Magnesium in PDB 8i05: Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
Enzymatic activity of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
All present enzymatic activity of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant:
4.1.1.47;
Protein crystallography data
The structure of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant, PDB code: 8i05
was solved by
J.H.Kim,
J.S.Kim,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.81 /
2.09
|
|
Space group
|
P 41 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
189.172,
189.172,
246.506,
90,
90,
90
|
|
R / Rfree (%)
|
20.9 /
25
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
(pdb code 8i05). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the
Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant, PDB code: 8i05:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 8i05
Go back to
Magnesium Binding Sites List in 8i05
Magnesium binding site 1 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg703
b:25.2
occ:1.00
|
OD1
|
A:ASN473
|
2.0
|
26.8
|
1.0
|
|
O2A
|
A:TPP702
|
2.2
|
24.9
|
1.0
|
|
OD1
|
A:ASP446
|
2.2
|
26.0
|
1.0
|
|
O
|
A:TYR475
|
2.2
|
25.3
|
1.0
|
|
O1B
|
A:TPP702
|
2.3
|
25.3
|
1.0
|
|
O
|
A:HOH935
|
2.3
|
26.1
|
1.0
|
|
CG
|
A:ASN473
|
3.0
|
26.6
|
1.0
|
|
CG
|
A:ASP446
|
3.2
|
25.1
|
1.0
|
|
C
|
A:TYR475
|
3.3
|
25.4
|
1.0
|
|
PA
|
A:TPP702
|
3.4
|
25.7
|
1.0
|
|
PB
|
A:TPP702
|
3.4
|
28.4
|
1.0
|
|
ND2
|
A:ASN473
|
3.4
|
25.7
|
1.0
|
|
O3A
|
A:TPP702
|
3.5
|
27.6
|
1.0
|
|
OD2
|
A:ASP446
|
3.6
|
25.2
|
1.0
|
|
N
|
A:TYR475
|
3.8
|
25.6
|
1.0
|
|
N
|
A:ASP446
|
3.9
|
24.9
|
1.0
|
|
O2B
|
A:TPP702
|
4.0
|
26.8
|
1.0
|
|
O7
|
A:TPP702
|
4.0
|
24.9
|
1.0
|
|
CA
|
A:TYR475
|
4.1
|
25.6
|
1.0
|
|
N
|
A:GLY477
|
4.1
|
25.4
|
1.0
|
|
N
|
A:ASN473
|
4.2
|
25.6
|
1.0
|
|
CB
|
A:ASN473
|
4.3
|
25.8
|
1.0
|
|
N
|
A:LEU476
|
4.4
|
25.3
|
1.0
|
|
CB
|
A:TYR475
|
4.5
|
25.8
|
1.0
|
|
CB
|
A:ASP446
|
4.5
|
25.0
|
1.0
|
|
N
|
A:PHE447
|
4.5
|
24.7
|
1.0
|
|
CA
|
A:LEU476
|
4.6
|
25.2
|
1.0
|
|
N
|
A:ALA474
|
4.6
|
25.7
|
1.0
|
|
CA
|
A:ASN473
|
4.6
|
25.8
|
1.0
|
|
CA
|
A:GLY445
|
4.6
|
24.8
|
1.0
|
|
O3B
|
A:TPP702
|
4.6
|
27.5
|
1.0
|
|
CA
|
A:ASP446
|
4.7
|
24.8
|
1.0
|
|
O1A
|
A:TPP702
|
