Magnesium in PDB 5tma: Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3
Enzymatic activity of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3
All present enzymatic activity of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3:
4.1.1.1;
Protein crystallography data
The structure of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3, PDB code: 5tma
was solved by
P.M.Alahuhta,
V.V.Lunin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
101.18 /
1.67
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.440,
124.440,
173.825,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17 /
20.3
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3
(pdb code 5tma). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3, PDB code: 5tma:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 5tma
Go back to
Magnesium Binding Sites List in 5tma
Magnesium binding site 1 out
of 2 in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:20.7
occ:1.00
|
O1A
|
A:TPP601
|
2.0
|
22.0
|
0.9
|
O2B
|
A:TPP601
|
2.0
|
21.9
|
0.9
|
O
|
A:GLY469
|
2.1
|
24.3
|
1.0
|
OD1
|
A:ASP440
|
2.1
|
22.1
|
1.0
|
O
|
A:HOH961
|
2.2
|
24.2
|
1.0
|
OD1
|
A:ASN467
|
2.2
|
25.4
|
1.0
|
PA
|
A:TPP601
|
3.1
|
22.6
|
0.9
|
CG
|
A:ASN467
|
3.2
|
28.9
|
1.0
|
PB
|
A:TPP601
|
3.2
|
27.8
|
0.9
|
C
|
A:GLY469
|
3.3
|
29.0
|
1.0
|
CG
|
A:ASP440
|
3.4
|
23.3
|
1.0
|
O3A
|
A:TPP601
|
3.5
|
23.7
|
0.9
|
ND2
|
A:ASN467
|
3.5
|
24.7
|
1.0
|
OD2
|
A:ASP440
|
3.9
|
28.1
|
1.0
|
O7
|
A:TPP601
|
4.0
|
23.3
|
0.9
|
N
|
A:ASP440
|
4.0
|
16.6
|
1.0
|
N
|
A:GLY469
|
4.1
|
27.2
|
1.0
|
N
|
A:GLY441
|
4.1
|
18.4
|
1.0
|
O3B
|
A:TPP601
|
4.1
|
27.0
|
0.9
|
N
|
A:THR471
|
4.1
|
28.3
|
1.0
|
CA
|
A:GLY469
|
4.2
|
26.3
|
1.0
|
N
|
A:TYR470
|
4.3
|
24.4
|
1.0
|
O
|
A:HOH719
|
4.3
|
38.0
|
1.0
|
CA
|
A:TYR470
|
4.4
|
26.0
|
1.0
|
O1B
|
A:TPP601
|
4.4
|
34.8
|
0.9
|
O2A
|
A:TPP601
|
4.4
|
21.5
|
0.9
|
O
|
A:ILE465
|
4.4
|
18.7
|
1.0
|
CB
|
A:ASN467
|
4.5
|
25.9
|
1.0
|
CB
|
A:ASP440
|
4.6
|
19.5
|
1.0
|
CA
|
A:GLY439
|
4.6
|
15.4
|
1.0
|
OG1
|
A:THR471
|
4.6
|
36.2
|
1.0
|
N
|
A:ASN467
|
4.7
|
21.7
|
1.0
|
O
|
A:HOH784
|
4.7
|
26.3
|
1.0
|
C
|
A:GLY439
|
4.7
|
15.3
|
1.0
|
C
|
A:ASN467
|
4.7
|
29.3
|
1.0
|
CA
|
A:ASP440
|
4.7
|
18.4
|
1.0
|
CB
|
A:THR471
|
4.8
|
32.6
