.7
|
1.0
|
|
N
|
D:ASN470
|
4.7
|
13.4
|
1.0
|
|
C
|
D:ASN469
|
4.7
|
15.5
|
1.0
|
|
CG
|
D:GLN473
|
4.8
|
11.8
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 5z2u
Go back to
Magnesium Binding Sites List in 5z2u
Magnesium binding site 5 out
of 8 in the Thdp-MN2+ Complex of R395A 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 R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg602
b:15.3
occ:1.00
|
O3B
|
E:TD6601
|
2.0
|
10.4
|
1.0
|
|
O
|
E:GLY471
|
2.0
|
13.3
|
1.0
|
|
OD1
|
E:ASP442
|
2.0
|
15.0
|
1.0
|
|
OD1
|
E:ASN469
|
2.1
|
13.8
|
1.0
|
|
O2A
|
E:TD6601
|
2.1
|
13.7
|
1.0
|
|
O
|
E:HOH784
|
2.2
|
13.2
|
1.0
|
|
CG
|
E:ASP442
|
3.0
|
13.8
|
1.0
|
|
C
|
E:GLY471
|
3.2
|
12.6
|
1.0
|
|
PB
|
E:TD6601
|
3.2
|
11.7
|
1.0
|
|
CG
|
E:ASN469
|
3.2
|
12.2
|
1.0
|
|
PA
|
E:TD6601
|
3.2
|
13.4
|
1.0
|
|
O3A
|
E:TD6601
|
3.3
|
14.5
|
1.0
|
|
OD2
|
E:ASP442
|
3.4
|
15.5
|
1.0
|
|
ND2
|
E:ASN469
|
3.6
|
12.4
|
1.0
|
|
N
|
E:ASP442
|
3.9
|
13.0
|
1.0
|
|
N
|
E:GLY471
|
3.9
|
13.5
|
1.0
|
|
N
|
E:GLY472
|
4.1
|
13.1
|
1.0
|
|
O7
|
E:TD6601
|
4.1
|
14.5
|
1.0
|
|
CA
|
E:GLY472
|
4.1
|
13.2
|
1.0
|
|
CA
|
E:GLY471
|
4.1
|
14.7
|
1.0
|
|
O2B
|
E:TD6601
|
4.1
|
11.4
|
1.0
|
|
N
|
E:GLN473
|
4.2
|
13.4
|
1.0
|
|
O1B
|
E:TD6601
|
4.2
|
14.9
|
1.0
|
|
CB
|
E:ASP442
|
4.3
|
10.0
|
1.0
|
|
O
|
E:HOH779
|
4.3
|
13.9
|
1.0
|
|
N
|
E:ASN469
|
4.3
|
11.7
|
1.0
|
|
O
|
E:VAL467
|
4.4
|
12.3
|
1.0
|
|
O1A
|
E:TD6601
|
4.5
|
15.1
|
1.0
|
|
N
|
E:LEU443
|
4.5
|
11.3
|
1.0
|
|
CB
|
E:ASN469
|
4.5
|
14.5
|
1.0
|
|
CA
|
E:ASP442
|
4.6
|
15.3
|
1.0
|
|
C
|
E:ASN469
|
4.7
|
14.1
|
1.0
|
|
CA
|
E:GLY441
|
4.7
|
11.6
|
1.0
|
|
N
|
E:ASN470
|
4.7
|
17.8
|
1.0
|
|
C
|
E:GLY472
|
4.7
|
15.4
|
1.0
|
|
CA
|
E:ASN469
|
4.7
|
13.4
|
1.0
|
|
C
|
E:GLY441
|
4.7
|
15.1
|
1.0
|
|
CG
|
E:GLN473
|
4.8
|
16.8
|
1.0
|
|
CG
|
E:LEU443
|
4.9
|
12.5
|
1.0
|
|
C
|
E:ASN470
|
5.0
|
14.8
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 5z2u
Go back to
Magnesium Binding Sites List in 5z2u
Magnesium binding site 6 out
of 8 in the Thdp-MN2+ Complex of R395A 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 R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg602
b:5.8
occ:1.00
|
OD1
|
F:ASP442
|
1.9
|
15.3
|
1.0
|
|
O
|
F:GLY471
|
2.0
|
18.4
|
1.0
|
|
O
|
F:HOH760
|
2.0
|
15.2
|
1.0
|
|
O12
|
F:TDP601
|
2.0
|
14.1
|
1.0
|
|
O22
|
F:TDP601
|
2.0
|
14.8
|
1.0
|
|
OD1
|
F:ASN469
|
2.2
|
