Magnesium in PDB 8y7s: Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
Protein crystallography data
The structure of Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1, PDB code: 8y7s
was solved by
Y.Li,
Y.F.Zhang,
Y.Y.Chen,
W.D.Liu,
P.Y.Yao,
Q.Q.Wu,
D.M.Zhu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.19 /
2.68
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
333.789,
98.696,
231.654,
90,
108.05,
90
|
|
R / Rfree (%)
|
18.9 /
23.6
|
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
(pdb code 8y7s). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the
Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1, PDB code: 8y7s:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 12 in 8y7s
Go back to
Magnesium Binding Sites List in 8y7s
Magnesium binding site 1 out
of 12 in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
 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 A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:35.1
occ:1.00
|
O1B
|
A:TPP601
|
1.8
|
41.2
|
1.0
|
|
OD1
|
A:ASN471
|
2.0
|
54.4
|
1.0
|
|
O1A
|
A:TPP601
|
2.1
|
37.8
|
1.0
|
|
OD1
|
A:ASP444
|
2.2
|
35.3
|
1.0
|
|
O
|
A:HOH704
|
2.2
|
32.1
|
1.0
|
|
O
|
A:ALA473
|
2.5
|
34.7
|
1.0
|
|
CG
|
A:ASN471
|
2.7
|
45.6
|
1.0
|
|
ND2
|
A:ASN471
|
3.0
|
51.6
|
1.0
|
|
PB
|
A:TPP601
|
3.0
|
31.5
|
1.0
|
|
O3A
|
A:TPP601
|
3.2
|
32.6
|
1.0
|
|
PA
|
A:TPP601
|
3.2
|
33.6
|
1.0
|
|
CG
|
A:ASP444
|
3.4
|
35.8
|
1.0
|
|
O3B
|
A:TPP601
|
3.6
|
31.4
|
1.0
|
|
C
|
A:ALA473
|
3.7
|
43.0
|
1.0
|
|
N
|
A:GLY475
|
3.8
|
33.1
|
1.0
|
|
O7
|
A:TPP601
|
3.9
|
28.4
|
1.0
|
|
OD2
|
A:ASP444
|
3.9
|
29.3
|
1.0
|
|
N
|
A:ASP444
|
4.0
|
33.1
|
1.0
|
|
CB
|
A:ASN471
|
4.1
|
33.7
|
1.0
|
|
N
|
A:ASN471
|
4.2
|
34.0
|
1.0
|
|
O2B
|
A:TPP601
|
4.2
|
32.3
|
1.0
|
|
CA
|
A:GLY475
|
4.3
|
32.5
|
1.0
|
|
N
|
A:ALA473
|
4.4
|
43.2
|
1.0
|
|
O
|
A:LEU469
|
4.4
|
35.0
|
1.0
|
|
N
|
A:GLY445
|
4.5
|
35.7
|
1.0
|
|
O2A
|
A:TPP601
|
4.5
|
45.0
|
1.0
|
|
CA
|
A:ASN471
|
4.6
|
34.1
|
1.0
|
|
CA
|
A:GLY443
|
4.6
|
34.4
|
1.0
|
|
CB
|
A:ASP444
|
4.6
|
28.3
|
1.0
|
|
N
|
A:TRP474
|
4.6
|
40.4
|
1.0
|
|
CA
|
A:ALA473
|
4.6
|
48.8
|
1.0
|
|
CA
|
A:TRP474
|
4.7
|
35.3
|
1.0
|
|
