Magnesium in PDB 8i01: Crystal Structure of Escherichia Coli Glyoxylate Carboligase
Enzymatic activity of Crystal Structure of Escherichia Coli Glyoxylate Carboligase
All present enzymatic activity of Crystal Structure of Escherichia Coli Glyoxylate Carboligase:
4.1.1.47;
Protein crystallography data
The structure of Crystal Structure of Escherichia Coli Glyoxylate Carboligase, PDB code: 8i01
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)
|
48.58 /
2.15
|
|
Space group
|
P 41 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
189.617,
189.617,
248.631,
90,
90,
90
|
|
R / Rfree (%)
|
19.1 /
23.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
(pdb code 8i01). 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, PDB code: 8i01:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 8i01
Go back to
Magnesium Binding Sites List in 8i01
Magnesium binding site 1 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
 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 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg703
b:19.8
occ:1.00
|
OD1
|
A:ASN473
|
2.0
|
20.0
|
1.0
|
|
O
|
A:TYR475
|
2.1
|
19.8
|
1.0
|
|
O2A
|
A:TPP702
|
2.1
|
19.5
|
1.0
|
|
OD1
|
A:ASP446
|
2.2
|
19.6
|
1.0
|
|
O1B
|
A:TPP702
|
2.2
|
19.9
|
1.0
|
|
O
|
A:HOH880
|
2.5
|
19.8
|
1.0
|
|
CG
|
A:ASN473
|
3.0
|
20.1
|
1.0
|
|
CG
|
A:ASP446
|
3.2
|
19.5
|
1.0
|
|
C
|
A:TYR475
|
3.3
|
19.9
|
1.0
|
|
PA
|
A:TPP702
|
3.3
|
20.4
|
1.0
|
|
PB
|
A:TPP702
|
3.3
|
19.8
|
1.0
|
|
ND2
|
A:ASN473
|
3.4
|
20.2
|
1.0
|
|
O3A
|
A:TPP702
|
3.4
|
19.8
|
1.0
|
|
OD2
|
A:ASP446
|
3.7
|
19.6
|
1.0
|
|
N
|
A:TYR475
|
3.8
|
20.0
|
1.0
|
|
N
|
A:ASP446
|
3.9
|
19.4
|
1.0
|
|
O7
|
A:TPP702
|
4.0
|
21.3
|
1.0
|
|
O2B
|
A:TPP702
|
4.0
|
21.8
|
1.0
|
|
N
|
A:GLY477
|
4.0
|
20.0
|
1.0
|
|
CA
|
A:TYR475
|
4.0
|
20.0
|
1.0
|
|
N
|
A:ASN473
|
4.2
|
20.0
|
1.0
|
|
N
|
A:LEU476
|
4.3
|
19.9
|
1.0
|
|
CB
|
A:ASN473
|
4.4
|
20.2
|
1.0
|
|
N
|
A:PHE447
|
4.5
|
19.2
|
1.0
|
|
CB
|
A:TYR475
|
4.5
|
20.2
|
1.0
|
|
CB
|
A:ASP446
|
4.5
|
19.4
|
1.0
|
|
CA
|
A:LEU476
|
4.5
|
19.8
|
1.0
|
|
N
|
A:ALA474
|
4.6
|
20.0
|
1.0
|
|
O3B
|
A:TPP702
|
4.6
|
19.9
|
1.0
|
|
O1A
|
A:TPP702
|
4.6
|
19.3
|
1.0
|
|
CA
|
A:ASN473
|
4.6
|
20.1
|
1.0
|
|
CA
|
A:GLY445
|
4.6
|
19.4
|
1.0
|
|
CA
|
A:ASP446
|
4.7
|
19.3
|
1.0
|
|
C
|
A:GLY445
|
4.7
|
19.3
|
1.0
|
|
O
|