13.4
|
1.0
|
|
CG
|
F:ASP442
|
3.0
|
15.8
|
1.0
|
|
C
|
F:GLY471
|
3.2
|
15.5
|
1.0
|
|
P1
|
F:TDP601
|
3.2
|
13.1
|
1.0
|
|
P2
|
F:TDP601
|
3.2
|
14.1
|
1.0
|
|
CG
|
F:ASN469
|
3.2
|
15.3
|
1.0
|
|
O11
|
F:TDP601
|
3.4
|
17.5
|
1.0
|
|
OD2
|
F:ASP442
|
3.4
|
17.1
|
1.0
|
|
ND2
|
F:ASN469
|
3.6
|
15.2
|
1.0
|
|
N
|
F:ASP442
|
3.8
|
11.7
|
1.0
|
|
N
|
F:GLY472
|
4.0
|
10.6
|
1.0
|
|
CA
|
F:GLY472
|
4.0
|
14.7
|
1.0
|
|
N
|
F:GLY471
|
4.1
|
15.9
|
1.0
|
|
O21
|
F:TDP601
|
4.1
|
12.8
|
1.0
|
|
N
|
F:GLN473
|
4.2
|
13.4
|
1.0
|
|
CA
|
F:GLY471
|
4.2
|
16.5
|
1.0
|
|
O5G
|
F:TDP601
|
4.2
|
15.2
|
1.0
|
|
CB
|
F:ASP442
|
4.2
|
15.4
|
1.0
|
|
O13
|
F:TDP601
|
4.3
|
11.1
|
1.0
|
|
N
|
F:ASN469
|
4.3
|
16.1
|
1.0
|
|
O23
|
F:TDP601
|
4.3
|
17.9
|
1.0
|
|
O
|
F:HOH735
|
4.3
|
18.7
|
1.0
|
|
O
|
F:VAL467
|
4.3
|
16.1
|
1.0
|
|
N
|
F:LEU443
|
4.5
|
14.8
|
1.0
|
|
CA
|
F:ASP442
|
4.5
|
14.7
|
1.0
|
|
CB
|
F:ASN469
|
4.5
|
19.3
|
1.0
|
|
CA
|
F:GLY441
|
4.6
|
13.9
|
1.0
|
|
C
|
F:GLY441
|
4.6
|
13.5
|
1.0
|
|
C
|
F:GLY472
|
4.7
|
15.2
|
1.0
|
|
CG
|
F:GLN473
|
4.8
|
16.0
|
1.0
|
|
CA
|
F:ASN469
|
4.8
|
18.1
|
1.0
|
|
N
|
F:ASN470
|
4.8
|
14.0
|
1.0
|
|
C
|
F:ASN469
|
4.8
|
16.9
|
1.0
|
|
CG
|
F:LEU443
|
5.0
|
17.1
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 5z2u
Go back to
Magnesium Binding Sites List in 5z2u
Magnesium binding site 7 out
of 8 in the Thdp-MN2+ Complex of R395A 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 R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg602
b:7.2
occ:1.00
|
OD1
|
G:ASP442
|
2.0
|
11.3
|
1.0
|
|
O2B
|
G:TD6601
|
2.0
|
14.1
|
1.0
|
|
O
|
G:GLY471
|
2.0
|
12.8
|
1.0
|
|
OD1
|
G:ASN469
|
2.0
|
12.4
|
1.0
|
|
O2A
|
G:TD6601
|
2.2
|
9.9
|
1.0
|
|
O
|
G:HOH773
|
2.6
|
12.4
|
1.0
|
|
CG
|
G:ASN469
|
3.0
|
11.9
|
1.0
|
|
CG
|
G:ASP442
|
3.1
|
10.0
|
1.0
|
|
C
|
G:GLY471
|
3.2
|
11.2
|
1.0
|
|
PB
|
G:TD6601
|
3.3
|
10.4
|
1.0
|
|
PA
|
G:TD6601
|
3.3
|
9.8
|
1.0
|
|
O3A
|
G:TD6601
|
3.4
|
12.0
|
1.0
|
|
ND2
|
G:ASN469
|
3.4
|
8.8
|
1.0
|
|
OD2
|
G:ASP442
|
3.6
|
9.7
|
1.0
|
|
N
|
G:ASP442
|
3.8
|
10.7
|
1.0
|
|
N
|
G:GLY471
|
4.0
|
11.7
|
1.0
|
|
O
|
G:HOH759
|
4.1
|
16.3
|
1.0
|
|
N
|
G:GLY472
|
4.1
|
11.1
|
1.0
|
|
CA
|
G:GLY472
|
4.2
|
11.2
|
1.0
|
|
CA
|
G:GLY471
|
4.2
|
12.9
|
1.0
|
|
O7
|
G:TD6601
|
4.2
|
12.8
|
1.0
|
|
N
|
G:GLN473
|
4.2
|
12.1
|
1.0
|
|
O3B
|
G:TD6601
|
4.2
|
10.2
|
1.0
|
|
N
|
G:ASN469
|
4.3
|
12.4