C
|
A:TRP474
|
4.7
|
35.8
|
1.0
|
|
C
|
A:GLY443
|
4.8
|
34.8
|
1.0
|
|
CA
|
A:ASP444
|
4.8
|
34.3
|
1.0
|
|
N
|
A:ARG472
|
4.9
|
28.2
|
1.0
|
|
C
|
A:ASN471
|
4.9
|
33.8
|
1.0
|
|
Magnesium binding site 2 out
of 12 in 8y7s
Go back to
Magnesium Binding Sites List in 8y7s
Magnesium binding site 2 out
of 12 in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
 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 A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:41.4
occ:1.00
|
OD1
|
B:ASN471
|
1.8
|
47.4
|
1.0
|
|
O2B
|
B:TPP601
|
1.9
|
33.1
|
1.0
|
|
OD1
|
B:ASP444
|
2.2
|
36.4
|
1.0
|
|
O1A
|
B:TPP601
|
2.2
|
39.3
|
1.0
|
|
CG
|
B:ASN471
|
2.5
|
37.9
|
1.0
|
|
ND2
|
B:ASN471
|
2.6
|
42.2
|
1.0
|
|
O
|
B:ALA473
|
2.7
|
36.0
|
1.0
|
|
PB
|
B:TPP601
|
3.0
|
31.1
|
1.0
|
|
O3A
|
B:TPP601
|
3.2
|
30.6
|
1.0
|
|
PA
|
B:TPP601
|
3.3
|
33.2
|
1.0
|
|
CG
|
B:ASP444
|
3.4
|
36.4
|
1.0
|
|
O3B
|
B:TPP601
|
3.6
|
30.8
|
1.0
|
|
N
|
B:ASP444
|
3.8
|
35.7
|
1.0
|
|
CB
|
B:ASN471
|
3.9
|
36.5
|
1.0
|
|
C
|
B:ALA473
|
3.9
|
37.9
|
1.0
|
|
N
|
B:ASN471
|
3.9
|
36.2
|
1.0
|
|
OD2
|
B:ASP444
|
4.0
|
36.1
|
1.0
|
|
N
|
B:GLY475
|
4.1
|
34.7
|
1.0
|
|
O7
|
B:TPP601
|
4.1
|
32.6
|
1.0
|
|
O
|
B:LEU469
|
4.1
|
33.7
|
1.0
|
|
O1B
|
B:TPP601
|
4.3
|
37.9
|
1.0
|
|
CA
|
B:GLY443
|
4.4
|
34.7
|
1.0
|
|
CA
|
B:ASN471
|
4.4
|
34.5
|
1.0
|
|
N
|
B:GLY445
|
4.4
|
38.8
|
1.0
|
|
N
|
B:ALA473
|
4.4
|
37.8
|
1.0
|
|
O2A
|
B:TPP601
|
4.5
|
28.9
|
1.0
|
|
CB
|
B:ASP444
|
4.5
|
27.6
|
1.0
|
|
CA
|
B:GLY475
|
4.6
|
30.8
|
1.0
|
|
C
|
B:GLY443
|
4.6
|
33.6
|
1.0
|
|
CA
|
B:ASP444
|
4.7
|
28.8
|
1.0
|
|
CA
|
B:ALA473
|
4.8
|
37.8
|
1.0
|
|
C
|
B:ASN471
|
4.8
|
36.4
|
1.0
|
|
OG1
|
B:THR394
|
4.9
|
33.2
|
1.0
|
|
N
|
B:ARG472
|
4.9
|
35.2
|
1.0
|
|
N
|
B:TRP474
|
4.9
|
31.9
|
1.0
|
|
CA
|
B:TRP474
|
5.0
|
29.0
|
1.0
|
|
C
|
B:TRP474
|
5.0
|
34.2
|
1.0
|
|
Magnesium binding site 3 out
of 12 in 8y7s
Go back to
Magnesium Binding Sites List in 8y7s
Magnesium binding site 3 out
of 12 in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
 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 A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg602
b:32.4
occ:1.00
|
