Magnesium in PDB 6vim: P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
Enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
All present enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid:
5.1.2.2;
Protein crystallography data
The structure of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid, PDB code: 6vim
was solved by
L.Grandinetti,
A.N.Sharma,
S.L.Bearne,
M.St Maurice,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
116.37 /
2.00
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
228.988,
150.356,
150.275,
90.00,
129.25,
90.00
|
|
R / Rfree (%)
|
15.8 /
19.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
(pdb code 6vim). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid, PDB code: 6vim:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 6vim
Go back to
Magnesium Binding Sites List in 6vim
Magnesium binding site 1 out
of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:13.0
occ:1.00
|
OE1
|
A:GLU221
|
1.9
|
16.2
|
1.0
|
|
O1
|
A:PBC402
|
2.0
|
32.4
|
1.0
|
|
O
|
A:HOH508
|
2.0
|
12.5
|
1.0
|
|
OE2
|
A:GLU247
|
2.1
|
16.5
|
1.0
|
|
OD2
|
A:ASP195
|
2.1
|
12.1
|
1.0
|
|
CG
|
A:ASP195
|
3.0
|
21.4
|
1.0
|
|
CD
|
A:GLU221
|
3.0
|
16.2
|
1.0
|
|
CD
|
A:GLU247
|
3.0
|
17.9
|
1.0
|
|
B
|
A:PBC402
|
3.0
|
65.7
|
1.0
|
|
OD1
|
A:ASP195
|
3.2
|
15.6
|
1.0
|
|
OE1
|
A:GLU247
|
3.3
|
18.4
|
1.0
|
|
O2
|
A:PBC402
|
3.3
|
23.6
|
1.0
|
|
CG
|
A:GLU221
|
3.6
|
14.5
|
1.0
|
|
OE2
|
A:GLU221
|
4.0
|
14.8
|
1.0
|
|
NZ
|
A:LYS164
|
4.0
|
12.1
|
1.0
|
|
ND2
|
A:ASN197
|
4.0
|
19.3
|
1.0
|
|
NZ
|
A:LYS166
|
4.0
|
18.9
|
1.0
|
|
OE2
|
A:GLU222
|
4.1
|
19.1
|
1.0
|
|
O
|
A:HOH654
|
4.1
|
14.2
|
1.0
|
|
NE2
|
A:HIS297
|
4.2
|
23.4
|
1.0
|
|
CB
|
A:ASP195
|
4.3
|
11.9
|
1.0
|
|
CD2
|
A:HIS297
|
4.4
|
24.1
|
1.0
|
|
CG
|
A:GLU247
|
4.4
|
18.6
|
1.0
|
|
CA
|
A:PBC402
|
4.5
|
15.8
|
1.0
|
|
CE
|
A:MET268
|
4.5
|
14.0
|
1.0
|
|
CE
|
A:LYS164
|
4.6
|
8.1
|
1.0
|
|
CG
|
A:ASN197
|
4.7
|
20.3
|
1.0
|
|
CB
|
A:GLU221
|
4.8
|
14.0
|
1.0
|
|
CD
|
A:GLU222
|
4.8
|
21.9
|
1.0
|
|
CG
|
A:GLU222
|
4.9
|
16.7
|
1.0
|
|
OD1
|
A:ASN197
|
4.9
|
17.1
|
1.0
|
|
CB2
|
A:PBC402
|
4.9
|
42.0
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 6vim
Go back to