4.7
|
24.6
|
1.0
|
|
O
|
A:VAL471
|
4.7
|
25.2
|
1.0
|
|
C
|
A:GLY445
|
4.7
|
24.7
|
1.0
|
|
C
|
A:ASN473
|
4.7
|
25.8
|
1.0
|
|
C
|
A:LEU476
|
4.9
|
25.4
|
1.0
|
|
CA
|
A:GLY477
|
4.9
|
25.6
|
1.0
|
|
C
|
A:ALA474
|
4.9
|
25.7
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 8i05
Go back to
Magnesium Binding Sites List in 8i05
Magnesium binding site 2 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg704
b:23.4
occ:0.39
|
OE1
|
A:GLU454
|
2.3
|
23.4
|
0.9
|
|
O
|
A:PHE451
|
2.5
|
23.6
|
1.0
|
|
CD
|
A:GLU454
|
3.2
|
23.3
|
1.0
|
|
C
|
A:PHE451
|
3.5
|
23.6
|
1.0
|
|
OE2
|
A:GLU454
|
3.6
|
23.2
|
1.0
|
|
CA
|
A:LEU452
|
3.6
|
23.5
|
1.0
|
|
CD2
|
A:LEU452
|
3.8
|
23.2
|
1.0
|
|
N
|
A:LEU452
|
4.0
|
23.6
|
1.0
|
|
C
|
A:LEU452
|
4.3
|
23.5
|
1.0
|
|
N
|
A:ILE453
|
4.3
|
23.7
|
1.0
|
|
O
|
A:GLN450
|
4.4
|
23.9
|
1.0
|
|
CG
|
A:GLU454
|
4.4
|
23.3
|
1.0
|
|
CB
|
A:LEU452
|
4.7
|
23.4
|
1.0
|
|
CD2
|
A:HIS50
|
4.7
|
23.0
|
1.0
|
|
CA
|
A:PHE451
|
4.8
|
23.8
|
1.0
|
|
N
|
A:GLU454
|
4.8
|
23.6
|
1.0
|
|
CG
|
A:LEU452
|
4.8
|
23.3
|
1.0
|
|
CB
|
A:GLU454
|
4.9
|
23.4
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 8i05
Go back to
Magnesium Binding Sites List in 8i05
Magnesium binding site 3 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg703
b:27.4
occ:1.00
|
O1A
|
B:TPP702
|
2.1
|
26.6
|
1.0
|
|
O
|
B:TYR475
|
2.2
|
26.1
|
1.0
|
|
OD1
|
B:ASN473
|
2.2
|
28.8
|
1.0
|
|
OD1
|
B:ASP446
|
2.2
|
27.3
|
1.0
|
|
O3B
|
B:TPP702
|
2.3
|
29.4
|
1.0
|
|
CG
|
B:ASN473
|
3.1
|
30.4
|
1.0
|
|
PA
|
B:TPP702
|
3.2
|
28.9
|
1.0
|
|
PB
|
B:TPP702
|
3.3
|
29.9
|
1.0
|
|
CG
|
B:ASP446
|
3.3
|
26.4
|
1.0
|
|
O3A
|
B:TPP702
|
3.3
|
31.1
|
1.0
|
|
C
|
B:TYR475
|
3.3
|
29.3
|
1.0
|
|
ND2
|
B:ASN473
|
3.4
|
27.9
|
1.0
|
|
OD2
|
B:ASP446
|
3.7
|
26.6
|
1.0
|
|
N
|
B:ASP446
|
3.8
|
23.0
|
1.0
|
|
N
|
B:TYR475
|
3.8
|
26.9
|
1.0
|
|
O2B
|
B:TPP702
|
4.0
|
28.4
|
1.0
|
|
O7
|
B:TPP702
|
4.0
|
28.2
|
1.0
|
|
CA
|
B:TYR475
|
4.1
|
28.9
|
1.0
|
|
N
|
B:GLY477
|
4.1
|
28.6
|
1.0
|
|
N
|
B:ASN473
|
4.2
|
25.6
|
1.0
|
|
N
|
B:LEU476
|
4.4
|
28.4
|
1.0
|
|
CB
|
B:TYR475
|
4.4
|
28.0
|
1.0
|
|
N
|
B:PHE447
|
4.4
|
22.9
|
1.0
|
|
CB
|
B:ASN473
|
4.4
|
26.8
|
1.0
|
|
CA
|
B:GLY445
|
4.5
|
25.0
|
1.0
