Magnesium in PDB 5dei: Benzoylformate Decarboxylase From Pseudomonas Putida
Enzymatic activity of Benzoylformate Decarboxylase From Pseudomonas Putida
All present enzymatic activity of Benzoylformate Decarboxylase From Pseudomonas Putida:
4.1.1.7;
Protein crystallography data
The structure of Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 5dei
was solved by
A.K.Bera,
M.S.Hasson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
27.41 /
1.30
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.166,
92.451,
93.715,
63.59,
72.42,
72.88
|
|
R / Rfree (%)
|
13.6 /
14.8
|
Other elements in 5dei:
The structure of Benzoylformate Decarboxylase From Pseudomonas Putida also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Benzoylformate Decarboxylase From Pseudomonas Putida
(pdb code 5dei). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 5dei:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 5dei
Go back to
Magnesium Binding Sites List in 5dei
Magnesium binding site 1 out
of 8 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:10.8
occ:1.00
|
O
|
C:ARG121
|
2.5
|
13.2
|
1.0
|
|
O
|
A:ARG121
|
2.5
|
12.8
|
1.0
|
|
O
|
C:LEU119
|
2.6
|
11.2
|
1.0
|
|
O
|
A:LEU119
|
2.6
|
11.8
|
1.0
|
|
O
|
C:ASN118
|
2.7
|
12.1
|
1.0
|
|
O
|
A:ASN118
|
2.8
|
12.6
|
1.0
|
|
O
|
C:HOH1050
|
3.2
|
19.3
|
1.0
|
|
C
|
C:LEU119
|
3.3
|
11.5
|
1.0
|
|
C
|
A:LEU119
|
3.4
|
11.8
|
1.0
|
|
HA
|
A:LEU119
|
3.4
|
14.0
|
1.0
|
|
HA
|
C:LEU119
|
3.4
|
13.8
|
1.0
|
|
HE1
|
C:MET80
|
3.6
|
13.0
|
0.4
|
|
HE1
|
A:MET80
|
3.6
|
17.4
|
0.5
|
|
H
|
C:ARG121
|
3.6
|
13.8
|
1.0
|
|
H
|
A:ARG121
|
3.6
|
14.1
|
1.0
|
|
C
|
C:ARG121
|
3.7
|
12.8
|
1.0
|
|
C
|
A:ARG121
|
3.7
|
12.7
|
1.0
|
|
HB2
|
A:ARG121
|
3.8
|
15.2
|
1.0
|
|
HB2
|
C:ARG121
|
3.8
|
15.8
|
1.0
|
|
N
|
C:ARG121
|
3.8
|
11.5
|
1.0
|
|
C
|
C:ASN118
|
3.8
|
11.5
|
1.0
|
|
N
|
A:ARG121
|
3.8
|
11.8
|
1.0
|
|
CA
|
C:LEU119
|
3.8
|
11.5
|
1.0
|
|
CA
|
A:LEU119
|
3.8
|
11.7
|
1.0
|
|
C
|
A:ASN118
|
3.8
|
11.7
|
1.0
|
|
HD12
|
