Calcium 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:
Calcium Binding Sites:
The binding sites of Calcium atom in the Benzoylformate Decarboxylase From Pseudomonas Putida
(pdb code 5dei). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Benzoylformate Decarboxylase From Pseudomonas Putida, PDB code: 5dei:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 5dei
Go back to
Calcium Binding Sites List in 5dei
Calcium binding site 1 out
of 6 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca606
b:26.0
occ:1.00
|
H
|
A:ASP188
|
2.3
|
18.8
|
1.0
|
|
HE
|
D:ARG185
|
2.4
|
31.3
|
1.0
|
|
HH21
|
D:ARG185
|
3.0
|
31.6
|
1.0
|
|
O
|
D:HOH902
|
3.1
|
23.3
|
1.0
|
|
HA
|
A:ASN187
|
3.1
|
16.5
|
1.0
|
|
HB2
|
A:ASN187
|
3.1
|
19.9
|
1.0
|
|
N
|
A:ASP188
|
3.2
|
15.7
|
1.0
|
|
NE
|
D:ARG185
|
3.2
|
26.1
|
1.0
|
|
HB2
|
A:ASP188
|
3.3
|
22.4
|
1.0
|
|
O
|
A:HOH1123
|
3.3
|
24.9
|
1.0
|
|
HG2
|
D:ARG185
|
3.4
|
23.7
|
1.0
|
|
CG
|
A:ASP188
|
3.7
|
27.6
|
1.0
|
|
NH2
|
D:ARG185
|
3.8
|
26.4
|
1.0
|
|
CA
|
A:ASN187
|
3.8
|
13.8
|
1.0
|
|
CB
|
A:ASP188
|
3.8
|
18.6
|
1.0
|
|
CB
|
A:ASN187
|
3.8
|
16.6
|
1.0
|
|
OD2
|
A:ASP188
|
3.9
|
35.1
|
1.0
|
|
CZ
|
D:ARG185
|
4.0
|
21.6
|
1.0
|
|
C
|
A:ASN187
|
4.0
|
14.5
|
1.0
|
|
HB2
|
D:ALA325
|
4.1
|
21.4
|
1.0
|
|
CG
|
D:ARG185
|
4.1
|
19.8
|
1.0
|
|
CA
|
A:ASP188
|
4.1
|
15.6
|
1.0
|
|
HG3
|
D:ARG185
|
4.1
|
23.7
|
1.0
|
|
OD1
|
A:ASP188
|
4.1
|
23.5
|
0.6
|
|
HB3
|
A:ASN187
|
4.2
|
19.9
|
1.0
|
|
CD
|
D:ARG185
|
4.2
|
25.5
|
1.0
|
|
HH12
|
A:ARG185
|
4.4
|
23.9
|
1.0
|
|
O
|
D:HOH774
|
4.4
|
39.5
|
1.0
|
|
HH22
|
D:ARG185
|
4.5
|
31.6
|
1.0
|
|
H
|
A:GLN189
|
4.6
|
21.2
|
1.0
|
|
HD21
|
A:ASN187
|
4.6
|
20.5
|
1.0
|
|
HA
|
A:ASP188
|
4.7
|
18.8
|
1.0
|
|
HB3
|
A:ASP188
|
4.7
|
22.4
|
1.0
|
|
HB1
|
D:ALA321
|
4.8
|
19.9
|
1.0
|
|
HD3
|
D:ARG185
|
4.8
|
30.6
|
1.0
|
|
O
|
A:HOH1280
|
4.8
|
35.9
|
1.0