A:VAL471
|
4.7
|
19.7
|
1.0
|
|
C
|
A:ASN473
|
4.7
|
20.1
|
1.0
|
|
C
|
A:LEU476
|
4.8
|
19.9
|
1.0
|
|
CA
|
A:GLY477
|
4.8
|
20.2
|
1.0
|
|
C
|
A:ALA474
|
4.9
|
20.0
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 8i01
Go back to
Magnesium Binding Sites List in 8i01
Magnesium binding site 2 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
 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 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg704
b:18.0
occ:0.39
|
OE1
|
A:GLU454
|
2.1
|
17.9
|
0.9
|
|
O
|
A:PHE451
|
2.8
|
18.2
|
1.0
|
|
CD
|
A:GLU454
|
3.1
|
17.9
|
1.0
|
|
OE2
|
A:GLU454
|
3.5
|
18.3
|
1.0
|
|
C
|
A:PHE451
|
3.8
|
18.2
|
1.0
|
|
CA
|
A:LEU452
|
3.8
|
18.1
|
1.0
|
|
CD2
|
A:LEU452
|
4.1
|
17.9
|
1.0
|
|
N
|
A:LEU452
|
4.2
|
18.2
|
1.0
|
|
CG
|
A:GLU454
|
4.3
|
17.8
|
1.0
|
|
N
|
A:ILE453
|
4.4
|
18.2
|
1.0
|
|
C
|
A:LEU452
|
4.4
|
18.1
|
1.0
|
|
O
|
A:GLN450
|
4.6
|
18.4
|
1.0
|
|
CD2
|
A:HIS50
|
4.7
|
17.6
|
1.0
|
|
N
|
A:GLU454
|
4.7
|
18.1
|
1.0
|
|
CB
|
A:GLU454
|
4.7
|
17.9
|
1.0
|
|
CB
|
A:LEU452
|
4.8
|
18.1
|
1.0
|
|
CG
|
A:LEU452
|
5.0
|
18.0
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 8i01
Go back to
Magnesium Binding Sites List in 8i01
Magnesium binding site 3 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
 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 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg703
b:23.7
occ:1.00
|
O
|
B:HOH963
|
2.1
|
23.2
|
1.0
|
|
O1A
|
B:TPP702
|
2.2
|
22.8
|
1.0
|
|
O
|
B:TYR475
|
2.2
|
22.8
|
1.0
|
|
O3B
|
B:TPP702
|
2.3
|
26.2
|
1.0
|
|
OD1
|
B:ASN473
|
2.3
|
25.2
|
1.0
|
|
OD1
|
B:ASP446
|
2.3
|
25.3
|
1.0
|
|
CG
|
B:ASN473
|
3.1
|
27.5
|
1.0
|
|
CG
|
B:ASP446
|
3.3
|
22.4
|
1.0
|
|
PB
|
B:TPP702
|
3.3
|
27.1
|
1.0
|
|
PA
|
B:TPP702
|
3.3
|
25.8
|
1.0
|
|
C
|
B:TYR475
|
3.3
|
27.5
|
1.0
|
|
O3A
|
B:TPP702
|
3.3
|
26.7
|
1.0
|
|
ND2
|
B:ASN473
|
3.4
|
27.1
|
1.0
|
|
OD2
|
B:ASP446
|
3.7
|
24.2
|
1.0
|
|
N
|
B:TYR475
|
3.8
|
28.0
|
1.0
|
|
N
|
B:ASP446
|
3.9
|
19.0
|
1.0
|
|
CA
|
B:TYR475
|
4.0
|
28.9
|
1.0
|
|
O2B
|
B:TPP702
|
4.1
|
28.3
|
1.0
|
|
N
|
B:GLY477
|
4.1
|
28.1
|
1.0
|
|
O7
|
B:TPP702
|
4.1
|
27.1
|
1.0
|
|
N
|
B:ASN473
|
4.3
|
21.6
|
1.0
|
|
CB
|
B:TYR475
|
4.4
|
28.2
|
1.0
|
|
N
|
B:LEU476
|
4.4
|
29.6
|
1.0
|
|
N
|
B:PHE447
|
4.4
|
19.2
|
1.0
|
|
CB
|
B:ASN473
|
4.5
|
23.3
|
1.0