|
|
CB
|
B:ASP446
|
4.5
|
23.7
|
1.0
|
|
O2A
|
B:TPP702
|
4.5
|
25.6
|
1.0
|
|
C
|
B:GLY445
|
4.5
|
25.9
|
1.0
|
|
O
|
B:VAL471
|
4.6
|
25.7
|
1.0
|
|
O1B
|
B:TPP702
|
4.6
|
28.8
|
1.0
|
|
CA
|
B:LEU476
|
4.6
|
28.8
|
1.0
|
|
CA
|
B:ASP446
|
4.6
|
23.2
|
1.0
|
|
CA
|
B:ASN473
|
4.7
|
29.2
|
1.0
|
|
N
|
B:ALA474
|
4.8
|
28.0
|
1.0
|
|
C
|
B:ASN473
|
4.9
|
28.5
|
1.0
|
|
C
|
B:LEU476
|
4.9
|
30.4
|
1.0
|
|
CA
|
B:GLY477
|
5.0
|
27.9
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 8i05
Go back to
Magnesium Binding Sites List in 8i05
Magnesium binding site 4 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg704
b:23.9
occ:0.49
|
O
|
B:PHE451
|
2.4
|
23.6
|
1.0
|
|
OE1
|
B:GLU454
|
2.8
|
24.2
|
0.8
|
|
C
|
B:PHE451
|
3.5
|
23.5
|
1.0
|
|
CD
|
B:GLU454
|
3.7
|
24.3
|
1.0
|
|
OE2
|
B:GLU454
|
3.9
|
24.2
|
1.0
|
|
CA
|
B:LEU452
|
4.0
|
23.8
|
1.0
|
|
CD2
|
B:LEU452
|
4.1
|
23.7
|
1.0
|
|
N
|
B:LEU452
|
4.2
|
23.6
|
1.0
|
|
O
|
B:GLN450
|
4.3
|
23.7
|
1.0
|
|
N
|
B:ILE453
|
4.6
|
24.0
|
1.0
|
|
C
|
B:LEU452
|
4.7
|
24.0
|
1.0
|
|
CD2
|
B:HIS50
|
4.7
|
24.0
|
1.0
|
|
CA
|
B:PHE451
|
4.7
|
23.4
|
1.0
|
|
CG
|
B:GLU454
|
4.9
|
24.6
|
1.0
|
|
CB
|
B:LEU452
|
5.0
|
23.7
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 8i05
Go back to
Magnesium Binding Sites List in 8i05
Magnesium binding site 5 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg703
b:29.2
occ:1.00
|
O2A
|
C:TPP702
|
2.1
|
29.7
|
1.0
|
|
O
|
C:TYR475
|
2.1
|
32.1
|
1.0
|
|
O1B
|
C:TPP702
|
2.2
|
30.5
|
1.0
|
|
OD1
|
C:ASN473
|
2.2
|
31.9
|
1.0
|
|
OD1
|
C:ASP446
|
2.3
|
32.0
|
1.0
|
|
O
|
C:HOH865
|
2.3
|
32.3
|
1.0
|
|
CG
|
C:ASN473
|
3.0
|
33.1
|
1.0
|
|
PA
|
C:TPP702
|
3.2
|
33.4
|
1.0
|
|
PB
|
C:TPP702
|
3.2
|
33.7
|
1.0
|
|
O3A
|
C:TPP702
|
3.2
|
31.6
|
1.0
|
|
ND2
|
C:ASN473
|
3.3
|
30.5
|
1.0
|
|
C
|
C:TYR475
|
3.3
|
31.9
|
1.0
|
|
CG
|
C:ASP446
|
3.3
|
32.3
|
1.0
|
|
OD2
|
C:ASP446
|
3.8
|
29.3
|
1.0
|
|
O2B
|
C:TPP702
|
3.8
|
33.6
|
1.0
|
|
O7
|
C:TPP702
|
3.8
|
31.3
|
1.0
|
|
N
|
C:ASP446
|
3.9
|
28.9
|
1.0
|
|
N
|
C:TYR475
|
3.9
|
29.2
|
1.0
|
|
N
|
C:GLY477
|
4.0
|
31.8
|
1.0
|
|
CA
|
C:TYR475
|
4.1
|
33.0
|
1.0
|
|
N
|
C:LEU476
|
4.3
|
31.9
|
1.0
|
|
N
|
C:ASN473
|
4.3
|
29.7
|
1.0
|
|
CB
|
C:ASN473
