Calcium in PDB 6bum: Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica
Enzymatic activity of Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica
All present enzymatic activity of Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica:
3.5.2.15;
Protein crystallography data
The structure of Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica, PDB code: 6bum
was solved by
K.Shi,
S.Cho,
J.L.Seffernick,
A.Bera,
L.P.Wackett,
H.Aihara,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.99 /
1.51
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.440,
88.690,
204.280,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
12.6 /
14.1
|
Other elements in 6bum:
The structure of Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica
(pdb code 6bum). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica, PDB code: 6bum:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6bum
Go back to
Calcium Binding Sites List in 6bum
Calcium binding site 1 out
of 4 in the Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:19.0
occ:0.57
|
O
|
A:PRO355
|
2.4
|
17.9
|
1.0
|
OE1
|
A:GLU301
|
2.4
|
17.0
|
1.0
|
O
|
A:GLN353
|
2.4
|
16.0
|
1.0
|
O
|
A:ALA350
|
2.4
|
15.5
|
1.0
|
O
|
A:GLY358
|
2.7
|
17.5
|
1.0
|
O
|
A:HOH529
|
2.7
|
26.6
|
1.0
|
HB1
|
A:ALA350
|
2.9
|
19.0
|
1.0
|
HB3
|
A:ALA350
|
2.9
|
19.0
|
1.0
|
O
|
A:GLY354
|
3.2
|
18.6
|
1.0
|
CD
|
A:GLU301
|
3.3
|
17.2
|
1.0
|
C
|
A:PRO355
|
3.3
|
17.9
|
1.0
|
CB
|
A:ALA350
|
3.3
|
15.8
|
1.0
|
H
|
A:GLN353
|
3.4
|
18.8
|
1.0
|
H
|
A:GLY358
|
3.4
|
19.7
|
1.0
|
C
|
A:GLN353
|
3.4
|
15.5
|
1.0
|
C
|
A:ALA350
|
3.5
|
14.6
|
1.0
|
C
|
A:GLY354
|
3.6
|
18.1
|
1.0
|
HA
|
A:ASP356
|
3.6
|
22.1
|
1.0
|
C
|
A:GLY358
|
3.6
|
16.6
|
1.0
|
H
|
A:GLY357
|
3.7
|
20.2
|
1.0
|
HG2
|
A:GLU301
|
3.8
|
19.4
|
1.0
|
OE2
|
A:GLU301
|
3.9
|
17.1
|
1.0
|
N
|
A:GLY358
|
4.0
|
16.4
|
1.0
|
CA
|
A:ALA350
|
4.0
|
14.0
|
1.0
|
HA2
|
A:GLY359
|
4.0
|
18.5
|
1.0
|
N
|
A:GLN353
|
4.0
|
15.7
|
1.0
|
N
|
A:ASP356
|
4.1
|
18.6
|
1.0
|
HA3