|
|
CA
|
B:GLY445
|
4.5
|
20.1
|
1.0
|
|
CB
|
B:ASP446
|
4.5
|
20.5
|
1.0
|
|
O1B
|
B:TPP702
|
4.6
|
26.9
|
1.0
|
|
C
|
B:GLY445
|
4.6
|
20.9
|
1.0
|
|
O2A
|
B:TPP702
|
4.6
|
22.5
|
1.0
|
|
CA
|
B:LEU476
|
4.6
|
27.8
|
1.0
|
|
O
|
B:VAL471
|
4.6
|
20.0
|
1.0
|
|
CA
|
B:ASP446
|
4.7
|
19.6
|
1.0
|
|
N
|
B:ALA474
|
4.7
|
26.1
|
1.0
|
|
CA
|
B:ASN473
|
4.8
|
24.4
|
1.0
|
|
C
|
B:ASN473
|
4.9
|
27.1
|
1.0
|
|
CA
|
B:GLY477
|
4.9
|
28.9
|
1.0
|
|
C
|
B:LEU476
|
4.9
|
27.4
|
1.0
|
|
C
|
B:ALA474
|
5.0
|
29.7
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 8i01
Go back to
Magnesium Binding Sites List in 8i01
Magnesium binding site 4 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
 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 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg704
b:18.8
occ:0.49
|
OE1
|
B:GLU454
|
2.3
|
19.1
|
0.8
|
|
O
|
B:PHE451
|
2.7
|
18.5
|
1.0
|
|
CD
|
B:GLU454
|
3.1
|
19.1
|
1.0
|
|
OE2
|
B:GLU454
|
3.5
|
21.0
|
1.0
|
|
C
|
B:PHE451
|
3.8
|
18.4
|
1.0
|
|
CA
|
B:LEU452
|
4.0
|
18.7
|
1.0
|
|
CD2
|
B:LEU452
|
4.1
|
18.6
|
1.0
|
|
CG
|
B:GLU454
|
4.3
|
19.4
|
1.0
|
|
N
|
B:LEU452
|
4.3
|
18.5
|
1.0
|
|
CD2
|
B:HIS50
|
4.5
|
18.9
|
1.0
|
|
C
|
B:LEU452
|
4.6
|
18.8
|
1.0
|
|
N
|
B:ILE453
|
4.6
|
18.8
|
1.0
|
|
O
|
B:GLN450
|
4.6
|
18.5
|
1.0
|
|
CB
|
B:GLU454
|
4.9
|
19.4
|
1.0
|
|
N
|
B:GLU454
|
4.9
|
19.2
|
1.0
|
|
CB
|
B:LEU452
|
5.0
|
18.6
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 8i01
Go back to
Magnesium Binding Sites List in 8i01
Magnesium binding site 5 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
 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 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg703
b:21.4
occ:1.00
|
OD1
|
C:ASN473
|
2.1
|
24.2
|
1.0
|
|
O
|
C:HOH982
|
2.2
|
23.0
|
1.0
|
|
O
|
C:TYR475
|
2.2
|
22.9
|
1.0
|
|
OD1
|
C:ASP446
|
2.2
|
23.7
|
1.0
|
|
O2A
|
C:TPP702
|
2.2
|
21.8
|
1.0
|
|
O1B
|
C:TPP702
|
2.2
|
21.1
|
1.0
|
|
CG
|
C:ASN473
|
3.0
|
24.1
|
1.0
|
|
CG
|
C:ASP446
|
3.3
|
24.0
|
1.0
|
|
PB
|
C:TPP702
|
3.3
|
26.7
|
1.0
|
|
PA
|
C:TPP702
|
3.3
|
24.5
|
1.0
|
|
ND2
|
C:ASN473
|
3.3
|
22.6
|
1.0
|
|
C
|
C:TYR475
|
3.3
|
24.2
|
1.0
|
|
O3A
|
C:TPP702
|
3.4
|
23.4
|
1.0
|
|
OD2
|
C:ASP446
|
3.8
|
22.7
|
1.0
|
|
N
|
C:TYR475
|
3.8
|
21.6
|
1.0
|
|
N
|
C:ASP446
|
3.8
|
20.3
|
1.0
|
|
O2B
|
C:TPP702
|
3.9