|
4.4
|
32.4
|
1.0
|
|
N
|
C:PHE447
|
4.4
|
30.0
|
1.0
|
|
CB
|
C:TYR475
|
4.5
|
33.0
|
1.0
|
|
CA
|
C:LEU476
|
4.5
|
30.8
|
1.0
|
|
O1A
|
C:TPP702
|
4.5
|
32.0
|
1.0
|
|
O3B
|
C:TPP702
|
4.5
|
32.7
|
1.0
|
|
CA
|
C:GLY445
|
4.6
|
31.9
|
1.0
|
|
CB
|
C:ASP446
|
4.6
|
30.2
|
1.0
|
|
C
|
C:GLY445
|
4.7
|
30.1
|
1.0
|
|
CA
|
C:ASP446
|
4.7
|
30.3
|
1.0
|
|
O
|
C:VAL471
|
4.7
|
28.8
|
1.0
|
|
CA
|
C:ASN473
|
4.8
|
32.0
|
1.0
|
|
C
|
C:LEU476
|
4.8
|
32.2
|
1.0
|
|
CA
|
C:GLY477
|
4.8
|
31.3
|
1.0
|
|
N
|
C:ALA474
|
4.8
|
30.1
|
1.0
|
|
C
|
C:ASN473
|
4.9
|
32.0
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 8i05
Go back to
Magnesium Binding Sites List in 8i05
Magnesium binding site 6 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg704
b:31.1
occ:1.00
|
O
|
C:PHE451
|
2.3
|
32.0
|
1.0
|
|
OE1
|
E:GLU454
|
2.4
|
27.1
|
0.6
|
|
OE1
|
C:GLU454
|
2.4
|
29.3
|
0.9
|
|
O
|
E:PHE451
|
2.7
|
32.1
|
1.0
|
|
CD
|
E:GLU454
|
3.2
|
30.1
|
1.0
|
|
CD
|
C:GLU454
|
3.3
|
31.5
|
1.0
|
|
C
|
C:PHE451
|
3.3
|
30.4
|
1.0
|
|
CA
|
C:LEU452
|
3.5
|
29.1
|
1.0
|
|
OE2
|
E:GLU454
|
3.6
|
31.4
|
1.0
|
|
OE2
|
C:GLU454
|
3.6
|
29.2
|
1.0
|
|
C
|
E:PHE451
|
3.7
|
30.9
|
1.0
|
|
CA
|
E:LEU452
|
3.8
|
28.5
|
1.0
|
|
N
|
C:LEU452
|
3.8
|
29.0
|
1.0
|
|
CD2
|
E:LEU452
|
3.9
|
29.2
|
1.0
|
|
CD2
|
C:LEU452
|
3.9
|
28.3
|
1.0
|
|
O
|
C:GLN450
|
4.1
|
30.1
|
1.0
|
|
N
|
E:LEU452
|
4.2
|
27.1
|
1.0
|
|
N
|
C:ILE453
|
4.2
|
32.6
|
1.0
|
|
C
|
C:LEU452
|
4.2
|
31.4
|
1.0
|
|
CG
|
E:GLU454
|
4.3
|
29.2
|
1.0
|
|
C
|
E:LEU452
|
4.3
|
29.5
|
1.0
|
|
N
|
E:ILE453
|
4.4
|
30.9
|
1.0
|
|
O
|
E:GLN450
|
4.5
|
27.4
|
1.0
|
|
CG
|
C:GLU454
|
4.5
|
30.2
|
1.0
|
|
CA
|
C:PHE451
|
4.6
|
29.3
|
1.0
|
|
CB
|
C:LEU452
|
4.6
|
28.4
|
1.0
|
|
CD2
|
E:HIS50
|
4.7
|
29.2
|
1.0
|
|
N
|
E:GLU454
|
4.7
|
30.6
|
1.0
|
|
CG
|
C:LEU452
|
4.7
|
30.2
|
1.0
|
|
CB
|
E:GLU454
|
4.8
|
29.9
|
1.0
|
|
N
|
C:GLU454
|
4.8
|
30.1
|
1.0
|
|
CB
|
E:LEU452
|
4.8
|
26.9
|
1.0
|
|
CG
|
E:LEU452
|
4.9
|
29.0
|
1.0
|
|
CD2
|
C:HIS50
|
4.9
|
27.6
|
1.0
|
|
CB
|
C:GLU454
|
5.0
|
30.7
|
1.0
|
|
CA
|
E:PHE451
|
5.0
|
27.1
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 8i05
Go back to
Magnesium Binding Sites List in 8i05