|
|
NH1
|
A:ARG185
|
4.8
|
19.9
|
1.0
|
|
HD2
|
D:ARG185
|
4.9
|
30.6
|
1.0
|
|
HH11
|
A:ARG185
|
4.9
|
23.9
|
1.0
|
|
CB
|
D:ALA325
|
5.0
|
17.8
|
1.0
|
|
Calcium binding site 2 out
of 6 in 5dei
Go back to
Calcium Binding Sites List in 5dei
Calcium binding site 2 out
of 6 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca607
b:13.4
occ:1.00
|
O21
|
A:TDP602
|
2.2
|
12.3
|
1.0
|
|
O
|
A:THR458
|
2.3
|
14.3
|
1.0
|
|
O12
|
A:TDP602
|
2.3
|
12.2
|
1.0
|
|
O
|
A:HOH752
|
2.3
|
15.0
|
1.0
|
|
OD1
|
A:ASP429
|
2.3
|
14.8
|
1.0
|
|
OD1
|
A:ASN456
|
2.3
|
13.3
|
1.0
|
|
H
|
A:THR458
|
3.2
|
17.0
|
1.0
|
|
CG
|
A:ASN456
|
3.3
|
21.7
|
1.0
|
|
H
|
A:GLY460
|
3.4
|
16.5
|
1.0
|
|
CG
|
A:ASP429
|
3.4
|
16.5
|
1.0
|
|
P1
|
A:TDP602
|
3.4
|
12.4
|
1.0
|
|
C
|
A:THR458
|
3.5
|
14.7
|
1.0
|
|
HD21
|
A:ASN456
|
3.5
|
35.3
|
1.0
|
|
P2
|
A:TDP602
|
3.5
|
12.8
|
1.0
|
|
H
|
A:ASN456
|
3.5
|
16.5
|
1.0
|
|
O11
|
A:TDP602
|
3.6
|
12.2
|
1.0
|
|
H
|
A:ASP429
|
3.6
|
14.7
|
1.0
|
|
H
|
A:GLY430
|
3.6
|
14.1
|
1.0
|
|
ND2
|
A:ASN456
|
3.8
|
29.4
|
1.0
|
|
OD2
|
A:ASP429
|
3.9
|
17.5
|
1.0
|
|
N
|
A:THR458
|
4.0
|
14.2
|
1.0
|
|
HA
|
A:TYR459
|
4.0
|
14.6
|
1.0
|
|
HG23
|
A:THR458
|
4.1
|
19.5
|
1.0
|
|
O5G
|
A:TDP602
|
4.1
|
12.9
|
1.0
|
|
N
|
A:GLY460
|
4.2
|
13.7
|
1.0
|
|
N
|
A:ASP429
|
4.2
|
12.2
|
1.0
|
|
HG22
|
A:THR458
|
4.3
|
19.5
|
1.0
|
|
O22
|
A:TDP602
|
4.3
|
13.4
|
1.0
|
|
O
|
A:MET454
|
4.3
|
13.2
|
1.0
|
|
N
|
A:ASN456
|
4.3
|
13.8
|
1.0
|
|
H
|
A:GLY457
|
4.3
|
18.4
|
1.0
|
|
HA3
|
A:GLY428
|
4.3
|
16.0
|
1.0
|
|
CA
|
A:THR458
|
4.3
|
14.7
|
1.0
|
|
N
|
A:GLY430
|
4.4
|
11.8
|
1.0
|
|
N
|
A:TYR459
|
4.4
|
13.1
|
1.0
|
|
O
|
A:HOH757
|
4.5
|
14.4
|
1.0
|
|
CB
|
A:ASN456
|
4.6
|
18.7
|
1.0
|
|
N
|
A:GLY457
|
4.6
|
15.3
|
1.0
|
|
O23
|
A:TDP602
|
4.6
|
13.7
|
1.0
|
|
CA
|
A:TYR459
|
4.6
|
12.2
|
1.0
|
|
HD22
|
A:ASN456
|
4.6
|
35.3
|
1.0
|
|
O13
|