Magnesium Binding Sites List in 6vim
Magnesium binding site 2 out
of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:15.8
occ:1.00
|
O2
|
B:PBC402
|
1.9
|
26.1
|
0.5
|
|
O2
|
B:PBC402
|
2.0
|
26.9
|
0.5
|
|
OE1
|
B:GLU221
|
2.0
|
18.4
|
1.0
|
|
OE1
|
B:GLU247
|
2.0
|
25.2
|
1.0
|
|
O
|
B:HOH515
|
2.1
|
17.9
|
1.0
|
|
OD2
|
B:ASP195
|
2.1
|
19.2
|
1.0
|
|
B
|
B:PBC402
|
2.9
|
29.0
|
0.5
|
|
CD
|
B:GLU247
|
3.0
|
18.5
|
1.0
|
|
CD
|
B:GLU221
|
3.0
|
21.6
|
1.0
|
|
B
|
B:PBC402
|
3.0
|
25.8
|
0.5
|
|
CG
|
B:ASP195
|
3.1
|
23.0
|
1.0
|
|
O1
|
B:PBC402
|
3.1
|
18.0
|
0.5
|
|
OE2
|
B:GLU247
|
3.3
|
19.6
|
1.0
|
|
O1
|
B:PBC402
|
3.3
|
23.0
|
0.5
|
|
OD1
|
B:ASP195
|
3.4
|
17.0
|
1.0
|
|
CG
|
B:GLU221
|
3.6
|
9.9
|
1.0
|
|
NE2
|
B:HIS297
|
3.7
|
17.3
|
0.5
|
|
ND2
|
B:ASN197
|
3.9
|
23.7
|
1.0
|
|
OE2
|
B:GLU221
|
4.0
|
21.9
|
1.0
|
|
NZ
|
B:LYS164
|
4.0
|
19.2
|
1.0
|
|
CD2
|
B:HIS297
|
4.0
|
9.8
|
0.5
|
|
O
|
B:HOH654
|
4.1
|
14.2
|
1.0
|
|
NZ
|
B:LYS166
|
4.2
|
22.2
|
1.0
|
|
OE2
|
B:GLU222
|
4.2
|
20.7
|
1.0
|
|
CD2
|
B:HIS297
|
4.3
|
12.2
|
0.5
|
|
CA
|
B:PBC402
|
4.3
|
20.6
|
0.5
|
|
NE2
|
B:HIS297
|
4.3
|
15.8
|
0.5
|
|
CG
|
B:GLU247
|
4.4
|
15.9
|
1.0
|
|
CB
|
B:ASP195
|
4.4
|
12.5
|
1.0
|
|
CA
|
B:PBC402
|
4.4
|
24.6
|
0.5
|
|
CE
|
B:MET268
|
4.4
|
15.8
|
1.0
|
|
CB1
|
B:PBC402
|
4.6
|
26.1
|
0.5
|
|
CE
|
B:LYS164
|
4.7
|
14.6
|
1.0
|
|
CE1
|
B:HIS297
|
4.7
|
22.4
|
0.5
|
|
CG
|
B:ASN197
|
4.8
|
26.0
|
1.0
|
|
CB1
|
B:PBC402
|
4.9
|
30.5
|
0.5
|
|
CB
|
B:GLU221
|
4.9
|
15.7
|
1.0
|
|
CD
|
B:GLU222
|
5.0
|
25.9
|
1.0
|
|
CB
|
B:GLU247
|
5.0
|
20.0
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 6vim
Go back to
Magnesium Binding Sites List in 6vim
Magnesium binding site 3 out
of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg401
b:12.4
occ:1.00
|
O2
|
C:PBC402
|
1.9
|
29.8
|
1.0
|
|
O
|
C:HOH517
|
2.0
|
11.4
|
1.0
|
|
OE1
|
C:GLU221
|
2.0
|
18.4
|
1.0
|
|
OE1
|
C:GLU247
|
2.0
|
13.2
|
1.0
|
|
OD2
|
C:ASP195
|
2.2
|
11.9
|
1.0
|
|
CD
|
C:GLU247
|
2.9
|
13.6
|
1.0
|
|
B
|
C:PBC402
|
3.0
|
56.1
|
1.0
|
|
CD
|
C:GLU221
|
3.0
|
12.6
|
1.0
|
|
CG
|
C:ASP195
|
3.1
|
16.6
|
1.0
|
|
OE2
|
C:GLU247
|
3.2
|
18.5
|
1.0
|
|
O1
|
C:PBC402
|
3.2
|