C:LEU119
|
4.2
|
16.2
|
1.0
|
|
CA
|
C:ARG121
|
4.2
|
12.0
|
1.0
|
|
CA
|
A:ARG121
|
4.2
|
11.9
|
1.0
|
|
HD12
|
A:LEU119
|
4.2
|
15.9
|
1.0
|
|
N
|
C:PRO120
|
4.3
|
12.1
|
1.0
|
|
N
|
A:PRO120
|
4.3
|
11.7
|
1.0
|
|
C
|
C:PRO120
|
4.3
|
11.7
|
1.0
|
|
HE2
|
C:MET80
|
4.3
|
25.1
|
0.6
|
|
C
|
A:PRO120
|
4.3
|
12.4
|
1.0
|
|
N
|
C:LEU119
|
4.3
|
11.6
|
1.0
|
|
N
|
A:LEU119
|
4.3
|
11.1
|
1.0
|
|
HE2
|
A:MET80
|
4.3
|
24.9
|
0.5
|
|
CE
|
C:MET80
|
4.5
|
10.8
|
0.4
|
|
CB
|
A:ARG121
|
4.5
|
12.7
|
1.0
|
|
CB
|
C:ARG121
|
4.5
|
13.2
|
1.0
|
|
CE
|
A:MET80
|
4.5
|
14.5
|
0.5
|
|
HE3
|
C:MET80
|
4.6
|
13.0
|
0.4
|
|
HD3
|
C:PRO122
|
4.6
|
15.8
|
1.0
|
|
HD3
|
A:PRO122
|
4.6
|
17.1
|
1.0
|
|
HA
|
A:PRO120
|
4.6
|
12.8
|
1.0
|
|
HB3
|
A:ASN118
|
4.6
|
16.1
|
1.0
|
|
CA
|
A:PRO120
|
4.6
|
10.7
|
1.0
|
|
HB3
|
C:ASN118
|
4.6
|
15.1
|
1.0
|
|
HE3
|
A:MET80
|
4.6
|
17.4
|
0.5
|
|
CA
|
C:PRO120
|
4.7
|
11.0
|
1.0
|
|
HA
|
C:PRO120
|
4.7
|
13.2
|
1.0
|
|
HE1
|
A:MET80
|
4.7
|
24.9
|
0.5
|
|
HE1
|
C:MET80
|
4.7
|
25.1
|
0.6
|
|
N
|
C:PRO122
|
4.8
|
12.4
|
1.0
|
|
N
|
A:PRO122
|
4.8
|
11.8
|
1.0
|
|
CE
|
C:MET80
|
5.0
|
20.9
|
0.6
|
|
Magnesium binding site 2 out
of 8 in 5dei
Go back to
Magnesium Binding Sites List in 5dei
Magnesium binding site 2 out
of 8 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg604
b:16.7
occ:1.00
|
H
|
A:LYS497
|
2.5
|
18.5
|
1.0
|
|
HG2
|
A:LYS497
|
2.9
|
32.3
|
1.0
|
|
HA
|
A:LEU496
|
3.0
|
17.8
|
1.0
|
|
O
|
A:HOH1241
|
3.1
|
40.7
|
1.0
|
|
O
|
A:HOH1002
|
3.1
|
37.6
|
1.0
|
|
O
|
A:HOH931
|
3.1
|
22.6
|
1.0
|
|
N
|
A:LYS497
|
3.3
|
15.4
|
1.0
|
|
HB3
|
A:LEU496
|
3.5
|
18.4
|
1.0
|
|
HD22
|
A:LEU496
|
3.5
|
20.1
|
1.0
|
|
CA
|
A:LEU496
|
3.8
|
14.8
|
1.0
|
|
CG
|
A:LYS497
|
3.8
|
26.9
|
1.0
|
|
C
|
A:LEU496
|
4.0
|
15.0
|
1.0
|
|
CB
|
A:LEU496
|
4.1
|
15.3
|
1.0
|
|
HD23
|
A:LEU496
|
4.1
|
20.1
|
1.0
|
|
O
|
A:LYS497
|
4.1
|
17.6
|
1.0
|
|
HG3
|
A:LYS497
|
4.1
|
32.3
|
1.0
|
|
HE2
|
A:LYS497
|
4.1
|
41.8
|
1.0
|
|
HG
|
A:SER507
|
4.2
|
17.7