Magnesium binding site 7 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg703
b:33.4
occ:1.00
|
O
|
D:TYR475
|
2.0
|
34.9
|
1.0
|
|
O1A
|
D:TPP702
|
2.1
|
32.4
|
1.0
|
|
O3B
|
D:TPP702
|
2.1
|
36.6
|
1.0
|
|
OD1
|
D:ASN473
|
2.2
|
35.2
|
1.0
|
|
O
|
D:HOH908
|
2.2
|
31.2
|
1.0
|
|
OD1
|
D:ASP446
|
2.4
|
32.8
|
1.0
|
|
CG
|
D:ASN473
|
3.1
|
37.1
|
1.0
|
|
C
|
D:TYR475
|
3.2
|
37.1
|
1.0
|
|
PB
|
D:TPP702
|
3.2
|
35.6
|
1.0
|
|
PA
|
D:TPP702
|
3.2
|
35.6
|
1.0
|
|
O3A
|
D:TPP702
|
3.3
|
33.8
|
1.0
|
|
CG
|
D:ASP446
|
3.4
|
34.1
|
1.0
|
|
ND2
|
D:ASN473
|
3.4
|
34.8
|
1.0
|
|
OD2
|
D:ASP446
|
3.7
|
32.5
|
1.0
|
|
N
|
D:TYR475
|
3.8
|
35.0
|
1.0
|
|
CA
|
D:TYR475
|
3.9
|
36.6
|
1.0
|
|
O2B
|
D:TPP702
|
3.9
|
36.9
|
1.0
|
|
N
|
D:GLY477
|
4.0
|
36.5
|
1.0
|
|
N
|
D:ASP446
|
4.0
|
29.0
|
1.0
|
|
O7
|
D:TPP702
|
4.0
|
32.9
|
1.0
|
|
N
|
D:LEU476
|
4.2
|
35.3
|
1.0
|
|
CB
|
D:TYR475
|
4.3
|
34.7
|
1.0
|
|
N
|
D:ASN473
|
4.4
|
34.2
|
1.0
|
|
CA
|
D:LEU476
|
4.4
|
36.9
|
1.0
|
|
N
|
D:PHE447
|
4.5
|
31.0
|
1.0
|
|
O1B
|
D:TPP702
|
4.5
|
36.9
|
1.0
|
|
CB
|
D:ASN473
|
4.5
|
31.1
|
1.0
|
|
O2A
|
D:TPP702
|
4.6
|
31.9
|
1.0
|
|
CB
|
D:ASP446
|
4.6
|
31.4
|
1.0
|
|
CA
|
D:GLY445
|
4.6
|
32.9
|
1.0
|
|
C
|
D:GLY445
|
4.7
|
32.6
|
1.0
|
|
N
|
D:ALA474
|
4.7
|
33.3
|
1.0
|
|
C
|
D:LEU476
|
4.7
|
35.8
|
1.0
|
|
CA
|
D:ASP446
|
4.8
|
31.3
|
1.0
|
|
CA
|
D:GLY477
|
4.8
|
35.4
|
1.0
|
|
CA
|
D:ASN473
|
4.8
|
33.9
|
1.0
|
|
O
|
D:VAL471
|
4.8
|
31.3
|
1.0
|
|
C
|
D:ASN473
|
4.8
|
34.9
|
1.0
|
|
C
|
D:ALA474
|
5.0
|
37.6
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 8i05
Go back to
Magnesium Binding Sites List in 8i05
Magnesium binding site 8 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg704
b:33.5
occ:1.00
|
OE1
|
D:GLU454
|
2.3
|
27.4
|
0.6
|
|
O
|
F:PHE451
|
2.4
|
29.9
|
1.0
|
|
O
|
D:PHE451
|
2.5
|
28.6
|
1.0
|
|
OE1
|
F:GLU454
|
2.5
|
27.4
|
0.8
|
|
CD
|
D:GLU454
|
3.1
|
29.2
|
1.0
|
|
CD
|
F:GLU454
|
3.3
|
30.7
|
1.0
|
|
OE2
|
D:GLU454
|
3.4
|
31.2
|
1.0
|
|
C
|
F:PHE451
|
3.5
|
31.1
|
1.0
|
|
C
|
D:PHE451
|
3.6
|
27.4
|
1.0
|
|
CA
|
D:LEU452
|
3.6
|
27.8
|
1.0
|
|
OE2
|
F:GLU454
|
3.6
|
32.1
|
1.0
|
|
CA
|
F:LEU452
|
3.7
|
29.0
|
1.0
|
|
CD2
|
D:LEU452
|
3.8
|
27.4
|
1.0
|
|
CD2
|
F:LEU452
|
3.8