20.9
|
1.0
|
|
OD1
|
C:ASP195
|
3.4
|
13.4
|
1.0
|
|
CG
|
C:GLU221
|
3.6
|
14.1
|
1.0
|
|
O
|
C:HOH600
|
4.0
|
14.4
|
1.0
|
|
ND2
|
C:ASN197
|
4.0
|
18.2
|
1.0
|
|
NZ
|
C:LYS164
|
4.1
|
11.8
|
1.0
|
|
OE2
|
C:GLU221
|
4.1
|
15.9
|
1.0
|
|
NZ
|
C:LYS166
|
4.1
|
24.1
|
1.0
|
|
NE2
|
C:HIS297
|
4.2
|
14.3
|
1.0
|
|
OE2
|
C:GLU222
|
4.2
|
15.6
|
1.0
|
|
CG
|
C:GLU247
|
4.3
|
9.8
|
1.0
|
|
CD2
|
C:HIS297
|
4.3
|
9.4
|
1.0
|
|
CB
|
C:ASP195
|
4.4
|
8.7
|
1.0
|
|
CA
|
C:PBC402
|
4.4
|
26.1
|
1.0
|
|
CE
|
C:MET268
|
4.5
|
7.6
|
1.0
|
|
CE
|
C:LYS164
|
4.7
|
10.3
|
1.0
|
|
CG
|
C:ASN197
|
4.8
|
20.7
|
1.0
|
|
CB
|
C:GLU221
|
4.8
|
10.2
|
1.0
|
|
CB1
|
C:PBC402
|
4.8
|
44.7
|
1.0
|
|
CB
|
C:GLU247
|
4.9
|
9.3
|
1.0
|
|
OD1
|
C:ASN197
|
4.9
|
19.4
|
1.0
|
|
CD
|
C:GLU222
|
4.9
|
13.4
|
1.0
|
|
CG
|
C:GLU222
|
5.0
|
14.8
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 6vim
Go back to
Magnesium Binding Sites List in 6vim
Magnesium binding site 4 out
of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg401
b:17.1
occ:1.00
|
O1
|
D:PBC402
|
1.8
|
29.7
|
0.5
|
|
OE1
|
D:GLU221
|
1.9
|
23.4
|
1.0
|
|
O1
|
D:PBC402
|
1.9
|
23.7
|
0.5
|
|
OE1
|
D:GLU247
|
2.1
|
16.5
|
1.0
|
|
OD2
|
D:ASP195
|
2.1
|
19.2
|
1.0
|
|
O
|
D:HOH512
|
2.2
|
22.6
|
1.0
|
|
B
|
D:PBC402
|
2.9
|
19.7
|
0.5
|
|
B
|
D:PBC402
|
2.9
|
31.0
|
0.5
|
|
CD
|
D:GLU221
|
3.0
|
30.2
|
1.0
|
|
CD
|
D:GLU247
|
3.0
|
14.4
|
1.0
|
|
O2
|
D:PBC402
|
3.1
|
10.1
|
0.5
|
|
CG
|
D:ASP195
|
3.1
|
24.2
|
1.0
|
|
O2
|
D:PBC402
|
3.2
|
32.4
|
0.5
|
|
OE2
|
D:GLU247
|
3.3
|
21.3
|
1.0
|
|
OD1
|
D:ASP195
|
3.5
|
19.4
|
1.0
|
|
CG
|
D:GLU221
|
3.7
|
16.0
|
1.0
|
|
NE2
|
D:HIS297
|
3.7
|
21.2
|
0.5
|
|
ND2
|
D:ASN197
|
3.9
|
24.2
|
1.0
|
|
NZ
|
D:LYS164
|
3.9
|
21.2
|
1.0
|
|
OE2
|
D:GLU221
|
3.9
|
21.1
|
1.0
|
|
NZ
|
D:LYS166
|
4.0
|
23.6
|
1.0
|
|
CD2
|
D:HIS297
|
4.0
|
5.8
|
0.5
|
|
O
|
D:HOH633
|
4.1
|
19.6
|
1.0
|
|
CA
|
D:PBC402
|
4.2
|
24.5
|
0.5
|
|
CD2
|
D:HIS297
|
4.3
|
11.9
|
0.5
|
|
OE2
|
D:GLU222
|
4.3
|
20.4
|
1.0
|
|
CA
|
D:PBC402
|
4.4
|
26.0
|
0.5
|
|
CB
|
D:ASP195
|
4.4
|
20.0
|
1.0
|
|
NE2
|
D:HIS297
|
4.4
|
20.7
|
0.5
|
|
CG
|
D:GLU247
|
4.4
|
19.4
|
1.0
|
|
CE
|
D:MET268
|
4.4
|
9.2
|
1.0
|
|
CB2
|