O3B
|
C:TPP601
|
1.8
|
29.9
|
1.0
|
|
O2A
|
C:TPP601
|
1.9
|
35.4
|
1.0
|
|
OD1
|
C:ASP444
|
2.0
|
25.5
|
1.0
|
|
OD1
|
C:ASN471
|
2.1
|
37.4
|
1.0
|
|
O
|
C:HOH701
|
2.4
|
28.7
|
1.0
|
|
O
|
C:ALA473
|
2.6
|
28.9
|
1.0
|
|
PB
|
C:TPP601
|
2.9
|
31.9
|
1.0
|
|
PA
|
C:TPP601
|
3.0
|
31.6
|
1.0
|
|
CG
|
C:ASN471
|
3.0
|
31.4
|
1.0
|
|
O3A
|
C:TPP601
|
3.1
|
24.9
|
1.0
|
|
CG
|
C:ASP444
|
3.2
|
30.9
|
1.0
|
|
ND2
|
C:ASN471
|
3.2
|
39.4
|
1.0
|
|
O1B
|
C:TPP601
|
3.6
|
18.4
|
1.0
|
|
N
|
C:ASP444
|
3.7
|
27.8
|
1.0
|
|
O7
|
C:TPP601
|
3.8
|
32.0
|
1.0
|
|
C
|
C:ALA473
|
3.8
|
34.0
|
1.0
|
|
OD2
|
C:ASP444
|
3.9
|
25.7
|
1.0
|
|
N
|
C:GLY475
|
4.0
|
25.2
|
1.0
|
|
N
|
C:GLY445
|
4.1
|
25.8
|
1.0
|
|
O2B
|
C:TPP601
|
4.2
|
28.1
|
1.0
|
|
O1A
|
C:TPP601
|
4.3
|
33.5
|
1.0
|
|
CA
|
C:GLY443
|
4.3
|
26.1
|
1.0
|
|
N
|
C:ASN471
|
4.3
|
30.3
|
1.0
|
|
CB
|
C:ASP444
|
4.4
|
27.1
|
1.0
|
|
CB
|
C:ASN471
|
4.4
|
26.8
|
1.0
|
|
C
|
C:GLY443
|
4.4
|
30.1
|
1.0
|
|
CA
|
C:ASP444
|
4.5
|
30.0
|
1.0
|
|
CA
|
C:TRP474
|
4.5
|
27.9
|
1.0
|
|
O
|
C:LEU469
|
4.5
|
28.5
|
1.0
|
|
N
|
C:ALA473
|
4.5
|
27.4
|
1.0
|
|
N
|
C:TRP474
|
4.6
|
32.2
|
1.0
|
|
C
|
C:TRP474
|
4.7
|
29.0
|
1.0
|
|
CA
|
C:ALA473
|
4.8
|
27.0
|
1.0
|
|
C
|
C:ASP444
|
4.8
|
29.5
|
1.0
|
|
CA
|
C:ASN471
|
4.8
|
25.7
|
1.0
|
|
CA
|
C:GLY475
|
4.9
|
22.0
|
1.0
|
|
Magnesium binding site 4 out
of 12 in 8y7s
Go back to
Magnesium Binding Sites List in 8y7s
Magnesium binding site 4 out
of 12 in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
 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 A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg602
b:38.7
occ:1.00
|
O3B
|
D:TPP601
|
1.8
|
41.4
|
1.0
|
|
OD1
|
D:ASN471
|
1.9
|
43.3
|
1.0
|
|
OD1
|
D:ASP444
|
2.2
|
33.8
|
1.0
|
|
O1A
|
D:TPP601
|
2.2
|
41.8
|
1.0
|
|
O
|
D:ALA473
|
2.6
|
34.5
|
1.0
|
|
CG
|
D:ASN471
|
2.7
|
37.5
|
1.0
|
|
PB
|
D:TPP601
|
2.9
|
30.7
|
1.0
|
|
ND2
|
D:ASN471
|
2.9
|
43.4
|
1.0
|
|
O3A
|
D:TPP601
|
3.1
|
32.8
|
1.0
|
|
PA
|
D:TPP601
|
3.2
|
36.6
|
1.0
|
|
CG
|
D:ASP444
|
3.4
|
34.4
|
1.0
|
|
O1B
|
D:TPP601
|
3.4
|
34.5
|
1.0
|
|
N
|
D:ASP444
|
3.8
|
32.2
|
1.0
|
|
C
|
D:ALA473
|
3.8
|
44.1
|
1.0
|
|
N
|