A:TDP602
|
4.6
|
13.2
|
1.0
|
|
CG2
|
A:THR458
|
4.6
|
16.2
|
1.0
|
|
CB
|
A:ASP429
|
4.7
|
13.1
|
1.0
|
|
HA3
|
A:GLY460
|
4.7
|
17.1
|
1.0
|
|
HA2
|
A:GLY428
|
4.7
|
16.0
|
1.0
|
|
CA
|
A:ASN456
|
4.7
|
15.6
|
1.0
|
|
C
|
A:ASN456
|
4.7
|
16.9
|
1.0
|
|
CA
|
A:ASP429
|
4.9
|
13.3
|
1.0
|
|
HA
|
A:ASN455
|
4.9
|
15.2
|
1.0
|
|
CA
|
A:GLY428
|
4.9
|
13.3
|
1.0
|
|
C
|
A:GLY428
|
4.9
|
11.9
|
1.0
|
|
HA3
|
A:GLY430
|
5.0
|
14.5
|
1.0
|
|
C
|
A:TYR459
|
5.0
|
14.6
|
1.0
|
|
HB3
|
A:ASP429
|
5.0
|
15.8
|
1.0
|
|
Calcium binding site 3 out
of 6 in 5dei
Go back to
Calcium Binding Sites List in 5dei
Calcium binding site 3 out
of 6 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca607
b:13.1
occ:1.00
|
O
|
B:HOH763
|
2.3
|
14.7
|
1.0
|
|
O
|
B:THR458
|
2.3
|
13.8
|
1.0
|
|
O23
|
B:TDP602
|
2.3
|
12.1
|
1.0
|
|
OD1
|
B:ASP429
|
2.3
|
14.4
|
1.0
|
|
O13
|
B:TDP602
|
2.3
|
12.3
|
1.0
|
|
OD1
|
B:ASN456
|
2.3
|
14.2
|
1.0
|
|
H
|
B:THR458
|
3.2
|
16.3
|
1.0
|
|
CG
|
B:ASN456
|
3.3
|
20.3
|
1.0
|
|
HD21
|
B:ASN456
|
3.4
|
30.6
|
1.0
|
|
CG
|
B:ASP429
|
3.4
|
15.6
|
1.0
|
|
H
|
B:GLY460
|
3.4
|
15.2
|
1.0
|
|
P1
|
B:TDP602
|
3.4
|
12.1
|
1.0
|
|
C
|
B:THR458
|
3.5
|
13.6
|
1.0
|
|
P2
|
B:TDP602
|
3.5
|
12.3
|
1.0
|
|
H
|
B:ASN456
|
3.5
|
17.4
|
1.0
|
|
H
|
B:GLY430
|
3.6
|
14.0
|
1.0
|
|
H
|
B:ASP429
|
3.6
|
15.2
|
1.0
|
|
O11
|
B:TDP602
|
3.6
|
11.8
|
1.0
|
|
ND2
|
B:ASN456
|
3.7
|
25.5
|
1.0
|
|
OD2
|
B:ASP429
|
3.9
|
17.8
|
1.0
|
|
N
|
B:THR458
|
4.0
|
13.6
|
1.0
|
|
HA
|
B:TYR459
|
4.0
|
14.8
|
1.0
|
|
HG23
|
B:THR458
|
4.1
|
18.9
|
1.0
|
|
O5G
|
B:TDP602
|
4.2
|
11.9
|
1.0
|
|
HG22
|
B:THR458
|
4.2
|
18.9
|
1.0
|
|
N
|
B:ASP429
|
4.2
|
12.7
|
1.0
|
|
N
|
B:GLY460
|
4.2
|
12.7
|
1.0
|
|
O22
|
B:TDP602
|
4.3
|
13.5
|
1.0
|
|
O
|
B:MET454
|
4.3
|
12.7
|
1.0
|
|
H
|
B:GLY457
|
4.3
|
17.3
|
1.0
|
|
HA3
|
B:GLY428
|
4.3
|
15.1
|
1.0
|
|
N
|
B:ASN456
|