D:PBC402
|
4.6
|
32.8
|
0.5
|
|
CE
|
D:LYS164
|
4.6
|
14.9
|
1.0
|
|
CE1
|
D:HIS297
|
4.7
|
16.4
|
0.5
|
|
CB2
|
D:PBC402
|
4.9
|
24.6
|
0.5
|
|
CG
|
D:ASN197
|
4.9
|
19.4
|
1.0
|
|
CB
|
D:GLU221
|
4.9
|
9.7
|
1.0
|
|
CB
|
D:GLU247
|
5.0
|
15.7
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 6vim
Go back to
Magnesium Binding Sites List in 6vim
Magnesium binding site 5 out
of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg401
b:12.7
occ:1.00
|
O1
|
E:PBC402
|
1.9
|
28.2
|
1.0
|
|
OE1
|
E:GLU221
|
2.0
|
15.0
|
1.0
|
|
O
|
E:HOH509
|
2.0
|
10.6
|
1.0
|
|
OE1
|
E:GLU247
|
2.1
|
15.1
|
1.0
|
|
OD2
|
E:ASP195
|
2.1
|
14.3
|
1.0
|
|
B
|
E:PBC402
|
2.9
|
54.7
|
1.0
|
|
CD
|
E:GLU247
|
3.0
|
17.3
|
1.0
|
|
CG
|
E:ASP195
|
3.0
|
18.6
|
1.0
|
|
CD
|
E:GLU221
|
3.1
|
15.8
|
1.0
|
|
O2
|
E:PBC402
|
3.2
|
28.3
|
1.0
|
|
OE2
|
E:GLU247
|
3.2
|
21.2
|
1.0
|
|
OD1
|
E:ASP195
|
3.4
|
17.5
|
1.0
|
|
CG
|
E:GLU221
|
3.7
|
14.3
|
1.0
|
|
NZ
|
E:LYS166
|
4.0
|
19.8
|
1.0
|
|
ND2
|
E:ASN197
|
4.0
|
14.5
|
1.0
|
|
NZ
|
E:LYS164
|
4.1
|
8.5
|
1.0
|
|
OE2
|
E:GLU221
|
4.1
|
13.4
|
1.0
|
|
O
|
E:HOH604
|
4.1
|
14.3
|
1.0
|
|
OE2
|
E:GLU222
|
4.2
|
16.4
|
1.0
|
|
NE2
|
E:HIS297
|
4.2
|
16.7
|
1.0
|
|
CB
|
E:ASP195
|
4.3
|
12.6
|
1.0
|
|
CD2
|
E:HIS297
|
4.3
|
13.6
|
1.0
|
|
CA
|
E:PBC402
|
4.4
|
19.3
|
1.0
|
|
CG
|
E:GLU247
|
4.4
|
18.7
|
1.0
|
|
CE
|
E:MET268
|
4.6
|
12.0
|
1.0
|
|
CE
|
E:LYS164
|
4.6
|
13.3
|
1.0
|
|
CG
|
E:ASN197
|
4.8
|
13.5
|
1.0
|
|
CB2
|
E:PBC402
|
4.8
|
31.1
|
1.0
|
|
CB
|
E:GLU221
|
4.9
|
12.4
|
1.0
|
|
CE
|
E:LYS166
|
4.9
|
26.5
|
1.0
|
|
O
|
E:HOH521
|
4.9
|
14.5
|
1.0
|
|
CD
|
E:GLU222
|
4.9
|
18.9
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 6vim
Go back to
Magnesium Binding Sites List in 6vim
Magnesium binding site 6 out
of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg401
b:14.2
occ:1.00
|
O1
|
F:PBC402
|
1.8
|
27.1
|
0.5
|
|
O1
|
F:PBC402
|
1.9
|
29.8
|
0.5
|
|
OE1
|
F:GLU221
|
2.0
|
16.1
|
1.0
|
|
OE1
|
F:GLU247
|
2.1
|
16.1
|
1.0
|
|
O
|
F:HOH522
|
2.1
|
15.4
|
1.0
|
|
OD2
|
F:ASP195
|
2.1
|
11.8
|
1.0
|
|
B
|
F:PBC402
|
2.9
|
24.0
|
0.5
|
|
CD
|
F:GLU247
|
3.0
|
18.7
|
1.0
|
|
CD
|
F:GLU221
|
3.0
|
23.7
|
1.0
|
|
B
|