|
0.5
|
|
CD2
|
A:LEU496
|
4.2
|
16.8
|
1.0
|
|
HH11
|
A:ARG485
|
4.3
|
22.7
|
1.0
|
|
CA
|
A:LYS497
|
4.3
|
17.8
|
1.0
|
|
HB3
|
A:LYS497
|
4.4
|
29.6
|
1.0
|
|
CB
|
A:LYS497
|
4.4
|
24.7
|
1.0
|
|
OG
|
A:SER507
|
4.4
|
14.8
|
0.5
|
|
C
|
A:LYS497
|
4.6
|
17.0
|
1.0
|
|
CG
|
A:LEU496
|
4.7
|
15.2
|
1.0
|
|
HH12
|
A:ARG485
|
4.8
|
22.7
|
1.0
|
|
NH1
|
A:ARG485
|
4.8
|
18.9
|
1.0
|
|
O
|
A:ALA495
|
4.8
|
18.3
|
1.0
|
|
CD
|
A:LYS497
|
4.9
|
28.3
|
1.0
|
|
HB2
|
A:LEU496
|
4.9
|
18.4
|
1.0
|
|
CE
|
A:LYS497
|
4.9
|
34.8
|
1.0
|
|
HD13
|
A:LEU496
|
5.0
|
20.1
|
1.0
|
|
HD21
|
A:LEU496
|
5.0
|
20.1
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 5dei
Go back to
Magnesium Binding Sites List in 5dei
Magnesium binding site 3 out
of 8 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg605
b:18.7
occ:1.00
|
H
|
D:ASP188
|
2.4
|
20.3
|
1.0
|
|
HE
|
A:ARG185
|
2.4
|
30.4
|
1.0
|
|
HH21
|
A:ARG185
|
3.0
|
36.9
|
1.0
|
|
O
|
A:HOH871
|
3.0
|
24.7
|
1.0
|
|
HB2
|
D:ASN187
|
3.2
|
20.6
|
1.0
|
|
HA
|
D:ASN187
|
3.2
|
18.1
|
1.0
|
|
N
|
D:ASP188
|
3.2
|
16.9
|
1.0
|
|
NE
|
A:ARG185
|
3.2
|
25.3
|
1.0
|
|
HG2
|
A:ARG185
|
3.3
|
23.6
|
1.0
|
|
HB2
|
D:ASP188
|
3.4
|
22.4
|
1.0
|
|
O
|
D:HOH1059
|
3.4
|
28.6
|
1.0
|
|
CG
|
D:ASP188
|
3.7
|
28.9
|
1.0
|
|
NH2
|
A:ARG185
|
3.7
|
30.7
|
1.0
|
|
CA
|
D:ASN187
|
3.8
|
15.1
|
1.0
|
|
OD2
|
D:ASP188
|
3.8
|
26.9
|
1.0
|
|
CB
|
D:ASP188
|
3.9
|
18.6
|
1.0
|
|
CB
|
D:ASN187
|
3.9
|
17.2
|
1.0
|
|
CZ
|
A:ARG185
|
4.0
|
25.6
|
1.0
|
|
HB2
|
A:ALA325
|
4.0
|
22.9
|
1.0
|
|
C
|
D:ASN187
|
4.0
|
16.6
|
1.0
|
|
CG
|
A:ARG185
|
4.0
|
19.6
|
1.0
|
|
OD1
|
D:ASP188
|
4.1
|
29.7
|
1.0
|
|
HG3
|
A:ARG185
|
4.1
|
23.6
|
1.0
|
|
CA
|
D:ASP188
|
4.2
|
16.4
|
1.0
|
|
CD
|
A:ARG185
|
4.2
|
26.1
|
1.0
|
|
HB3
|
D:ASN187
|
4.3
|
20.6
|
1.0
|
|
HH12
|
D:ARG185
|
4.4
|
22.1
|
1.0
|
|
O
|
A:HOH937
|
4.5
|
42.0
|
1.0
|
|
HH22
|
A:ARG185
|
4.5
|
36.9
|
1.0
|
|
H
|
D:GLN189
|
4.7
|
22.2
|
1.0
|
|
HA
|
D:ASP188
|
4.7
|
19.7
|
1.0
|
|
O
|
D:HOH1221
|
4.8