|
26.9
|
1.0
|
|
N
|
F:LEU452
|
4.0
|
27.4
|
1.0
|
|
N
|
D:LEU452
|
4.0
|
26.9
|
1.0
|
|
C
|
D:LEU452
|
4.3
|
29.2
|
1.0
|
|
N
|
D:ILE453
|
4.3
|
28.2
|
1.0
|
|
O
|
F:GLN450
|
4.3
|
30.8
|
1.0
|
|
C
|
F:LEU452
|
4.4
|
29.2
|
1.0
|
|
N
|
F:ILE453
|
4.4
|
29.8
|
1.0
|
|
O
|
D:GLN450
|
4.4
|
30.5
|
1.0
|
|
CD2
|
D:HIS50
|
4.4
|
29.0
|
1.0
|
|
CG
|
D:GLU454
|
4.4
|
29.7
|
1.0
|
|
CG
|
F:GLU454
|
4.6
|
29.2
|
1.0
|
|
CB
|
D:LEU452
|
4.6
|
28.3
|
1.0
|
|
CD2
|
F:HIS50
|
4.6
|
28.6
|
1.0
|
|
CA
|
F:PHE451
|
4.7
|
31.3
|
1.0
|
|
CB
|
F:LEU452
|
4.7
|
28.9
|
1.0
|
|
CG
|
F:LEU452
|
4.8
|
31.2
|
1.0
|
|
CG
|
D:LEU452
|
4.8
|
30.6
|
1.0
|
|
N
|
D:GLU454
|
4.8
|
29.3
|
1.0
|
|
CA
|
D:PHE451
|
4.9
|
25.3
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 8i05
Go back to
Magnesium Binding Sites List in 8i05
Magnesium binding site 9 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg703
b:32.3
occ:1.00
|
OD1
|
E:ASP446
|
2.1
|
36.2
|
1.0
|
|
O
|
E:TYR475
|
2.2
|
34.1
|
1.0
|
|
OD1
|
E:ASN473
|
2.2
|
37.6
|
1.0
|
|
O1A
|
E:TPP702
|
2.2
|
37.1
|
1.0
|
|
O3B
|
E:TPP702
|
2.2
|
37.5
|
1.0
|
|
O
|
E:HOH835
|
2.4
|
34.9
|
1.0
|
|
CG
|
E:ASN473
|
3.1
|
37.9
|
1.0
|
|
CG
|
E:ASP446
|
3.2
|
35.8
|
1.0
|
|
PA
|
E:TPP702
|
3.3
|
35.6
|
1.0
|
|
C
|
E:TYR475
|
3.3
|
35.9
|
1.0
|
|
PB
|
E:TPP702
|
3.3
|
41.8
|
1.0
|
|
O3A
|
E:TPP702
|
3.4
|
35.1
|
1.0
|
|
ND2
|
E:ASN473
|
3.5
|
36.6
|
1.0
|
|
N
|
E:TYR475
|
3.7
|
36.3
|
1.0
|
|
OD2
|
E:ASP446
|
3.7
|
34.2
|
1.0
|
|
N
|
E:ASP446
|
3.8
|
33.8
|
1.0
|
|
CA
|
E:TYR475
|
4.0
|
38.0
|
1.0
|
|
O2B
|
E:TPP702
|
4.0
|
34.3
|
1.0
|
|
O7
|
E:TPP702
|
4.1
|
38.5
|
1.0
|
|
N
|
E:GLY477
|
4.2
|
36.0
|
1.0
|
|
N
|
E:ASN473
|
4.2
|
33.9
|
1.0
|
|
CB
|
E:TYR475
|
4.4
|
38.3
|
1.0
|
|
N
|
E:PHE447
|
4.4
|
33.3
|
1.0
|
|
N
|
E:LEU476
|
4.4
|
36.8
|
1.0
|
|
CB
|
E:ASP446
|
4.5
|
32.3
|
1.0
|
|
CB
|
E:ASN473
|
4.5
|
36.0
|
1.0
|
|
O
|
E:VAL471
|
4.6
|
31.2
|
1.0
|
|
O2A
|
E:TPP702
|
4.6
|
31.6
|
1.0
|
|
CA
|
E:GLY445
|
4.6
|
32.7
|
1.0
|
|
N
|
E:ALA474
|
4.6
|
35.0
|
1.0
|
|
CA
|
E:ASP446
|
4.6
|
31.4
|
1.0
|
|
C
|
E:GLY445
|
4.6
|
32.8
|
1.0
|
|
O1B
|
E:TPP702
|
4.6
|
37.2
|
1.0
|
|
CA
|
E:LEU476
|
4.7
|
38.1
|
1.0
|
|
CA
|
E:ASN473
|
4.7
|
36.6
|
1.0
|
|
C
|
E:ASN473
|