F:PBC402
|
3.0
|
11.2
|
0.5
|
|
CG
|
F:ASP195
|
3.1
|
21.8
|
1.0
|
|
O2
|
F:PBC402
|
3.2
|
11.8
|
0.5
|
|
OE2
|
F:GLU247
|
3.2
|
19.6
|
1.0
|
|
O2
|
F:PBC402
|
3.4
|
44.8
|
0.5
|
|
OD1
|
F:ASP195
|
3.4
|
18.5
|
1.0
|
|
CG
|
F:GLU221
|
3.7
|
10.7
|
1.0
|
|
NE2
|
F:HIS297
|
3.8
|
10.3
|
0.5
|
|
ND2
|
F:ASN197
|
4.0
|
20.9
|
1.0
|
|
OE2
|
F:GLU221
|
4.0
|
20.5
|
1.0
|
|
NZ
|
F:LYS164
|
4.0
|
12.5
|
1.0
|
|
CD2
|
F:HIS297
|
4.1
|
9.1
|
0.5
|
|
NZ
|
F:LYS166
|
4.1
|
21.2
|
1.0
|
|
O
|
F:HOH668
|
4.2
|
10.7
|
1.0
|
|
OE2
|
F:GLU222
|
4.2
|
20.5
|
1.0
|
|
CA
|
F:PBC402
|
4.3
|
15.9
|
0.5
|
|
CA
|
F:PBC402
|
4.3
|
23.4
|
0.5
|
|
CG
|
F:GLU247
|
4.4
|
15.5
|
1.0
|
|
CB
|
F:ASP195
|
4.4
|
14.7
|
1.0
|
|
CD2
|
F:HIS297
|
4.4
|
15.6
|
0.5
|
|
NE2
|
F:HIS297
|
4.5
|
16.2
|
0.5
|
|
CE
|
F:MET268
|
4.5
|
15.2
|
1.0
|
|
CB2
|
F:PBC402
|
4.6
|
22.5
|
0.5
|
|
CB2
|
F:PBC402
|
4.7
|
27.2
|
0.5
|
|
CE
|
F:LYS164
|
4.7
|
10.9
|
1.0
|
|
CE1
|
F:HIS297
|
4.7
|
15.1
|
0.5
|
|
CG
|
F:ASN197
|
4.8
|
28.3
|
1.0
|
|
CB
|
F:GLU221
|
4.9
|
15.8
|
1.0
|
|
CD
|
F:GLU222
|
5.0
|
27.9
|
1.0
|
|
CB
|
F:GLU247
|
5.0
|
15.6
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 6vim
Go back to
Magnesium Binding Sites List in 6vim
Magnesium binding site 7 out
of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg401
b:11.7
occ:1.00
|
O
|
G:HOH524
|
2.0
|
12.5
|
1.0
|
|
OE2
|
G:GLU221
|
2.0
|
14.5
|
1.0
|
|
O2
|
G:PBC402
|
2.0
|
32.0
|
1.0
|
|
OE1
|
G:GLU247
|
2.0
|
13.4
|
1.0
|
|
OD2
|
G:ASP195
|
2.2
|
13.1
|
1.0
|
|
CD
|
G:GLU247
|
3.0
|
22.2
|
1.0
|
|
CD
|
G:GLU221
|
3.0
|
11.8
|
1.0
|
|
CG
|
G:ASP195
|
3.0
|
23.4
|
1.0
|
|
B
|
G:PBC402
|
3.1
|
55.2
|
1.0
|
|
OE2
|
G:GLU247
|
3.3
|
18.7
|
1.0
|
|
OD1
|
G:ASP195
|
3.3
|
17.8
|
1.0
|
|
O1
|
G:PBC402
|
3.4
|
25.0
|
1.0
|
|
CG
|
G:GLU221
|
3.7
|
17.7
|
1.0
|
|
NZ
|
G:LYS164
|
3.9
|
13.8
|
1.0
|
|
OE1
|
G:GLU221
|
4.0
|
14.2
|
1.0
|
|
ND2
|
G:ASN197
|
4.0
|
19.0
|
1.0
|
|
O
|
G:HOH638
|
4.1
|
12.1
|
1.0
|
|
OE2
|
G:GLU222
|
4.1
|
15.8
|
1.0
|
|
NZ
|
G:LYS166
|
4.1
|
22.6
|
1.0
|
|
NE2
|
G:HIS297
|
4.2
|
17.5
|
1.0
|
|
CG
|
G:GLU247
|
4.3
|
14.6
|
1.0
|
|
CB
|
G:ASP195
|
4.3
|
13.5
|
1.0
|
|
CD2
|
G:HIS297
|
4.3
|
15.0
|
1.0
|
|
CE
|
G:MET268
|
4.4