|
1.0
|
C
|
A:TYR470
|
4.8
|
26.1
|
1.0
|
CA
|
A:ASN467
|
4.8
|
26.6
|
1.0
|
CA
|
A:GLY441
|
4.9
|
17.8
|
1.0
|
O
|
A:ASN467
|
4.9
|
27.7
|
1.0
|
N
|
A:TYR468
|
4.9
|
27.9
|
1.0
|
C
|
A:ASP440
|
4.9
|
18.2
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 5tma
Go back to
Magnesium Binding Sites List in 5tma
Magnesium binding site 2 out
of 2 in the Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:24.7
occ:1.00
|
O2A
|
B:TPP601
|
2.0
|
17.9
|
0.8
|
O1B
|
B:TPP601
|
2.1
|
21.1
|
0.8
|
OD1
|
B:ASP440
|
2.2
|
24.5
|
1.0
|
OD1
|
B:ASN467
|
2.2
|
23.3
|
1.0
|
O
|
B:HOH962
|
2.2
|
23.9
|
1.0
|
O
|
B:GLY469
|
2.2
|
26.3
|
1.0
|
CG
|
B:ASN467
|
3.1
|
26.6
|
1.0
|
PA
|
B:TPP601
|
3.1
|
21.5
|
0.8
|
PB
|
B:TPP601
|
3.3
|
24.1
|
0.8
|
CG
|
B:ASP440
|
3.4
|
24.1
|
1.0
|
C
|
B:GLY469
|
3.4
|
29.6
|
1.0
|
O3A
|
B:TPP601
|
3.4
|
23.8
|
0.8
|
ND2
|
B:ASN467
|
3.4
|
28.9
|
1.0
|
N
|
B:ASP440
|
4.0
|
19.2
|
1.0
|
OD2
|
B:ASP440
|
4.0
|
31.8
|
1.0
|
O7
|
B:TPP601
|
4.0
|
22.2
|
0.8
|
N
|
B:GLY441
|
4.1
|
20.2
|
1.0
|
N
|
B:GLY469
|
4.1
|
26.8
|
1.0
|
O2B
|
B:TPP601
|
4.2
|
26.7
|
0.8
|
N
|
B:THR471
|
4.2
|
28.2
|
1.0
|
O
|
B:ILE465
|
4.3
|
21.6
|
1.0
|
N
|
B:TYR470
|
4.3
|
27.6
|
1.0
|
CA
|
B:GLY469
|
4.3
|
27.1
|
1.0
|
O1A
|
B:TPP601
|
4.3
|
23.0
|
0.8
|
CA
|
B:TYR470
|
4.4
|
29.6
|
1.0
|
O3B
|
B:TPP601
|
4.4
|
28.9
|
0.8
|
CB
|
B:ASN467
|
4.5
|
23.7
|
1.0
|
CA
|
B:GLY439
|
4.5
|
17.7
|
1.0
|
N
|
B:ASN467
|
4.5
|
23.0
|
1.0
|
CB
|
B:ASP440
|
4.6
|
21.9
|
1.0
|
C
|
B:GLY439
|
4.6
|
19.5
|
1.0
|
CA
|
B:ASP440
|
4.6
|
19.5
|
1.0
|
O
|
B:HOH1021
|
4.7
|
29.0
|
1.0
|
C
|
B:ASN467
|
4.7
|
25.9
|
1.0
|
CA
|
B:ASN467
|
4.8
|
21.5
|
1.0
|
OG1
|
B:THR471
|
4.8
|
33.4
|
1.0
|
C
|
B:TYR470
|
4.8
|
30.7
|
1.0
|
C
|
B:ASP440
|
4.9
|
20.9
|
1.0
|
O
|
B:HOH777
|
4.9
|
40.0
|
1.0
|
CA
|
B:GLY441
|
4.9
|
20.0
|
1.0
|
N
|
B:TYR468
|
4.9
|
28.4
|
1.0
|
|
Reference:
D.W.Sammond,
N.Kastelowitz,
B.S.Donohoe,
M.Alahuhta,
V.V.Lunin,
D.Chung,
N.S.Sarai,
H.Yin,
A.Mittal,
M.E.Himmel,
A.M.Guss,
Y.J.Bomble.
An Iterative Computational Design Approach to Increase the Thermal Endurance of A Mesophilic Enzyme. Biotechnol Biofuels V. 11 189 2018.
ISSN: ESSN 1754-6834
PubMed: 30002729
DOI: 10.1186/S13068-018-1178-9
Page generated: Mon Dec 14 21:12:42 2020
|