|
24.4
|
1.0
|
|
O7
|
C:TPP702
|
4.0
|
24.2
|
1.0
|
|
CA
|
C:TYR475
|
4.1
|
23.9
|
1.0
|
|
N
|
C:GLY477
|
4.1
|
23.1
|
1.0
|
|
N
|
C:ASN473
|
4.2
|
23.0
|
1.0
|
|
CB
|
C:ASN473
|
4.4
|
23.8
|
1.0
|
|
N
|
C:LEU476
|
4.4
|
25.4
|
1.0
|
|
CB
|
C:TYR475
|
4.4
|
24.8
|
1.0
|
|
N
|
C:PHE447
|
4.5
|
22.6
|
1.0
|
|
CB
|
C:ASP446
|
4.5
|
21.4
|
1.0
|
|
CA
|
C:GLY445
|
4.5
|
22.5
|
1.0
|
|
CA
|
C:LEU476
|
4.6
|
22.9
|
1.0
|
|
O3B
|
C:TPP702
|
4.6
|
23.2
|
1.0
|
|
O1A
|
C:TPP702
|
4.6
|
23.9
|
1.0
|
|
O
|
C:VAL471
|
4.6
|
23.0
|
1.0
|
|
N
|
C:ALA474
|
4.6
|
21.5
|
1.0
|
|
C
|
C:GLY445
|
4.6
|
22.4
|
1.0
|
|
CA
|
C:ASN473
|
4.7
|
23.0
|
1.0
|
|
CA
|
C:ASP446
|
4.7
|
23.3
|
1.0
|
|
C
|
C:ASN473
|
4.8
|
22.6
|
1.0
|
|
C
|
C:LEU476
|
4.9
|
23.6
|
1.0
|
|
CA
|
C:GLY477
|
4.9
|
23.5
|
1.0
|
|
C
|
C:ALA474
|
5.0
|
23.7
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 8i01
Go back to
Magnesium Binding Sites List in 8i01
Magnesium binding site 6 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
 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 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg703
b:29.0
occ:1.00
|
O1A
|
D:TPP702
|
2.1
|
27.6
|
1.0
|
|
O
|
D:TYR475
|
2.2
|
30.3
|
1.0
|
|
O3B
|
D:TPP702
|
2.2
|
30.1
|
1.0
|
|
OD1
|
D:ASN473
|
2.2
|
28.8
|
1.0
|
|
OD1
|
D:ASP446
|
2.2
|
29.0
|
1.0
|
|
O
|
D:HOH908
|
2.3
|
29.7
|
1.0
|
|
CG
|
D:ASN473
|
3.1
|
32.3
|
1.0
|
|
PA
|
D:TPP702
|
3.2
|
30.6
|
1.0
|
|
PB
|
D:TPP702
|
3.2
|
32.4
|
1.0
|
|
O3A
|
D:TPP702
|
3.3
|
30.2
|
1.0
|
|
CG
|
D:ASP446
|
3.3
|
27.9
|
1.0
|
|
C
|
D:TYR475
|
3.4
|
30.9
|
1.0
|
|
ND2
|
D:ASN473
|
3.4
|
31.8
|
1.0
|
|
N
|
D:ASP446
|
3.8
|
26.1
|
1.0
|
|
OD2
|
D:ASP446
|
3.8
|
28.2
|
1.0
|
|
N
|
D:TYR475
|
3.9
|
30.5
|
1.0
|
|
O7
|
D:TPP702
|
4.0
|
30.0
|
1.0
|
|
O2B
|
D:TPP702
|
4.0
|
35.2
|
1.0
|
|
N
|
D:GLY477
|
4.1
|
33.0
|
1.0
|
|
CA
|
D:TYR475
|
4.1
|
31.8
|
1.0
|
|
N
|
D:PHE447
|
4.3
|
25.6
|
1.0
|
|
N
|
D:LEU476
|
4.4
|
31.8
|
1.0
|
|
N
|
D:ASN473
|
4.4
|
29.4
|
1.0
|
|
CA
|
D:GLY445
|
4.4
|
26.3
|
1.0
|
|
C
|
D:GLY445
|
4.5
|
26.5
|
1.0
|
|
CB
|
D:TYR475
|
4.5
|
32.7
|
1.0
|
|
CB
|
D:ASP446
|
4.5
|
25.7
|
1.0
|
|
CB
|
D:ASN473
|
4.5
|
29.4
|
1.0
|
|
O2A
|
D:TPP702
|
4.5
|
26.4
|
1.0
|
|
CA
|
D:LEU476
|
4.5
|
31.2
|
1.0
|
|
O1B
|
D:TPP702
|
4.5
|
32.5
|
1.0
|
|
CA
|
D:ASP446
|
4.6
|
24.7
|
1.0
|
|
O
|
D:VAL471
|
4.7