4.3
|
14.5
|
1.0
|
|
CA
|
B:THR458
|
4.3
|
12.7
|
1.0
|
|
O
|
B:HOH711
|
4.4
|
37.6
|
1.0
|
|
N
|
B:GLY430
|
4.4
|
11.6
|
1.0
|
|
N
|
B:TYR459
|
4.5
|
12.8
|
1.0
|
|
O
|
B:HOH765
|
4.5
|
15.1
|
1.0
|
|
CB
|
B:ASN456
|
4.5
|
17.1
|
1.0
|
|
HD22
|
B:ASN456
|
4.5
|
30.6
|
1.0
|
|
N
|
B:GLY457
|
4.6
|
14.4
|
1.0
|
|
CG2
|
B:THR458
|
4.6
|
15.8
|
1.0
|
|
O21
|
B:TDP602
|
4.6
|
13.2
|
1.0
|
|
CA
|
B:TYR459
|
4.6
|
12.3
|
1.0
|
|
CB
|
B:ASP429
|
4.6
|
14.6
|
1.0
|
|
O12
|
B:TDP602
|
4.7
|
13.2
|
1.0
|
|
HA2
|
B:GLY428
|
4.7
|
15.1
|
1.0
|
|
CA
|
B:ASN456
|
4.7
|
15.8
|
1.0
|
|
HA3
|
B:GLY460
|
4.7
|
14.8
|
1.0
|
|
C
|
B:ASN456
|
4.7
|
16.6
|
1.0
|
|
HA
|
B:ASN455
|
4.8
|
15.7
|
1.0
|
|
CA
|
B:ASP429
|
4.8
|
13.1
|
1.0
|
|
CA
|
B:GLY428
|
4.9
|
12.6
|
1.0
|
|
HA3
|
B:GLY430
|
4.9
|
15.0
|
1.0
|
|
HB3
|
B:ASN456
|
4.9
|
20.5
|
1.0
|
|
C
|
B:GLY428
|
4.9
|
11.9
|
1.0
|
|
C
|
B:TYR459
|
5.0
|
12.1
|
1.0
|
|
HB3
|
B:ASP429
|
5.0
|
17.6
|
1.0
|
|
Calcium binding site 4 out
of 6 in 5dei
Go back to
Calcium Binding Sites List in 5dei
Calcium binding site 4 out
of 6 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca608
b:25.8
occ:1.00
|
HE
|
C:ARG185
|
2.3
|
32.0
|
1.0
|
|
H
|
B:ASP188
|
2.4
|
21.2
|
1.0
|
|
HH21
|
C:ARG185
|
2.9
|
37.8
|
1.0
|
|
O
|
C:HOH848
|
3.1
|
23.2
|
1.0
|
|
HA
|
B:ASN187
|
3.1
|
18.8
|
1.0
|
|
HB2
|
B:ASN187
|
3.2
|
21.3
|
1.0
|
|
NE
|
C:ARG185
|
3.2
|
26.6
|
1.0
|
|
N
|
B:ASP188
|
3.2
|
17.7
|
1.0
|
|
HB2
|
B:ASP188
|
3.3
|
23.2
|
1.0
|
|
HG2
|
C:ARG185
|
3.4
|
23.8
|
1.0
|
|
O
|
B:HOH1108
|
3.4
|
24.7
|
1.0
|
|
NH2
|
C:ARG185
|
3.6
|
31.5
|
1.0
|
|
CG
|
B:ASP188
|
3.7
|
28.1
|
1.0
|
|
CA
|
B:ASN187
|
3.8
|
15.7
|
1.0
|
|
CZ
|
C:ARG185
|
3.8
|
24.6
|
1.0
|
|
CB
|
B:ASN187
|
3.9
|
17.7
|
1.0
|
|
CB
|
B:ASP188
|
3.9
|
19.4
|
1.0
|
|
OD2
|
B:ASP188
|
3.9
|
32.1
|
1.0
|
|
C
|
B:ASN187
|
4.0
|
16.1
|
1.0
|
|
CG
|
C:ARG185
|
4.0
|
19.8