D:GLY475
|
3.9
|
30.9
|
1.0
|
|
OD2
|
D:ASP444
|
4.0
|
35.4
|
1.0
|
|
O7
|
D:TPP601
|
4.0
|
37.8
|
1.0
|
|
CB
|
D:ASN471
|
4.1
|
25.1
|
1.0
|
|
N
|
D:ASN471
|
4.2
|
27.5
|
1.0
|
|
O2B
|
D:TPP601
|
4.2
|
27.9
|
1.0
|
|
O
|
D:LEU469
|
4.2
|
34.9
|
1.0
|
|
CA
|
D:GLY443
|
4.3
|
36.4
|
1.0
|
|
O2A
|
D:TPP601
|
4.4
|
40.4
|
1.0
|
|
CA
|
D:GLY475
|
4.4
|
35.6
|
1.0
|
|
N
|
D:GLY445
|
4.5
|
32.9
|
1.0
|
|
N
|
D:ALA473
|
4.5
|
32.5
|
1.0
|
|
CB
|
D:ASP444
|
4.5
|
27.4
|
1.0
|
|
C
|
D:GLY443
|
4.6
|
38.6
|
1.0
|
|
CA
|
D:ASN471
|
4.6
|
27.1
|
1.0
|
|
CA
|
D:ASP444
|
4.7
|
30.2
|
1.0
|
|
N
|
D:TRP474
|
4.7
|
36.3
|
1.0
|
|
CA
|
D:TRP474
|
4.7
|
31.7
|
1.0
|
|
CA
|
D:ALA473
|
4.8
|
35.9
|
1.0
|
|
C
|
D:TRP474
|
4.8
|
34.2
|
1.0
|
|
Magnesium binding site 5 out
of 12 in 8y7s
Go back to
Magnesium Binding Sites List in 8y7s
Magnesium binding site 5 out
of 12 in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
 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 A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg602
b:70.9
occ:1.00
|
O3B
|
E:TPP601
|
1.8
|
38.6
|
1.0
|
|
OD1
|
E:ASN471
|
1.9
|
40.0
|
1.0
|
|
O1A
|
E:TPP601
|
2.1
|
43.0
|
1.0
|
|
OD1
|
E:ASP444
|
2.3
|
36.8
|
1.0
|
|
O
|
E:ALA473
|
2.7
|
31.5
|
1.0
|
|
CG
|
E:ASN471
|
2.8
|
33.3
|
1.0
|
|
ND2
|
E:ASN471
|
3.0
|
57.7
|
1.0
|
|
PB
|
E:TPP601
|
3.1
|
57.9
|
1.0
|
|
CG
|
E:ASP444
|
3.2
|
32.9
|
1.0
|
|
PA
|
E:TPP601
|
3.2
|
37.5
|
1.0
|
|
O3A
|
E:TPP601
|
3.3
|
43.1
|
1.0
|
|
OD2
|
E:ASP444
|
3.5
|
29.7
|
1.0
|
|
N
|
E:GLY475
|
3.7
|
35.5
|
1.0
|
|
N
|
E:ASP444
|
3.8
|
34.7
|
1.0
|
|
C
|
E:ALA473
|
3.9
|
32.5
|
1.0
|
|
O1B
|
E:TPP601
|
3.9
|
26.9
|
1.0
|
|
O7
|
E:TPP601
|
4.0
|
33.2
|
1.0
|
|
N
|
E:ASN471
|
4.0
|
35.2
|
1.0
|
|
O
|
E:LEU469
|
4.1
|
40.9
|
1.0
|
|
CB
|
E:ASN471
|
4.2
|
33.7
|
1.0
|
|
O2B
|
E:TPP601
|
4.2
|
30.8
|
1.0
|
|
N
|
E:GLY445
|
4.3
|
34.2
|
1.0
|
|
CA
|
E:GLY475
|
4.3
|
29.9
|
1.0
|
|
CA
|
E:GLY443
|
4.3
|
35.7
|
1.0
|
|
CB
|
E:ASP444
|
4.4
|
25.9
|
1.0
|
|
O2A
|
E:TPP601
|
4.5
|
38.3
|
1.0
|
|
C
|
E:GLY443
|
4.5
|
35.0
|
1.0
|
|
N
|
E:ALA473
|
4.5
|
35.4
|
1.0
|
|
CA
|
E:ASN471
|
4.6
|
33.6
|
1.0
|
|
CA
|
E:ASP444
|
4.6
|
33.3
|
1.0
|
|
C
|
E:TRP474
|
4.6