|
28.0
|
1.0
|
|
N
|
D:ALA474
|
4.8
|
28.9
|
1.0
|
|
CA
|
D:ASN473
|
4.8
|
30.7
|
1.0
|
|
C
|
D:LEU476
|
4.8
|
34.3
|
1.0
|
|
CA
|
D:GLY477
|
4.9
|
31.6
|
1.0
|
|
C
|
D:ASN473
|
5.0
|
30.7
|
1.0
|
|
CB
|
D:PHE447
|
5.0
|
23.6
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 8i01
Go back to
Magnesium Binding Sites List in 8i01
Magnesium binding site 7 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
 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 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg704
b:30.5
occ:1.00
|
OE1
|
D:GLU454
|
2.3
|
21.9
|
0.6
|
|
OE1
|
F:GLU454
|
2.3
|
24.4
|
0.8
|
|
O
|
F:PHE451
|
2.4
|
22.2
|
1.0
|
|
O
|
D:PHE451
|
2.6
|
24.7
|
1.0
|
|
CD
|
D:GLU454
|
3.0
|
24.1
|
1.0
|
|
CD
|
F:GLU454
|
3.3
|
25.3
|
1.0
|
|
OE2
|
D:GLU454
|
3.3
|
27.0
|
1.0
|
|
C
|
F:PHE451
|
3.5
|
23.9
|
1.0
|
|
OE2
|
F:GLU454
|
3.6
|
26.5
|
1.0
|
|
C
|
D:PHE451
|
3.7
|
24.8
|
1.0
|
|
CA
|
F:LEU452
|
3.7
|
23.1
|
1.0
|
|
CA
|
D:LEU452
|
3.7
|
23.2
|
1.0
|
|
CD2
|
D:LEU452
|
3.9
|
22.4
|
1.0
|
|
CD2
|
F:LEU452
|
3.9
|
25.1
|
1.0
|
|
N
|
F:LEU452
|
4.0
|
20.9
|
1.0
|
|
N
|
D:LEU452
|
4.1
|
22.7
|
1.0
|
|
O
|
F:GLN450
|
4.2
|
23.2
|
1.0
|
|
N
|
F:ILE453
|
4.3
|
24.4
|
1.0
|
|
CG
|
D:GLU454
|
4.3
|
24.1
|
1.0
|
|
N
|
D:ILE453
|
4.3
|
23.4
|
1.0
|
|
C
|
D:LEU452
|
4.3
|
23.3
|
1.0
|
|
C
|
F:LEU452
|
4.4
|
24.1
|
1.0
|
|
O
|
D:GLN450
|
4.5
|
23.4
|
1.0
|
|
CG
|
F:GLU454
|
4.5
|
22.5
|
1.0
|
|
CD2
|
D:HIS50
|
4.6
|
24.4
|
1.0
|
|
CA
|
F:PHE451
|
4.7
|
25.2
|
1.0
|
|
CB
|
F:LEU452
|
4.8
|
23.3
|
1.0
|
|
CB
|
D:LEU452
|
4.8
|
23.3
|
1.0
|
|
CD2
|
F:HIS50
|
4.8
|
25.0
|
1.0
|
|
N
|
D:GLU454
|
4.8
|
22.7
|
1.0
|
|
CG
|
F:LEU452
|
4.8
|
25.5
|
1.0
|
|
N
|
F:GLU454
|
4.9
|
22.7
|
1.0
|
|
CG
|
D:LEU452
|
4.9
|
24.6
|
1.0
|
|
CA
|
D:PHE451
|
4.9
|
23.6
|
1.0
|
|
CB
|
D:GLU454
|
5.0
|
21.6
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 8i01
Go back to
Magnesium Binding Sites List in 8i01
Magnesium binding site 8 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
 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 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg703
b:26.8
occ:1.00
|
OD1
|
E:ASN473
|
2.1
|
31.6
|
1.0
|
|
O1A
|
E:TPP702
|
2.2
|
28.6
|
1.0
|
|
OD1
|
E:ASP446
|
2.2
|
27.7
|
1.0
|
|
O
|
E:TYR475
|
2.2
|
31.3
|
1.0
|
|
O3B
|
E:TPP702
|
2.3
|
31.9
|
1.0
|
|
O
|