|
A:GLY354
|
4.1
|
21.2
|
1.0
|
N
|
A:PRO355
|
4.1
|
17.5
|
1.0
|
HB2
|
A:GLN353
|
4.1
|
17.4
|
1.0
|
O3
|
A:PDO404
|
4.1
|
34.0
|
1.0
|
HB2
|
A:ALA350
|
4.2
|
19.0
|
1.0
|
CG
|
A:GLU301
|
4.2
|
16.2
|
1.0
|
N
|
A:GLY357
|
4.2
|
16.8
|
1.0
|
CA
|
A:GLY354
|
4.2
|
17.6
|
1.0
|
CA
|
A:ASP356
|
4.2
|
18.4
|
1.0
|
N
|
A:GLY354
|
4.2
|
16.1
|
1.0
|
CA
|
A:PRO355
|
4.3
|
17.7
|
1.0
|
CA
|
A:GLN353
|
4.3
|
15.1
|
1.0
|
H
|
A:HIS352
|
4.4
|
19.1
|
1.0
|
CA
|
A:GLY358
|
4.4
|
16.7
|
1.0
|
O
|
A:HOH656
|
4.5
|
24.4
|
1.0
|
N
|
A:GLY359
|
4.5
|
15.5
|
1.0
|
HA
|
A:GLU351
|
4.5
|
18.6
|
1.0
|
N
|
A:GLU351
|
4.6
|
15.0
|
1.0
|
HO3
|
A:PDO404
|
4.6
|
40.8
|
1.0
|
C
|
A:ASP356
|
4.6
|
17.9
|
1.0
|
HA
|
A:ALA350
|
4.6
|
16.8
|
1.0
|
CA
|
A:GLY359
|
4.6
|
15.4
|
1.0
|
HA
|
A:PRO355
|
4.7
|
21.3
|
1.0
|
N
|
A:HIS352
|
4.7
|
15.9
|
1.0
|
CB
|
A:GLN353
|
4.7
|
14.5
|
1.0
|
H31
|
A:PDO404
|
4.7
|
43.0
|
1.0
|
HG3
|
A:GLU301
|
4.7
|
19.4
|
1.0
|
HA3
|
A:GLY358
|
4.8
|
20.0
|
1.0
|
HD2
|
A:PRO355
|
4.8
|
22.0
|
1.0
|
HA3
|
A:GLY359
|
4.8
|
18.5
|
1.0
|
H
|
A:ASP356
|
4.8
|
22.3
|
1.0
|
H
|
A:ALA350
|
4.8
|
17.0
|
1.0
|
C
|
A:GLY357
|
4.9
|
16.1
|
1.0
|
CA
|
A:GLU351
|
4.9
|
15.5
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6bum
Go back to
Calcium Binding Sites List in 6bum
Calcium binding site 2 out
of 4 in the Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:18.2
occ:0.50
|
O
|
B:GLN353
|
2.4
|
17.9
|
1.0
|
O
|
B:ALA350
|
2.4
|
17.7
|
1.0
|
O
|
B:PRO355
|
2.4
|
18.8
|
1.0
|
OE1
|
B:GLU301
|
2.4
|
18.9
|
1.0
|
O
|
B:GLY358
|
2.7
|
18.3
|
1.0
|
O
|
B:HOH554
|
2.9
|
26.0
|
1.0
|
HB3
|
B:ALA350
|
2.9
|
19.8
|
1.0
|
HB1
|
B:ALA350
|
2.9
|
19.8
|
1.0
|
O
|
B:GLY354
|
3.1
|
19.8
|
1.0
|
CD
|
B:GLU301
|
3.3
|
18.6
|
1.0
|
H
|
B:GLN353
|
3.3
|
19.7
|
1.0
|
C
|
B:PRO355
|
3.3
|
18.8
|
1.0
|
CB
|
B:ALA350
|
3.4
|
16.5
|
1.0
|
C
|
B:GLN353
|
3.4
|
17.5
|
1.0
|
H
|
B:GLY358
|
3.4
|
22.8
|
1.0
|
C
|
B:ALA350
|
3.4
|
16.7
|
1.0
|
C
|
B:GLY354
|
3.5
|
19.1
|
1.0
|
C
|
B:GLY358
|