|
31.4
|
1.0
|
|
CA
|
E:TRP474
|
4.7
|
28.2
|
1.0
|
|
N
|
E:TRP474
|
4.8
|
32.7
|
1.0
|
|
CA
|
E:ALA473
|
4.8
|
34.3
|
1.0
|
|
N
|
E:ARG472
|
5.0
|
24.8
|
1.0
|
|
Magnesium binding site 6 out
of 12 in 8y7s
Go back to
Magnesium Binding Sites List in 8y7s
Magnesium binding site 6 out
of 12 in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
 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 A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg602
b:36.7
occ:1.00
|
O2A
|
F:TPP601
|
2.0
|
37.4
|
1.0
|
|
O3B
|
F:TPP601
|
2.0
|
29.6
|
1.0
|
|
OD1
|
F:ASP444
|
2.1
|
31.2
|
1.0
|
|
OD1
|
F:ASN471
|
2.4
|
38.5
|
1.0
|
|
O
|
F:ALA473
|
2.9
|
33.6
|
1.0
|
|
ND2
|
F:ASN471
|
2.9
|
35.9
|
1.0
|
|
CG
|
F:ASN471
|
3.0
|
32.8
|
1.0
|
|
PB
|
F:TPP601
|
3.0
|
35.2
|
1.0
|
|
PA
|
F:TPP601
|
3.0
|
40.2
|
1.0
|
|
O3A
|
F:TPP601
|
3.0
|
30.5
|
1.0
|
|
CG
|
F:ASP444
|
3.4
|
34.1
|
1.0
|
|
N
|
F:ASP444
|
3.4
|
29.5
|
1.0
|
|
O1B
|
F:TPP601
|
3.5
|
25.5
|
1.0
|
|
O7
|
F:TPP601
|
3.9
|
32.1
|
1.0
|
|
CA
|
F:GLY443
|
4.0
|
35.7
|
1.0
|
|
N
|
F:GLY445
|
4.0
|
30.6
|
1.0
|
|
C
|
F:ALA473
|
4.1
|
35.6
|
1.0
|
|
C
|
F:GLY443
|
4.2
|
31.5
|
1.0
|
|
O
|
F:LEU469
|
4.2
|
28.2
|
1.0
|
|
N
|
F:GLY475
|
4.2
|
31.2
|
1.0
|
|
OD2
|
F:ASP444
|
4.2
|
31.1
|
1.0
|
|
O1A
|
F:TPP601
|
4.2
|
35.9
|
1.0
|
|
N
|
F:ASN471
|
4.2
|
24.6
|
1.0
|
|
CB
|
F:ASP444
|
4.3
|
27.7
|
1.0
|
|
CA
|
F:ASP444
|
4.3
|
30.2
|
1.0
|
|
O2B
|
F:TPP601
|
4.3
|
30.8
|
1.0
|
|
CB
|
F:ASN471
|
4.4
|
24.9
|
1.0
|
|
C
|
F:ASP444
|
4.7
|
29.3
|
1.0
|
|
N
|
F:ALA473
|
4.7
|
33.7
|
1.0
|
|
CA
|
F:GLY475
|
4.8
|
27.6
|
1.0
|
|
CA
|
F:ASN471
|
4.8
|
26.7
|
1.0
|
|
OG1
|
F:THR394
|
4.9
|
39.5
|
1.0
|
|
Magnesium binding site 7 out
of 12 in 8y7s
Go back to
Magnesium Binding Sites List in 8y7s
Magnesium binding site 7 out
of 12 in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
 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 A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg602
b:30.5
occ:1.00
|
O2B
|
G:TPP601
|
1.8
|
29.4
|
1.0
|
|
O2A
|
G:TPP601
|
2.0
|
35.8
|
1.0
|
|
OD1
|
G:ASP444
|
2.1
|
38.0
|
1.0
|
|
OD1
|
G:ASN471
|
2.2
|
33.0
|
1.0
|
|
O
|
G:ALA473
|
2.4
|
26.9
|
1.0
|
|
O
|