|
38.9
|
1.0
|
|
HB3
|
D:ASP188
|
4.8
|
22.4
|
1.0
|
|
HB1
|
A:ALA321
|
4.8
|
19.4
|
1.0
|
|
HD3
|
A:ARG185
|
4.8
|
31.3
|
1.0
|
|
NH1
|
D:ARG185
|
4.9
|
18.4
|
1.0
|
|
HD2
|
A:ARG185
|
4.9
|
31.3
|
1.0
|
|
CB
|
A:ALA325
|
4.9
|
19.1
|
1.0
|
|
HH11
|
D:ARG185
|
5.0
|
22.1
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 5dei
Go back to
Magnesium Binding Sites List in 5dei
Magnesium binding site 4 out
of 8 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:10.3
occ:1.00
|
O
|
D:ARG121
|
2.6
|
12.6
|
1.0
|
|
O
|
B:ARG121
|
2.6
|
12.8
|
1.0
|
|
O
|
B:LEU119
|
2.6
|
12.0
|
1.0
|
|
O
|
D:LEU119
|
2.6
|
12.4
|
1.0
|
|
O
|
D:ASN118
|
2.7
|
12.0
|
1.0
|
|
O
|
B:ASN118
|
2.8
|
12.2
|
1.0
|
|
O
|
B:HOH1065
|
3.2
|
19.8
|
1.0
|
|
C
|
B:LEU119
|
3.3
|
10.6
|
1.0
|
|
C
|
D:LEU119
|
3.3
|
11.0
|
1.0
|
|
HA
|
D:LEU119
|
3.4
|
13.4
|
1.0
|
|
HA
|
B:LEU119
|
3.4
|
13.8
|
1.0
|
|
HE1
|
B:MET80
|
3.5
|
15.4
|
0.5
|
|
H
|
B:ARG121
|
3.6
|
14.2
|
1.0
|
|
H
|
D:ARG121
|
3.6
|
14.7
|
1.0
|
|
HE1
|
D:MET80
|
3.6
|
12.3
|
0.4
|
|
C
|
D:ARG121
|
3.7
|
12.0
|
1.0
|
|
C
|
B:ARG121
|
3.7
|
12.4
|
1.0
|
|
HB2
|
D:ARG121
|
3.8
|
16.5
|
1.0
|
|
HB2
|
B:ARG121
|
3.8
|
16.1
|
1.0
|
|
N
|
B:ARG121
|
3.8
|
11.8
|
1.0
|
|
C
|
D:ASN118
|
3.8
|
11.1
|
1.0
|
|
N
|
D:ARG121
|
3.8
|
12.2
|
1.0
|
|
CA
|
D:LEU119
|
3.8
|
11.2
|
1.0
|
|
CA
|
B:LEU119
|
3.8
|
11.5
|
1.0
|
|
C
|
B:ASN118
|
3.8
|
11.9
|
1.0
|
|
CA
|
D:ARG121
|
4.2
|
12.2
|
1.0
|
|
CA
|
B:ARG121
|
4.2
|
12.8
|
1.0
|
|
HD12
|
D:LEU119
|
4.2
|
17.3
|
1.0
|
|
HD12
|
B:LEU119
|
4.2
|
16.9
|
1.0
|
|
N
|
B:PRO120
|
4.3
|
12.0
|
1.0
|
|
N
|
D:PRO120
|
4.3
|
12.0
|
1.0
|
|
N
|
D:LEU119
|
4.3
|
11.0
|
1.0
|
|
C
|
D:PRO120
|
4.3
|
13.8
|
1.0
|
|
N
|
B:LEU119
|
4.3
|
11.8
|
1.0
|
|
HE2
|
D:MET80
|
4.3
|
25.0
|
0.6
|
|
HE2
|
B:MET80
|
4.3
|
23.1
|
0.5
|
|
C
|
B:PRO120
|
4.3
|
11.9
|
1.0
|
|
CE
|
B:MET80
|
4.4
|
12.8
|
0.5
|
|
CB
|
D:ARG121
|
4.5
|
13.8
|
1.0
|
|
CB
|
B:ARG121
|
4.5
|
13.4
|
1.0
|
|
CE
|
D:MET80
|
4.5
|
10.2
|
0.4
|
|
HE3
|