|
1.0
|
|
OD1
|
B:ASP188
|
4.1
|
30.3
|
1.0
|
|
HB2
|
C:ALA325
|
4.1
|
24.4
|
1.0
|
|
HG3
|
C:ARG185
|
4.1
|
23.8
|
1.0
|
|
CA
|
B:ASP188
|
4.2
|
17.6
|
1.0
|
|
CD
|
C:ARG185
|
4.2
|
26.0
|
1.0
|
|
HB3
|
B:ASN187
|
4.2
|
21.3
|
1.0
|
|
HH12
|
B:ARG185
|
4.4
|
25.0
|
1.0
|
|
HH22
|
C:ARG185
|
4.4
|
37.8
|
1.0
|
|
O
|
C:HOH751
|
4.5
|
42.3
|
1.0
|
|
H
|
B:GLN189
|
4.6
|
22.0
|
1.0
|
|
HA
|
B:ASP188
|
4.7
|
21.2
|
1.0
|
|
HD3
|
C:ARG185
|
4.8
|
31.2
|
1.0
|
|
HB1
|
C:ALA321
|
4.8
|
19.5
|
1.0
|
|
HD2
|
C:ARG185
|
4.8
|
31.2
|
1.0
|
|
HB3
|
B:ASP188
|
4.8
|
23.2
|
1.0
|
|
NH1
|
B:ARG185
|
4.8
|
20.8
|
1.0
|
|
O
|
C:HOH1261
|
4.8
|
37.3
|
1.0
|
|
HH11
|
B:ARG185
|
4.9
|
25.0
|
1.0
|
|
CB
|
C:ALA325
|
5.0
|
20.3
|
1.0
|
|
Calcium binding site 5 out
of 6 in 5dei
Go back to
Calcium Binding Sites List in 5dei
Calcium binding site 5 out
of 6 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca603
b:14.0
occ:1.00
|
O12
|
C:TDP602
|
2.3
|
12.9
|
1.0
|
|
O22
|
C:TDP602
|
2.3
|
13.6
|
1.0
|
|
OD1
|
C:ASP429
|
2.3
|
15.3
|
1.0
|
|
O
|
C:THR458
|
2.3
|
13.5
|
1.0
|
|
O
|
C:HOH743
|
2.3
|
14.4
|
1.0
|
|
OD1
|
C:ASN456
|
2.3
|
15.0
|
1.0
|
|
H
|
C:THR458
|
3.3
|
17.0
|
1.0
|
|
CG
|
C:ASN456
|
3.3
|
18.8
|
1.0
|
|
P1
|
C:TDP602
|
3.4
|
12.3
|
1.0
|
|
H
|
C:GLY460
|
3.4
|
14.8
|
1.0
|
|
CG
|
C:ASP429
|
3.4
|
15.7
|
1.0
|
|
HD21
|
C:ASN456
|
3.4
|
32.9
|
1.0
|
|
P2
|
C:TDP602
|
3.5
|
12.2
|
1.0
|
|
C
|
C:THR458
|
3.5
|
13.0
|
1.0
|
|
H
|
C:GLY430
|
3.5
|
14.0
|
1.0
|
|
H
|
C:ASN456
|
3.5
|
17.5
|
1.0
|
|
H
|
C:ASP429
|
3.6
|
15.1
|
1.0
|
|
O11
|
C:TDP602
|
3.6
|
11.9
|
1.0
|
|
ND2
|
C:ASN456
|
3.7
|
27.4
|
1.0
|
|
OD2
|
C:ASP429
|
4.0
|
17.2
|
1.0
|
|
N
|
C:THR458
|
4.0
|
14.2
|
1.0
|
|
HA
|
C:TYR459
|
4.0
|
15.3
|
1.0
|
|
O5G
|
C:TDP602
|
4.1
|
12.1
|
1.0
|
|
N
|
C:ASP429
|
4.2
|
12.6
|
1.0
|
|
N
|
C:GLY460
|
4.2
|
12.3
|
1.0
|
|
HG23
|
C:THR458
|
4.2
|
18.6