G:HOH704
|
2.4
|
25.1
|
1.0
|
|
PB
|
G:TPP601
|
3.1
|
44.0
|
1.0
|
|
PA
|
G:TPP601
|
3.1
|
38.1
|
1.0
|
|
CG
|
G:ASN471
|
3.2
|
37.2
|
1.0
|
|
CG
|
G:ASP444
|
3.2
|
33.8
|
1.0
|
|
O3A
|
G:TPP601
|
3.3
|
29.3
|
1.0
|
|
ND2
|
G:ASN471
|
3.4
|
28.3
|
1.0
|
|
C
|
G:ALA473
|
3.6
|
36.8
|
1.0
|
|
N
|
G:ASP444
|
3.8
|
34.1
|
1.0
|
|
N
|
G:GLY475
|
3.8
|
32.4
|
1.0
|
|
OD2
|
G:ASP444
|
3.8
|
27.5
|
1.0
|
|
O7
|
G:TPP601
|
3.9
|
31.5
|
1.0
|
|
O3B
|
G:TPP601
|
3.9
|
28.5
|
1.0
|
|
N
|
G:GLY445
|
4.1
|
31.0
|
1.0
|
|
O1B
|
G:TPP601
|
4.2
|
28.5
|
1.0
|
|
CA
|
G:TRP474
|
4.3
|
32.6
|
1.0
|
|
N
|
G:ALA473
|
4.4
|
37.2
|
1.0
|
|
CB
|
G:ASP444
|
4.4
|
28.4
|
1.0
|
|
O1A
|
G:TPP601
|
4.4
|
32.4
|
1.0
|
|
N
|
G:ASN471
|
4.4
|
28.0
|
1.0
|
|
N
|
G:TRP474
|
4.4
|
33.0
|
1.0
|
|
CA
|
G:GLY443
|
4.5
|
25.1
|
1.0
|
|
C
|
G:TRP474
|
4.5
|
36.4
|
1.0
|
|
CA
|
G:ASP444
|
4.5
|
32.0
|
1.0
|
|
CB
|
G:ASN471
|
4.6
|
32.9
|
1.0
|
|
C
|
G:GLY443
|
4.6
|
35.8
|
1.0
|
|
CA
|
G:ALA473
|
4.6
|
36.0
|
1.0
|
|
O
|
G:LEU469
|
4.7
|
37.1
|
1.0
|
|
CA
|
G:GLY475
|
4.7
|
29.6
|
1.0
|
|
C
|
G:ASP444
|
4.8
|
31.7
|
1.0
|
|
CA
|
G:ASN471
|
5.0
|
29.6
|
1.0
|
|
Magnesium binding site 8 out
of 12 in 8y7s
Go back to
Magnesium Binding Sites List in 8y7s
Magnesium binding site 8 out
of 12 in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
 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 A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg602
b:39.7
occ:1.00
|
OD1
|
H:ASN471
|
1.8
|
50.0
|
1.0
|
|
OD1
|
H:ASP444
|
2.0
|
55.5
|
1.0
|
|
O2A
|
H:TPP601
|
2.2
|
30.1
|
1.0
|
|
O
|
H:ALA473
|
2.3
|
35.9
|
1.0
|
|
O2B
|
H:TPP601
|
2.5
|
36.3
|
1.0
|
|
CG
|
H:ASP444
|
2.7
|
45.7
|
1.0
|
|
CG
|
H:ASN471
|
2.8
|
50.0
|
1.0
|
|
OD2
|
H:ASP444
|
2.8
|
41.7
|
1.0
|
|
ND2
|
H:ASN471
|
3.3
|
50.0
|
1.0
|
|
PA
|
H:TPP601
|
3.5
|
38.4
|
1.0
|
|
C
|
H:ALA473
|
3.5
|
38.9
|
1.0
|
|
PB
|
H:TPP601
|
3.7
|
34.7
|
1.0
|
|
O3A
|
H:TPP601
|
3.8
|
33.3
|
1.0
|
|
N
|
H:ASP444
|
3.8
|
32.5
|
1.0
|
|
N
|
H:ASN471
|
3.9
|
46.0
|
1.0
|
|
N
|
H:ALA473
|
4.0
|
49.3
|
1.0
|
|
N
|
H:GLY475
|
4.0
|
36.0
|
1.0
|
|
CB
|
H:ASP444
|
4.1
|
37.0
|
1.0
|
|
CB
|
H:ASN471
|
4.2
|
50.0
|
1.0
|
|
O7
|
H:TPP601
|
4.2