4.7
|
37.2
|
1.0
|
|
C
|
E:ALA474
|
4.9
|
38.2
|
1.0
|
|
CA
|
E:GLY477
|
4.9
|
38.9
|
1.0
|
|
C
|
E:LEU476
|
5.0
|
37.0
|
1.0
|
|
CB
|
E:PHE447
|
5.0
|
31.3
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 8i05
Go back to
Magnesium Binding Sites List in 8i05
Magnesium binding site 10 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg703
b:37.2
occ:1.00
|
O2A
|
F:TPP702
|
2.1
|
35.2
|
1.0
|
|
O
|
F:TYR475
|
2.2
|
35.3
|
1.0
|
|
OD1
|
F:ASN473
|
2.2
|
38.9
|
1.0
|
|
O2B
|
F:TPP702
|
2.2
|
36.7
|
1.0
|
|
O
|
F:HOH935
|
2.2
|
35.0
|
1.0
|
|
OD1
|
F:ASP446
|
2.3
|
36.1
|
1.0
|
|
CG
|
F:ASN473
|
3.1
|
40.2
|
1.0
|
|
PA
|
F:TPP702
|
3.2
|
37.7
|
1.0
|
|
PB
|
F:TPP702
|
3.2
|
40.1
|
1.0
|
|
O3A
|
F:TPP702
|
3.3
|
40.4
|
1.0
|
|
CG
|
F:ASP446
|
3.3
|
35.2
|
1.0
|
|
C
|
F:TYR475
|
3.3
|
41.0
|
1.0
|
|
ND2
|
F:ASN473
|
3.4
|
36.5
|
1.0
|
|
OD2
|
F:ASP446
|
3.8
|
32.8
|
1.0
|
|
N
|
F:ASP446
|
3.8
|
31.4
|
1.0
|
|
O7
|
F:TPP702
|
3.9
|
39.2
|
1.0
|
|
N
|
F:TYR475
|
3.9
|
38.1
|
1.0
|
|
N
|
F:GLY477
|
4.0
|
40.4
|
1.0
|
|
O1B
|
F:TPP702
|
4.0
|
39.5
|
1.0
|
|
CA
|
F:TYR475
|
4.1
|
39.6
|
1.0
|
|
N
|
F:ASN473
|
4.3
|
33.5
|
1.0
|
|
N
|
F:PHE447
|
4.4
|
33.4
|
1.0
|
|
N
|
F:LEU476
|
4.4
|
39.1
|
1.0
|
|
CB
|
F:TYR475
|
4.4
|
40.0
|
1.0
|
|
CA
|
F:GLY445
|
4.5
|
34.8
|
1.0
|
|
CB
|
F:ASN473
|
4.5
|
36.2
|
1.0
|
|
O1A
|
F:TPP702
|
4.5
|
33.1
|
1.0
|
|
O3B
|
F:TPP702
|
4.5
|
38.9
|
1.0
|
|
C
|
F:GLY445
|
4.5
|
34.1
|
1.0
|
|
CB
|
F:ASP446
|
4.5
|
31.7
|
1.0
|
|
CA
|
F:LEU476
|
4.6
|
38.9
|
1.0
|
|
CA
|
F:ASP446
|
4.6
|
31.6
|
1.0
|
|
O
|
F:VAL471
|
4.7
|
33.5
|
1.0
|
|
N
|
F:ALA474
|
4.8
|
37.2
|
1.0
|
|
CA
|
F:GLY477
|
4.8
|
39.4
|
1.0
|
|
CA
|
F:ASN473
|
4.8
|
37.7
|
1.0
|
|
C
|
F:LEU476
|
4.9
|
40.3
|
1.0
|
|
C
|
F:ASN473
|
5.0
|
38.3
|
1.0
|
|
CB
|
F:PHE447
|
5.0
|
31.3
|
1.0
|
|
Reference:
J.H.Kim,
H.Cheon,
H.J.Jo,
J.W.Kim,
G.Y.Kim,
H.R.Seo,
P.W.Seo,
J.S.Kim,
J.B.Park.
Engineering of Two Thiamine Diphosphate-Dependent Enzymes For the Regioselective Condensation of C1-Formaldehyde Into C4-Erythrulose Int.J.Biol.Macromol. V. 253 27674 2023.
ISSN: ISSN 0141-8130
DOI: 10.1016/J.IJBIOMAC.2023.127674
Page generated: Fri Oct 4 08:59:51 2024
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