|
1.0
|
|
HA3
|
C:GLY428
|
4.3
|
14.5
|
1.0
|
|
O21
|
C:TDP602
|
4.3
|
13.2
|
1.0
|
|
O
|
C:MET454
|
4.3
|
14.0
|
1.0
|
|
N
|
C:GLY430
|
4.3
|
11.7
|
1.0
|
|
HG22
|
C:THR458
|
4.3
|
18.6
|
1.0
|
|
N
|
C:ASN456
|
4.3
|
14.6
|
1.0
|
|
CA
|
C:THR458
|
4.4
|
13.7
|
1.0
|
|
H
|
C:GLY457
|
4.4
|
18.2
|
1.0
|
|
N
|
C:TYR459
|
4.5
|
12.0
|
1.0
|
|
O
|
C:HOH761
|
4.5
|
14.5
|
1.0
|
|
CB
|
C:ASN456
|
4.5
|
18.3
|
1.0
|
|
HD22
|
C:ASN456
|
4.6
|
32.9
|
1.0
|
|
O13
|
C:TDP602
|
4.6
|
12.3
|
1.0
|
|
CA
|
C:TYR459
|
4.6
|
12.8
|
1.0
|
|
O23
|
C:TDP602
|
4.6
|
13.0
|
1.0
|
|
CB
|
C:ASP429
|
4.6
|
13.3
|
1.0
|
|
HA2
|
C:GLY428
|
4.6
|
14.5
|
1.0
|
|
N
|
C:GLY457
|
4.6
|
15.1
|
1.0
|
|
CG2
|
C:THR458
|
4.7
|
15.5
|
1.0
|
|
CA
|
C:ASN456
|
4.7
|
15.7
|
1.0
|
|
HA3
|
C:GLY460
|
4.8
|
16.0
|
1.0
|
|
C
|
C:ASN456
|
4.8
|
17.2
|
1.0
|
|
CA
|
C:GLY428
|
4.8
|
12.1
|
1.0
|
|
CA
|
C:ASP429
|
4.8
|
13.1
|
1.0
|
|
HA
|
C:ASN455
|
4.8
|
15.0
|
1.0
|
|
HA3
|
C:GLY430
|
4.9
|
14.4
|
1.0
|
|
C
|
C:GLY428
|
4.9
|
12.0
|
1.0
|
|
C
|
C:TYR459
|
5.0
|
14.6
|
1.0
|
|
HB3
|
C:ASN456
|
5.0
|
21.9
|
1.0
|
|
HD1
|
C:TYR459
|
5.0
|
16.2
|
1.0
|
|
HB3
|
C:ASP429
|
5.0
|
15.9
|
1.0
|
|
Calcium binding site 6 out
of 6 in 5dei
Go back to
Calcium Binding Sites List in 5dei
Calcium binding site 6 out
of 6 in the Benzoylformate Decarboxylase From Pseudomonas Putida
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Benzoylformate Decarboxylase From Pseudomonas Putida within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca604
b:12.7
occ:1.00
|
O
|
D:THR458
|
2.3
|
13.8
|
1.0
|
|
O13
|
D:TDP602
|
2.3
|
12.4
|
1.0
|
|
O
|
D:HOH749
|
2.3
|
14.7
|
1.0
|
|
OD1
|
D:ASP429
|
2.3
|
14.8
|
1.0
|
|
O23
|
D:TDP602
|
2.3
|
12.3
|
1.0
|
|
OD1
|
D:ASN456
|
2.3
|
14.3
|
1.0
|
|
H
|
D:THR458
|
3.2
|
16.9
|
1.0
|
|
CG
|
D:ASN456
|
3.3
|
17.4
|
1.0
|
|
H
|
D:GLY460
|
3.4
|
15.5
|
1.0
|
|
CG
|
D:ASP429