|
13.8
|
1.0
|
|
CA
|
G:PBC402
|
4.5
|
19.4
|
1.0
|
|
CE
|
G:LYS164
|
4.6
|
11.2
|
1.0
|
|
CG
|
G:ASN197
|
4.8
|
19.5
|
1.0
|
|
CB
|
G:GLU221
|
4.8
|
11.9
|
1.0
|
|
CB1
|
G:PBC402
|
4.9
|
25.1
|
1.0
|
|
CD
|
G:GLU222
|
4.9
|
19.8
|
1.0
|
|
O
|
G:HOH521
|
4.9
|
17.0
|
1.0
|
|
CG
|
G:GLU222
|
4.9
|
17.1
|
1.0
|
|
CB
|
G:GLU247
|
5.0
|
14.8
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 6vim
Go back to
Magnesium Binding Sites List in 6vim
Magnesium binding site 8 out
of 8 in the P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of P. Putida Mandelate Racemase Co-Crystallized with Phenylboronic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg401
b:16.0
occ:1.00
|
O2
|
H:PBC402
|
1.8
|
33.5
|
1.0
|
|
OE1
|
H:GLU221
|
2.0
|
24.8
|
1.0
|
|
O
|
H:HOH526
|
2.0
|
18.8
|
1.0
|
|
OE1
|
H:GLU247
|
2.0
|
19.3
|
1.0
|
|
OD2
|
H:ASP195
|
2.1
|
19.5
|
1.0
|
|
B
|
H:PBC402
|
2.9
|
37.5
|
1.0
|
|
CD
|
H:GLU247
|
3.0
|
19.3
|
1.0
|
|
CD
|
H:GLU221
|
3.0
|
25.0
|
1.0
|
|
CG
|
H:ASP195
|
3.0
|
19.8
|
1.0
|
|
O1
|
H:PBC402
|
3.2
|
23.9
|
1.0
|
|
OE2
|
H:GLU247
|
3.2
|
15.6
|
1.0
|
|
OD1
|
H:ASP195
|
3.4
|
18.4
|
1.0
|
|
CG
|
H:GLU221
|
3.6
|
15.2
|
1.0
|
|
ND2
|
H:ASN197
|
3.9
|
22.4
|
1.0
|
|
OE2
|
H:GLU221
|
3.9
|
23.8
|
1.0
|
|
O
|
H:HOH651
|
4.1
|
14.9
|
1.0
|
|
NZ
|
H:LYS164
|
4.1
|
19.5
|
1.0
|
|
OE2
|
H:GLU222
|
4.1
|
19.3
|
1.0
|
|
NE2
|
H:HIS297
|
4.1
|
22.4
|
1.0
|
|
NZ
|
H:LYS166
|
4.2
|
22.6
|
1.0
|
|
CD2
|
H:HIS297
|
4.3
|
15.8
|
1.0
|
|
CA
|
H:PBC402
|
4.3
|
27.2
|
1.0
|
|
CB
|
H:ASP195
|
4.3
|
16.0
|
1.0
|
|
CG
|
H:GLU247
|
4.3
|
20.6
|
1.0
|
|
CE
|
H:MET268
|
4.5
|
17.8
|
1.0
|
|
CE
|
H:LYS164
|
4.7
|
13.3
|
1.0
|
|
CB1
|
H:PBC402
|
4.7
|
24.2
|
1.0
|
|
CG
|
H:ASN197
|
4.8
|
22.3
|
1.0
|
|
CD
|
H:GLU222
|
4.9
|
21.7
|
1.0
|
|
CB
|
H:GLU221
|
4.9
|
12.8
|
1.0
|
|
O
|
H:HOH544
|
4.9
|
18.2
|
1.0
|
|
CB
|
H:GLU247
|
5.0
|
17.6
|
1.0
|
|
Reference:
A.N.Sharma,
L.Grandinetti,
E.R.Johnson,
M.St Maurice,
S.L.Bearne.
Potent Inhibition of Mandelate Racemase By Boronic Acids: Boron As A Mimic of A Carbon Acid Center. Biochemistry V. 59 3026 2020.
ISSN: ISSN 0006-2960
PubMed: 32786399
DOI: 10.1021/ACS.BIOCHEM.0C00478
Page generated: Tue Oct 1 22:05:50 2024
|