|
1.0
|
|
O
|
G:VAL467
|
4.3
|
12.0
|
1.0
|
|
CB
|
G:ASP442
|
4.3
|
11.0
|
1.0
|
|
O1B
|
G:TD6601
|
4.3
|
10.6
|
1.0
|
|
CB
|
G:ASN469
|
4.4
|
11.0
|
1.0
|
|
O1A
|
G:TD6601
|
4.4
|
12.7
|
1.0
|
|
N
|
G:LEU443
|
4.6
|
8.1
|
1.0
|
|
CA
|
G:ASP442
|
4.6
|
12.9
|
1.0
|
|
CA
|
G:GLY441
|
4.6
|
9.8
|
1.0
|
|
N
|
G:ASN470
|
4.7
|
12.3
|
1.0
|
|
C
|
G:ASN469
|
4.7
|
11.2
|
1.0
|
|
CA
|
G:ASN469
|
4.7
|
11.7
|
1.0
|
|
C
|
G:GLY441
|
4.7
|
10.1
|
1.0
|
|
CG
|
G:GLN473
|
4.7
|
11.2
|
1.0
|
|
C
|
G:GLY472
|
4.7
|
12.2
|
1.0
|
|
C
|
G:ASN470
|
5.0
|
11.8
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 5z2u
Go back to
Magnesium Binding Sites List in 5z2u
Magnesium binding site 8 out
of 8 in the Thdp-MN2+ Complex of R395A 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 8 of Thdp-MN2+ Complex of R395A Variant of Ecmend Soaked with 2- Ketoglutarate For 5 Min within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg602
b:1.0
occ:1.00
|
OD1
|
H:ASP442
|
1.9
|
14.4
|
1.0
|
|
O2A
|
H:TD6601
|
1.9
|
15.0
|
1.0
|
|
O
|
H:GLY471
|
2.0
|
19.2
|
1.0
|
|
O3B
|
H:TD6601
|
2.1
|
12.9
|
1.0
|
|
OD1
|
H:ASN469
|
2.1
|
14.8
|
1.0
|
|
O
|
H:HOH881
|
2.3
|
17.0
|
1.0
|
|
CG
|
H:ASP442
|
3.0
|
14.8
|
1.0
|
|
CG
|
H:ASN469
|
3.1
|
16.1
|
1.0
|
|
PA
|
H:TD6601
|
3.2
|
14.6
|
1.0
|
|
C
|
H:GLY471
|
3.3
|
16.9
|
1.0
|
|
PB
|
H:TD6601
|
3.3
|
14.8
|
1.0
|
|
O3A
|
H:TD6601
|
3.4
|
13.2
|
1.0
|
|
OD2
|
H:ASP442
|
3.5
|
14.7
|
1.0
|
|
ND2
|
H:ASN469
|
3.6
|
13.4
|
1.0
|
|
N
|
H:ASP442
|
3.8
|
13.8
|
1.0
|
|
N
|
H:GLY471
|
4.0
|
15.5
|
1.0
|
|
O7
|
H:TD6601
|
4.1
|
13.8
|
1.0
|
|
N
|
H:GLY472
|
4.2
|
15.3
|
1.0
|
|
O
|
H:HOH748
|
4.2
|
15.6
|
1.0
|
|
N
|
H:ASN469
|
4.2
|
15.5
|
1.0
|
|
CB
|
H:ASP442
|
4.2
|
11.4
|
1.0
|
|
CA
|
H:GLY471
|
4.2
|
15.9
|
1.0
|
|
CA
|
H:GLY472
|
4.2
|
16.1
|
1.0
|
|
O1B
|
H:TD6601
|
4.2
|
11.5
|
1.0
|
|
O1A
|
H:TD6601
|
4.3
|
12.7
|
1.0
|
|
O
|
H:VAL467
|
4.3
|
16.8
|
1.0
|
|
N
|
H:GLN473
|
4.3
|
16.3
|
1.0
|
|
O2B
|
H:TD6601
|
4.3
|
12.1
|
1.0
|
|
CB
|
H:ASN469
|
4.5
|
15.8
|
1.0
|
|
N
|
H:LEU443
|
4.5
|
12.7
|
1.0
|
|
CA
|
H:ASP442
|
4.5
|
13.7
|
1.0
|
|
CA
|
H:GLY441
|
4.6
|
13.0
|
1.0
|
|
C
|
H:GLY441
|
4.6
|
15.0
|
1.0
|
|
CA
|
H:ASN469
|
4.7
|
14.9
|
1.0
|
|
N
|
H:ASN470
|
4.7
|
16.8
|
1.0
|
|
C
|
H:ASN469
|
4.7
|
16.5
|
1.0
|
|
CG
|
H:GLN473
|
4.8
|
16.9
|
1.0
|
|
C
|
H:GLY472
|
4.8
|
17.9
|
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
|