|
3.4
|
14.6
|
1.0
|
|
P1
|
D:TDP602
|
3.4
|
11.9
|
1.0
|
|
HD21
|
D:ASN456
|
3.4
|
27.9
|
1.0
|
|
C
|
D:THR458
|
3.5
|
14.0
|
1.0
|
|
P2
|
D:TDP602
|
3.5
|
12.4
|
1.0
|
|
H
|
D:GLY430
|
3.5
|
14.1
|
1.0
|
|
H
|
D:ASN456
|
3.5
|
16.8
|
1.0
|
|
O11
|
D:TDP602
|
3.6
|
11.6
|
1.0
|
|
H
|
D:ASP429
|
3.6
|
15.3
|
1.0
|
|
ND2
|
D:ASN456
|
3.8
|
23.3
|
1.0
|
|
OD2
|
D:ASP429
|
3.9
|
17.2
|
1.0
|
|
N
|
D:THR458
|
4.0
|
14.1
|
1.0
|
|
HA
|
D:TYR459
|
4.0
|
14.2
|
1.0
|
|
O5G
|
D:TDP602
|
4.1
|
11.7
|
1.0
|
|
HG23
|
D:THR458
|
4.2
|
18.5
|
1.0
|
|
N
|
D:ASP429
|
4.2
|
12.7
|
1.0
|
|
N
|
D:GLY460
|
4.2
|
12.9
|
1.0
|
|
HG22
|
D:THR458
|
4.3
|
18.5
|
1.0
|
|
HA3
|
D:GLY428
|
4.3
|
14.5
|
1.0
|
|
O22
|
D:TDP602
|
4.3
|
13.8
|
1.0
|
|
O
|
D:MET454
|
4.3
|
13.5
|
1.0
|
|
N
|
D:ASN456
|
4.3
|
14.0
|
1.0
|
|
N
|
D:GLY430
|
4.3
|
11.7
|
1.0
|
|
CA
|
D:THR458
|
4.4
|
13.9
|
1.0
|
|
H
|
D:GLY457
|
4.4
|
18.7
|
1.0
|
|
N
|
D:TYR459
|
4.4
|
13.3
|
1.0
|
|
O
|
D:HOH779
|
4.5
|
14.1
|
1.0
|
|
CB
|
D:ASN456
|
4.6
|
17.6
|
1.0
|
|
HD22
|
D:ASN456
|
4.6
|
27.9
|
1.0
|
|
O21
|
D:TDP602
|
4.6
|
13.4
|
1.0
|
|
CA
|
D:TYR459
|
4.6
|
11.8
|
1.0
|
|
O12
|
D:TDP602
|
4.6
|
12.4
|
1.0
|
|
N
|
D:GLY457
|
4.6
|
15.6
|
1.0
|
|
CB
|
D:ASP429
|
4.6
|
14.5
|
1.0
|
|
CG2
|
D:THR458
|
4.7
|
15.4
|
1.0
|
|
HA2
|
D:GLY428
|
4.7
|
14.5
|
1.0
|
|
HA3
|
D:GLY460
|
4.7
|
17.5
|
1.0
|
|
CA
|
D:ASN456
|
4.8
|
15.6
|
1.0
|
|
C
|
D:ASN456
|
4.8
|
15.9
|
1.0
|
|
CA
|
D:ASP429
|
4.8
|
13.1
|
1.0
|
|
HA
|
D:ASN455
|
4.8
|
16.8
|
1.0
|
|
CA
|
D:GLY428
|
4.8
|
12.1
|
1.0
|
|
HA3
|
D:GLY430
|
4.9
|
14.3
|
1.0
|
|
C
|
D:GLY428
|
4.9
|
13.1
|
1.0
|
|
HB3
|
D:ASN456
|
5.0
|
21.2
|
1.0
|
|
C
|
D:TYR459
|
5.0
|
13.8
|
1.0
|
|
HB3
|
D:ASP429
|
5.0
|
17.4
|
1.0
|
|
Reference:
A.K.Bera,
M.S.Hasson.
Benzoylformate Decarboxylase From Pseudomonas Putida To Be Published.
Page generated: Wed Jul 9 05:08:00 2025
|