B:MET80
|
4.6
|
15.4
|
0.5
|
|
HB3
|
D:ASN118
|
4.6
|
17.2
|
1.0
|
|
HB3
|
B:ASN118
|
4.6
|
16.2
|
1.0
|
|
HD3
|
B:PRO122
|
4.6
|
17.6
|
1.0
|
|
HA
|
B:PRO120
|
4.6
|
13.6
|
1.0
|
|
CA
|
D:PRO120
|
4.6
|
11.4
|
1.0
|
|
HA
|
D:PRO120
|
4.6
|
13.7
|
1.0
|
|
CA
|
B:PRO120
|
4.7
|
11.3
|
1.0
|
|
HE1
|
D:MET80
|
4.7
|
25.0
|
0.6
|
|
HE3
|
D:MET80
|
4.7
|
12.3
|
0.4
|
|
HD3
|
D:PRO122
|
4.7
|
14.5
|
1.0
|
|
HE1
|
B:MET80
|
4.7
|
23.1
|
0.5
|
|
N
|
B:PRO122
|
4.8
|
11.9
|
1.0
|
|
N
|
D:PRO122
|
4.8
|
12.2
|
1.0
|
|
CE
|
D:MET80
|
5.0
|
20.8
|
0.6
|
|
CE
|
B:MET80
|
5.0
|
19.3
|
0.5
|
|
HD2
|
B:PRO122
|
5.0
|
17.6
|
1.0
|
|
HE2
|
B:MET80
|
5.0
|
15.4
|
0.5
|
|
Magnesium binding site 5 out
of 8 in 5dei
Go back to
Magnesium Binding Sites List in 5dei
Magnesium binding site 5 out
of 8 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:18.8
occ:1.00
|
HE
|
B:ARG185
|
2.3
|
28.3
|
1.0
|
|
H
|
C:ASP188
|
2.4
|
20.0
|
1.0
|
|
HH21
|
B:ARG185
|
2.9
|
35.9
|
1.0
|
|
O
|
B:HOH956
|
3.1
|
23.6
|
1.0
|
|
HB2
|
C:ASN187
|
3.1
|
23.9
|
1.0
|
|
NE
|
B:ARG185
|
3.1
|
23.6
|
1.0
|
|
HA
|
C:ASN187
|
3.2
|
20.2
|
1.0
|
|
N
|
C:ASP188
|
3.2
|
16.6
|
1.0
|
|
HB2
|
C:ASP188
|
3.3
|
23.4
|
1.0
|
|
HG2
|
B:ARG185
|
3.3
|
24.3
|
1.0
|
|
O
|
C:HOH1112
|
3.4
|
26.4
|
1.0
|
|
NH2
|
B:ARG185
|
3.6
|
29.9
|
1.0
|
|
CG
|
C:ASP188
|
3.7
|
29.1
|
1.0
|
|
CA
|
C:ASN187
|
3.8
|
16.8
|
1.0
|
|
CZ
|
B:ARG185
|
3.8
|
24.2
|
1.0
|
|
CB
|
C:ASP188
|
3.8
|
19.5
|
1.0
|
|
CB
|
C:ASN187
|
3.9
|
19.9
|
1.0
|
|
OD2
|
C:ASP188
|
3.9
|
31.3
|
1.0
|
|
OD1
|
C:ASP188
|
4.0
|
31.6
|
1.0
|
|
HB2
|
B:ALA325
|
4.0
|
24.1
|
1.0
|
|
C
|
C:ASN187
|
4.0
|
16.1
|
1.0
|
|
CG
|
B:ARG185
|
4.0
|
20.3
|
1.0
|
|
HG3
|
B:ARG185
|
4.1
|
24.3
|
1.0
|
|
CA
|
C:ASP188
|
4.2
|
16.8
|
1.0
|
|
CD
|
B:ARG185
|
4.2
|
23.2
|
1.0
|
|
HB3
|
C:ASN187
|
4.3
|
23.9
|
1.0
|
|
O
|
B:HOH957
|
4.3
|
39.5
|
1.0
|
|
HH22
|
B:ARG185
|
4.3
|
35.9
|
1.0
|
|
HH12
|
C:ARG185
|
4.4
|
25.4
|
1.0
|
|
H
|
C:GLN189
|
4.7
|
21.2
|
1.0
|
|
HA
|
C:ASP188
|
4.7
|