3.6
|
18.1
|
1.0
|
HA
|
B:ASP356
|
3.7
|
23.3
|
1.0
|
HO3
|
B:PDO406
|
3.7
|
47.5
|
1.0
|
H
|
B:GLY357
|
3.7
|
21.8
|
1.0
|
HG2
|
B:GLU301
|
3.9
|
21.8
|
1.0
|
OE2
|
B:GLU301
|
3.9
|
18.2
|
1.0
|
N
|
B:GLN353
|
4.0
|
16.4
|
1.0
|
HA2
|
B:GLY359
|
4.0
|
20.4
|
1.0
|
CA
|
B:ALA350
|
4.0
|
15.3
|
1.0
|
N
|
B:GLY358
|
4.0
|
19.0
|
1.0
|
HB2
|
B:GLN353
|
4.0
|
19.9
|
1.0
|
HA3
|
B:GLY354
|
4.1
|
21.2
|
1.0
|
N
|
B:PRO355
|
4.1
|
19.0
|
1.0
|
N
|
B:ASP356
|
4.1
|
19.2
|
1.0
|
CA
|
B:GLY354
|
4.2
|
17.7
|
1.0
|
N
|
B:GLY354
|
4.2
|
17.2
|
1.0
|
HB2
|
B:ALA350
|
4.2
|
19.8
|
1.0
|
CG
|
B:GLU301
|
4.2
|
18.2
|
1.0
|
N
|
B:GLY357
|
4.2
|
18.2
|
1.0
|
CA
|
B:GLN353
|
4.2
|
16.6
|
1.0
|
O3
|
B:PDO406
|
4.2
|
39.6
|
1.0
|
CA
|
B:ASP356
|
4.2
|
19.4
|
1.0
|
CA
|
B:PRO355
|
4.3
|
19.4
|
1.0
|
H
|
B:HIS352
|
4.3
|
20.3
|
1.0
|
O
|
B:HOH680
|
4.4
|
25.7
|
1.0
|
CA
|
B:GLY358
|
4.4
|
18.8
|
1.0
|
N
|
B:GLY359
|
4.5
|
17.0
|
1.0
|
HA
|
B:GLU351
|
4.5
|
19.0
|
1.0
|
N
|
B:GLU351
|
4.5
|
16.0
|
1.0
|
CA
|
B:GLY359
|
4.6
|
17.0
|
1.0
|
HA
|
B:ALA350
|
4.6
|
18.4
|
1.0
|
C
|
B:ASP356
|
4.6
|
19.3
|
1.0
|
CB
|
B:GLN353
|
4.7
|
16.6
|
1.0
|
N
|
B:HIS352
|
4.7
|
16.9
|
1.0
|
HA
|
B:PRO355
|
4.7
|
23.3
|
1.0
|
HA3
|
B:GLY358
|
4.8
|
22.6
|
1.0
|
HA3
|
B:GLY359
|
4.8
|
20.4
|
1.0
|
HG3
|
B:GLU301
|
4.8
|
21.8
|
1.0
|
H
|
B:ASP356
|
4.8
|
23.0
|
1.0
|
H
|
B:ALA350
|
4.8
|
18.7
|
1.0
|
HD2
|
B:PRO355
|
4.9
|
24.5
|
1.0
|
CA
|
B:GLU351
|
4.9
|
15.8
|
1.0
|
H32
|
B:PDO406
|
4.9
|
50.9
|
1.0
|
C
|
B:GLY357
|
4.9
|
18.4
|
1.0
|
H
|
B:GLY354
|
5.0
|
20.6
|
1.0
|
N
|
B:ALA350
|
5.0
|
15.6
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6bum
Go back to
Calcium Binding Sites List in 6bum
Calcium binding site 3 out
of 4 in the Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca402
b:19.0
occ:0.54
|
O
|
C:PRO355
|
2.4
|
18.6
|
1.0
|
OE1
|
C:GLU301
|
2.4
|
17.8
|
1.0
|
O
|
C:GLN353
|
2.4
|
17.5
|
1.0
|
O
|
C:ALA350
|
2.4
|
17.6
|
1.0
|
HO1
|
C:PDO405
|
2.4
|
44.9
|
1.0
|
O
|
C:GLY358
|
2.7