|
38.6
|
1.0
|
|
N
|
H:GLY445
|
4.3
|
39.1
|
1.0
|
|
O3B
|
H:TPP601
|
4.3
|
47.7
|
1.0
|
|
CA
|
H:ALA473
|
4.3
|
47.6
|
1.0
|
|
O
|
H:LEU469
|
4.4
|
46.7
|
1.0
|
|
CA
|
H:ASN471
|
4.4
|
42.0
|
1.0
|
|
CA
|
H:ASP444
|
4.5
|
34.8
|
1.0
|
|
N
|
H:TRP474
|
4.5
|
39.6
|
1.0
|
|
N
|
H:ARG472
|
4.6
|
33.3
|
1.0
|
|
C
|
H:ASN471
|
4.6
|
41.9
|
1.0
|
|
CA
|
H:TRP474
|
4.7
|
37.1
|
1.0
|
|
CA
|
H:GLY475
|
4.7
|
35.6
|
1.0
|
|
CA
|
H:GLY443
|
4.7
|
32.0
|
1.0
|
|
C
|
H:GLY443
|
4.7
|
34.0
|
1.0
|
|
O1A
|
H:TPP601
|
4.7
|
31.6
|
1.0
|
|
C
|
H:TRP474
|
4.8
|
34.0
|
1.0
|
|
O1B
|
H:TPP601
|
4.9
|
39.6
|
1.0
|
|
C
|
H:ASN470
|
4.9
|
39.6
|
1.0
|
|
C
|
H:ASP444
|
4.9
|
37.4
|
1.0
|
|
CA
|
H:ASN470
|
5.0
|
37.1
|
1.0
|
|
Magnesium binding site 9 out
of 12 in 8y7s
Go back to
Magnesium Binding Sites List in 8y7s
Magnesium binding site 9 out
of 12 in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
 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 A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg602
b:42.6
occ:1.00
|
OD1
|
I:ASN471
|
1.9
|
54.8
|
1.0
|
|
O2B
|
I:TPP601
|
2.0
|
43.2
|
1.0
|
|
OD1
|
I:ASP444
|
2.1
|
40.2
|
1.0
|
|
O2A
|
I:TPP601
|
2.5
|
47.9
|
1.0
|
|
CG
|
I:ASN471
|
2.6
|
54.3
|
1.0
|
|
ND2
|
I:ASN471
|
2.8
|
53.4
|
1.0
|
|
O
|
I:ALA473
|
2.9
|
39.4
|
1.0
|
|
PB
|
I:TPP601
|
3.1
|
48.2
|
1.0
|
|
O3A
|
I:TPP601
|
3.3
|
48.5
|
1.0
|
|
CG
|
I:ASP444
|
3.3
|
43.0
|
1.0
|
|
PA
|
I:TPP601
|
3.5
|
43.5
|
1.0
|
|
O3B
|
I:TPP601
|
3.5
|
43.1
|
1.0
|
|
N
|
I:ASP444
|
3.7
|
48.6
|
1.0
|
|
OD2
|
I:ASP444
|
3.9
|
42.0
|
1.0
|
|
N
|
I:ASN471
|
4.0
|
45.1
|
1.0
|
|
O
|
I:LEU469
|
4.0
|
49.0
|
1.0
|
|
CB
|
I:ASN471
|
4.1
|
49.6
|
1.0
|
|
C
|
I:ALA473
|
4.2
|
47.2
|
1.0
|
|
CA
|
I:GLY443
|
4.2
|
32.7
|
1.0
|
|
N
|
I:GLY475
|
4.2
|
39.7
|
1.0
|
|
O7
|
I:TPP601
|
4.4
|
50.7
|
1.0
|
|
O1B
|
I:TPP601
|
4.4
|
45.1
|
1.0
|
|
N
|
I:GLY445
|
4.5
|
42.0
|
1.0
|
|
C
|
I:GLY443
|
4.5
|
39.9
|
1.0
|
|
CB
|
I:ASP444
|
4.5
|
36.4
|
1.0
|
|
CA
|
I:ASN471
|
4.6
|
41.8
|
1.0
|
|
CA
|
I:ASP444
|
4.6
|
48.6
|
1.0
|
|
N
|
I:ALA473
|
4.7
|
44.2
|
1.0
|
|
O1A
|
I:TPP601
|
4.7
|
42.0
|
1.0
|
|
CA
|
I:TRP474
|
4.9
|
40.8
|
1.0
|
|
Magnesium binding site 10 out