E:HOH920
|
2.3
|
29.0
|
1.0
|
|
CG
|
E:ASN473
|
3.0
|
32.0
|
1.0
|
|
PA
|
E:TPP702
|
3.3
|
31.9
|
1.0
|
|
PB
|
E:TPP702
|
3.3
|
32.4
|
1.0
|
|
CG
|
E:ASP446
|
3.3
|
29.4
|
1.0
|
|
ND2
|
E:ASN473
|
3.3
|
31.3
|
1.0
|
|
O3A
|
E:TPP702
|
3.3
|
31.0
|
1.0
|
|
C
|
E:TYR475
|
3.4
|
32.3
|
1.0
|
|
OD2
|
E:ASP446
|
3.8
|
29.8
|
1.0
|
|
N
|
E:TYR475
|
3.8
|
31.5
|
1.0
|
|
N
|
E:ASP446
|
3.9
|
26.1
|
1.0
|
|
O2B
|
E:TPP702
|
4.0
|
30.8
|
1.0
|
|
O7
|
E:TPP702
|
4.0
|
30.8
|
1.0
|
|
CA
|
E:TYR475
|
4.0
|
31.9
|
1.0
|
|
N
|
E:GLY477
|
4.1
|
33.1
|
1.0
|
|
N
|
E:ASN473
|
4.3
|
28.6
|
1.0
|
|
CB
|
E:ASN473
|
4.4
|
28.2
|
1.0
|
|
CB
|
E:TYR475
|
4.4
|
33.1
|
1.0
|
|
N
|
E:LEU476
|
4.4
|
32.5
|
1.0
|
|
N
|
E:PHE447
|
4.4
|
25.2
|
1.0
|
|
CA
|
E:GLY445
|
4.5
|
27.1
|
1.0
|
|
CB
|
E:ASP446
|
4.5
|
26.2
|
1.0
|
|
O2A
|
E:TPP702
|
4.6
|
29.0
|
1.0
|
|
O1B
|
E:TPP702
|
4.6
|
31.4
|
1.0
|
|
CA
|
E:LEU476
|
4.6
|
33.8
|
1.0
|
|
C
|
E:GLY445
|
4.6
|
26.2
|
1.0
|
|
N
|
E:ALA474
|
4.6
|
30.1
|
1.0
|
|
O
|
E:VAL471
|
4.7
|
27.3
|
1.0
|
|
CA
|
E:ASP446
|
4.7
|
25.4
|
1.0
|
|
CA
|
E:ASN473
|
4.7
|
31.6
|
1.0
|
|
C
|
E:ASN473
|
4.8
|
30.9
|
1.0
|
|
CA
|
E:GLY477
|
4.9
|
34.4
|
1.0
|
|
C
|
E:LEU476
|
4.9
|
34.2
|
1.0
|
|
C
|
E:ALA474
|
5.0
|
32.9
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 8i01
Go back to
Magnesium Binding Sites List in 8i01
Magnesium binding site 9 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
 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 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg704
b:29.6
occ:1.00
|
OE1
|
E:GLU454
|
2.3
|
22.4
|
0.6
|
|
OE1
|
C:GLU454
|
2.4
|
24.0
|
0.9
|
|
O
|
C:PHE451
|
2.5
|
23.5
|
1.0
|
|
O
|
E:PHE451
|
2.5
|
26.4
|
1.0
|
|
CD
|
E:GLU454
|
3.1
|
25.1
|
1.0
|
|
OE2
|
E:GLU454
|
3.3
|
27.9
|
1.0
|
|
CD
|
C:GLU454
|
3.4
|
25.7
|
1.0
|
|
C
|
E:PHE451
|
3.5
|
25.1
|
1.0
|
|
C
|
C:PHE451
|
3.5
|
24.0
|
1.0
|
|
CA
|
E:LEU452
|
3.6
|
23.4
|
1.0
|
|
OE2
|
C:GLU454
|
3.7
|
25.2
|
1.0
|
|
CA
|
C:LEU452
|
3.8
|
23.6
|
1.0
|
|
CD2
|
E:LEU452
|
3.8
|
22.8
|
1.0
|
|
CD2
|
C:LEU452
|
4.0
|
22.8
|
1.0
|
|
N
|
E:LEU452
|
4.0
|
23.7
|
1.0
|
|
N
|
C:LEU452
|
4.1
|
25.1
|
1.0
|
|
C
|
E:LEU452
|
4.2
|
23.8
|
1.0
|
|
N
|
E:ILE453
|
4.2
|
24.4
|
1.0
|
|
O
|
E:GLN450
|
4.4
|
24.7
|
1.0
|
|
N
|
C:ILE453
|
4.4
|
23.4
|
1.0
|
|
CG
|
E:GLU454
|
4.4
|
23.0
|
1.0
|
|
O
|
C:GLN450