20.2
|
1.0
|
|
HB3
|
C:ASP188
|
4.8
|
23.4
|
1.0
|
|
HD3
|
B:ARG185
|
4.8
|
27.9
|
1.0
|
|
HD2
|
B:ARG185
|
4.8
|
27.9
|
1.0
|
|
HB1
|
B:ALA321
|
4.8
|
20.9
|
1.0
|
|
NH1
|
C:ARG185
|
4.9
|
21.1
|
1.0
|
|
CB
|
B:ALA325
|
4.9
|
20.1
|
1.0
|
|
O
|
B:HOH1280
|
4.9
|
37.9
|
1.0
|
|
HH11
|
C:ARG185
|
5.0
|
25.4
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 5dei
Go back to
Magnesium Binding Sites List in 5dei
Magnesium binding site 6 out
of 8 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:17.2
occ:1.00
|
H
|
B:LYS497
|
2.5
|
19.9
|
1.0
|
|
HA
|
B:LEU496
|
3.1
|
18.0
|
1.0
|
|
O
|
B:HOH970
|
3.1
|
21.0
|
1.0
|
|
O
|
B:HOH1042
|
3.1
|
37.2
|
1.0
|
|
O
|
B:HOH1233
|
3.3
|
41.1
|
1.0
|
|
N
|
B:LYS497
|
3.3
|
16.6
|
1.0
|
|
HG2
|
B:LYS497
|
3.4
|
34.4
|
1.0
|
|
HB3
|
B:LEU496
|
3.4
|
18.5
|
1.0
|
|
HD22
|
B:LEU496
|
3.6
|
19.8
|
1.0
|
|
CA
|
B:LEU496
|
3.8
|
15.0
|
1.0
|
|
HB3
|
B:LYS497
|
4.0
|
29.0
|
1.0
|
|
C
|
B:LEU496
|
4.0
|
14.0
|
1.0
|
|
CB
|
B:LEU496
|
4.0
|
15.4
|
1.0
|
|
HD23
|
B:LEU496
|
4.1
|
19.8
|
1.0
|
|
HE2
|
B:LYS497
|
4.1
|
34.6
|
1.0
|
|
O
|
B:LYS497
|
4.1
|
17.9
|
1.0
|
|
HH11
|
B:ARG485
|
4.2
|
25.6
|
1.0
|
|
CD2
|
B:LEU496
|
4.2
|
16.5
|
1.0
|
|
CG
|
B:LYS497
|
4.2
|
28.6
|
1.0
|
|
CA
|
B:LYS497
|
4.3
|
15.9
|
1.0
|
|
HG
|
B:SER507
|
4.3
|
22.8
|
0.5
|
|
CB
|
B:LYS497
|
4.4
|
24.1
|
1.0
|
|
OG
|
B:SER507
|
4.5
|
19.0
|
0.5
|
|
O
|
B:HOH1189
|
4.7
|
39.5
|
1.0
|
|
C
|
B:LYS497
|
4.7
|
15.8
|
1.0
|
|
HH12
|
B:ARG485
|
4.7
|
25.6
|
1.0
|
|
NH1
|
B:ARG485
|
4.7
|
21.3
|
1.0
|
|
CG
|
B:LEU496
|
4.8
|
13.4
|
1.0
|
|
HB2
|
B:LEU496
|
4.8
|
18.5
|
1.0
|
|
O
|
B:ALA495
|
4.9
|
18.5
|
1.0
|
|
CE
|
B:LYS497
|
4.9
|
28.9
|
1.0
|
|
HG3
|
B:LYS497
|
4.9
|
34.4
|
1.0
|
|
HD3
|
B:LYS497
|
4.9
|
33.8
|
1.0
|
|
CD
|
B:LYS497
|
5.0
|
28.2
|
1.0
|
|
HD13
|
B:LEU496
|
5.0
|
19.2
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 5dei
Go back to
Magnesium Binding Sites List in 5dei
Magnesium binding site 7 out
of 8 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:19.1