of 12 in 8y7s
Go back to
Magnesium Binding Sites List in 8y7s
Magnesium binding site 10 out
of 12 in the Crystal Structure of A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1
 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 A Benzaldehyde Lyase Mutant M6 From Herbiconiux Sp. Salv-R1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg602
b:40.0
occ:1.00
|
OD1
|
J:ASN471
|
1.9
|
44.3
|
1.0
|
|
O2B
|
J:TPP601
|
2.0
|
39.0
|
1.0
|
|
OD1
|
J:ASP444
|
2.1
|
38.4
|
1.0
|
|
O2A
|
J:TPP601
|
2.3
|
37.6
|
1.0
|
|
O
|
J:ALA473
|
2.7
|
45.5
|
1.0
|
|
CG
|
J:ASN471
|
2.9
|
45.5
|
1.0
|
|
PB
|
J:TPP601
|
3.1
|
32.3
|
1.0
|
|
ND2
|
J:ASN471
|
3.3
|
33.5
|
1.0
|
|
O3A
|
J:TPP601
|
3.3
|
33.8
|
1.0
|
|
CG
|
J:ASP444
|
3.3
|
36.6
|
1.0
|
|
PA
|
J:TPP601
|
3.3
|
40.7
|
1.0
|
|
N
|
J:ASP444
|
3.6
|
40.1
|
1.0
|
|
O3B
|
J:TPP601
|
3.6
|
35.8
|
1.0
|
|
C
|
J:ALA473
|
4.0
|
45.8
|
1.0
|
|
N
|
J:ASN471
|
4.0
|
28.1
|
1.0
|
|
O
|
J:LEU469
|
4.1
|
37.9
|
1.0
|
|
OD2
|
J:ASP444
|
4.1
|
35.2
|
1.0
|
|
N
|
J:GLY475
|
4.1
|
29.8
|
1.0
|
|
CA
|
J:GLY443
|
4.2
|
33.4
|
1.0
|
|
O7
|
J:TPP601
|
4.2
|
37.4
|
1.0
|
|
N
|
J:GLY445
|
4.2
|
32.1
|
1.0
|
|
CB
|
J:ASN471
|
4.3
|
40.5
|
1.0
|
|
CB
|
J:ASP444
|
4.3
|
36.3
|
1.0
|
|
C
|
J:GLY443
|
4.3
|
37.4
|
1.0
|
|
O1B
|
J:TPP601
|
4.4
|
26.7
|
1.0
|
|
CA
|
J:ASP444
|
4.4
|
37.6
|
1.0
|
|
N
|
J:ALA473
|
4.5
|
42.9
|
1.0
|
|
O1A
|
J:TPP601
|
4.5
|
34.1
|
1.0
|
|
CA
|
J:ASN471
|
4.6
|
28.6
|
1.0
|
|
CA
|
J:TRP474
|
4.7
|
33.6
|
1.0
|
|
N
|
J:TRP474
|
4.8
|
35.3
|
1.0
|
|
CA
|
J:ALA473
|
4.9
|
43.0
|
1.0
|
|
C
|
J:ASP444
|
4.9
|
37.5
|
1.0
|
|
CA
|
J:GLY475
|
4.9
|
27.8
|
1.0
|
|
C
|
J:TRP474
|
4.9
|
34.7
|
1.0
|
|
N
|
J:ARG472
|
5.0
|
31.3
|
1.0
|
|
C
|
J:ASN471
|
5.0
|
32.6
|
1.0
|
|
Reference:
Y.Zhang,
Y.Li,
Y.Chen,
W.Liu,
Q.Zhao,
J.Feng,
P.Yao,
Q.Wu,
D.Zhu.
Manipulating Activity and Chemoselectivity of A Benzaldehyde Lyase For Efficient Synthesis of Alpha-Hydroxymethyl Ketones and One-Pot Enantio-Complementary Conversion to 1,2-Diols Acs Catalysis V. 14 9687 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.4C01804
Page generated: Tue Feb 25 11:00:17 2025
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