|
4.4
|
23.1
|
1.0
|
|
C
|
C:LEU452
|
4.4
|
22.7
|
1.0
|
|
CD2
|
E:HIS50
|
4.5
|
24.2
|
1.0
|
|
CG
|
C:GLU454
|
4.6
|
25.3
|
1.0
|
|
CB
|
E:LEU452
|
4.6
|
24.0
|
1.0
|
|
CG
|
E:LEU452
|
4.7
|
23.6
|
1.0
|
|
CA
|
C:PHE451
|
4.8
|
21.9
|
1.0
|
|
CA
|
E:PHE451
|
4.8
|
23.3
|
1.0
|
|
CD2
|
C:HIS50
|
4.8
|
23.3
|
1.0
|
|
CB
|
C:LEU452
|
4.8
|
22.4
|
1.0
|
|
N
|
E:GLU454
|
4.8
|
21.6
|
1.0
|
|
CG
|
C:LEU452
|
4.9
|
22.7
|
1.0
|
|
N
|
C:GLU454
|
5.0
|
22.1
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 8i01
Go back to
Magnesium Binding Sites List in 8i01
Magnesium binding site 10 out
of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase
 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 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg703
b:33.1
occ:1.00
|
O
|
F:TYR475
|
2.2
|
35.0
|
1.0
|
|
O2B
|
F:TPP702
|
2.2
|
38.2
|
1.0
|
|
OD1
|
F:ASP446
|
2.3
|
34.1
|
1.0
|
|
O2A
|
F:TPP702
|
2.3
|
34.4
|
1.0
|
|
O
|
F:HOH962
|
2.3
|
32.6
|
1.0
|
|
OD1
|
F:ASN473
|
2.3
|
35.8
|
1.0
|
|
CG
|
F:ASN473
|
3.2
|
37.6
|
1.0
|
|
PB
|
F:TPP702
|
3.2
|
41.3
|
1.0
|
|
O3A
|
F:TPP702
|
3.3
|
37.5
|
1.0
|
|
PA
|
F:TPP702
|
3.3
|
37.5
|
1.0
|
|
C
|
F:TYR475
|
3.3
|
39.2
|
1.0
|
|
CG
|
F:ASP446
|
3.3
|
31.5
|
1.0
|
|
ND2
|
F:ASN473
|
3.5
|
39.3
|
1.0
|
|
N
|
F:TYR475
|
3.7
|
37.9
|
1.0
|
|
OD2
|
F:ASP446
|
3.8
|
31.9
|
1.0
|
|
N
|
F:ASP446
|
3.9
|
27.5
|
1.0
|
|
CA
|
F:TYR475
|
3.9
|
39.8
|
1.0
|
|
O7
|
F:TPP702
|
4.0
|
37.0
|
1.0
|
|
O1B
|
F:TPP702
|
4.1
|
38.6
|
1.0
|
|
N
|
F:GLY477
|
4.1
|
42.5
|
1.0
|
|
CB
|
F:TYR475
|
4.3
|
39.6
|
1.0
|
|
N
|
F:ASN473
|
4.3
|
30.4
|
1.0
|
|
N
|
F:LEU476
|
4.4
|
41.5
|
1.0
|
|
N
|
F:PHE447
|
4.4
|
28.4
|
1.0
|
|
O3B
|
F:TPP702
|
4.5
|
41.5
|
1.0
|
|
CA
|
F:GLY445
|
4.5
|
29.7
|
1.0
|
|
CB
|
F:ASN473
|
4.5
|
33.3
|
1.0
|
|
CB
|
F:ASP446
|
4.6
|
28.9
|
1.0
|
|
C
|
F:GLY445
|
4.6
|
29.4
|
1.0
|
|
O1A
|
F:TPP702
|
4.6
|
30.1
|
1.0
|
|
N
|
F:ALA474
|
4.7
|
34.7
|
1.0
|
|
CA
|
F:ASP446
|
4.7
|
29.4
|
1.0
|
|
CA
|
F:LEU476
|
4.7
|
41.7
|
1.0
|
|
O
|
F:VAL471
|
4.7
|
27.9
|
1.0
|
|
CA
|
F:ASN473
|
4.8
|
34.3
|
1.0
|
|
CA
|
F:GLY477
|
4.8
|
43.6
|
1.0
|
|
C
|
F:ASN473
|
4.9
|
36.8
|
1.0
|
|
C
|
F:ALA474
|
4.9
|
38.6
|
1.0
|
|
C
|
F:LEU476
|
4.9
|
41.5
|
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 08:59:08 2024
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