occ:1.00
|
HG3
|
B:GLN494
|
3.2
|
20.2
|
1.0
|
|
HB2
|
B:GLN494
|
3.3
|
17.3
|
1.0
|
|
OE1
|
B:GLN494
|
3.4
|
20.3
|
1.0
|
|
CG
|
B:GLN494
|
3.8
|
16.9
|
1.0
|
|
CB
|
B:GLN494
|
4.0
|
14.4
|
1.0
|
|
CD
|
B:GLN494
|
4.0
|
15.3
|
1.0
|
|
HA
|
B:GLN494
|
4.2
|
17.7
|
1.0
|
|
CA
|
B:GLN494
|
4.6
|
14.7
|
1.0
|
|
HG2
|
B:GLN494
|
4.7
|
20.2
|
1.0
|
|
HB3
|
B:GLN494
|
4.8
|
17.3
|
1.0
|
|
O
|
B:HOH1029
|
5.0
|
32.8
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 5dei
Go back to
Magnesium Binding Sites List in 5dei
Magnesium binding site 8 out
of 8 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg603
b:16.4
occ:1.00
|
H
|
D:LYS497
|
2.5
|
19.7
|
1.0
|
|
HG2
|
D:LYS497
|
3.0
|
30.9
|
1.0
|
|
HA
|
D:LEU496
|
3.1
|
17.5
|
1.0
|
|
O
|
D:HOH824
|
3.1
|
21.2
|
1.0
|
|
O
|
D:HOH1042
|
3.2
|
37.8
|
1.0
|
|
N
|
D:LYS497
|
3.3
|
16.4
|
1.0
|
|
HB3
|
D:LEU496
|
3.4
|
18.1
|
1.0
|
|
HD22
|
D:LEU496
|
3.6
|
22.2
|
1.0
|
|
CA
|
D:LEU496
|
3.8
|
14.6
|
1.0
|
|
CG
|
D:LYS497
|
3.9
|
25.8
|
1.0
|
|
C
|
D:LEU496
|
4.1
|
13.6
|
1.0
|
|
CB
|
D:LEU496
|
4.1
|
15.1
|
1.0
|
|
HD23
|
D:LEU496
|
4.1
|
22.2
|
1.0
|
|
O
|
D:LYS497
|
4.1
|
18.9
|
1.0
|
|
HH11
|
D:ARG485
|
4.2
|
25.0
|
1.0
|
|
CD2
|
D:LEU496
|
4.3
|
18.5
|
1.0
|
|
HB3
|
D:LYS497
|
4.3
|
31.3
|
1.0
|
|
CA
|
D:LYS497
|
4.3
|
17.5
|
1.0
|
|
HE2
|
D:LYS497
|
4.3
|
40.9
|
1.0
|
|
HG3
|
D:LYS497
|
4.3
|
30.9
|
1.0
|
|
CB
|
D:LYS497
|
4.4
|
26.1
|
1.0
|
|
HG
|
D:SER507
|
4.5
|
22.7
|
0.5
|
|
C
|
D:LYS497
|
4.7
|
15.1
|
1.0
|
|
OG
|
D:SER507
|
4.7
|
18.9
|
0.5
|
|
NH1
|
D:ARG485
|
4.7
|
20.9
|
1.0
|
|
HH12
|
D:ARG485
|
4.8
|
25.0
|
1.0
|
|
CG
|
D:LEU496
|
4.8
|
14.3
|
1.0
|
|
O
|
D:ALA495
|
4.8
|
19.1
|
1.0
|
|
HB2
|
D:LEU496
|
4.8
|
18.1
|
1.0
|
|
CD
|
D:LYS497
|
4.9
|
28.4
|
1.0
|
|
HD3
|
D:LYS497
|
4.9
|
34.1
|
1.0
|
|
HD3
|
D:ARG485
|
4.9
|
19.9
|
1.0
|
|
Reference:
A.K.Bera,
M.S.Hasson.
Benzoylformate Decarboxylase From Pseudomonas Putida To Be Published.
Page generated: Sun Sep 29 02:43:10 2024
|