|
18.0
|
1.0
|
O1
|
C:PDO405
|
2.9
|
37.4
|
1.0
|
HB1
|
C:ALA350
|
3.0
|
19.8
|
1.0
|
HB3
|
C:ALA350
|
3.0
|
19.8
|
1.0
|
O
|
C:GLY354
|
3.1
|
19.3
|
1.0
|
H12
|
C:PDO405
|
3.3
|
48.2
|
1.0
|
CD
|
C:GLU301
|
3.3
|
18.0
|
1.0
|
C
|
C:PRO355
|
3.3
|
18.1
|
1.0
|
H
|
C:GLN353
|
3.3
|
20.9
|
1.0
|
C
|
C:GLN353
|
3.4
|
17.4
|
1.0
|
H
|
C:GLY358
|
3.4
|
19.3
|
1.0
|
CB
|
C:ALA350
|
3.4
|
16.5
|
1.0
|
C
|
C:ALA350
|
3.4
|
17.5
|
1.0
|
C
|
C:GLY354
|
3.5
|
18.5
|
1.0
|
C1
|
C:PDO405
|
3.6
|
40.2
|
1.0
|
H
|
C:GLY357
|
3.6
|
20.6
|
1.0
|
HA
|
C:ASP356
|
3.6
|
22.0
|
1.0
|
C
|
C:GLY358
|
3.7
|
17.6
|
1.0
|
HG2
|
C:GLU301
|
3.9
|
20.2
|
1.0
|
OE2
|
C:GLU301
|
3.9
|
18.0
|
1.0
|
N
|
C:GLY358
|
4.0
|
16.1
|
1.0
|
N
|
C:GLN353
|
4.0
|
17.4
|
1.0
|
CA
|
C:ALA350
|
4.0
|
17.1
|
1.0
|
HB2
|
C:GLN353
|
4.0
|
20.5
|
1.0
|
HA2
|
C:GLY359
|
4.0
|
21.2
|
1.0
|
N
|
C:PRO355
|
4.1
|
18.2
|
1.0
|
HA3
|
C:GLY354
|
4.1
|
21.5
|
1.0
|
N
|
C:ASP356
|
4.1
|
19.0
|
1.0
|
H22
|
C:PDO405
|
4.1
|
47.6
|
1.0
|
N
|
C:GLY357
|
4.2
|
17.2
|
1.0
|
CA
|
C:GLY354
|
4.2
|
17.9
|
1.0
|
N
|
C:GLY354
|
4.2
|
18.1
|
1.0
|
CG
|
C:GLU301
|
4.2
|
16.8
|
1.0
|
CA
|
C:ASP356
|
4.2
|
18.4
|
1.0
|
CA
|
C:GLN353
|
4.2
|
17.4
|
1.0
|
HB2
|
C:ALA350
|
4.2
|
19.8
|
1.0
|
CA
|
C:PRO355
|
4.3
|
19.1
|
1.0
|
O
|
C:HOH621
|
4.3
|
25.7
|
1.0
|
H
|
C:HIS352
|
4.4
|
20.5
|
1.0
|
H11
|
C:PDO405
|
4.4
|
48.2
|
1.0
|
CA
|
C:GLY358
|
4.4
|
17.1
|
1.0
|
C2
|
C:PDO405
|
4.5
|
39.6
|
1.0
|
N
|
C:GLY359
|
4.5
|
17.3
|
1.0
|
HA
|
C:GLU351
|
4.5
|
20.5
|
1.0
|
N
|
C:GLU351
|
4.6
|
17.3
|
1.0
|
C
|
C:ASP356
|
4.6
|
18.1
|
1.0
|
HA
|
C:ALA350
|
4.6
|
20.6
|
1.0
|
CB
|
C:GLN353
|
4.6
|
17.1
|
1.0
|
CA
|
C:GLY359
|
4.7
|
17.7
|
1.0
|
HA
|
C:PRO355
|
4.7
|
22.9
|
1.0
|
N
|
C:HIS352
|
4.7
|
17.1
|
1.0
|
HG3
|
C:GLU301
|
4.8
|
20.2
|
1.0
|
HA3
|
C:GLY358
|
4.8
|
20.5
|
1.0
|
H
|
C:ASP356
|
4.8
|
22.8
|
1.0
|
HD2
|
C:PRO355
|
4.8
|
23.8
|
1.0
|
HA3
|
C:GLY359
|
4.8
|
21.2
|
1.0
|
H
|
C:ALA350
|
4.9
|
19.2
|
1.0
|
C
|
C:GLY357
|
4.9
|
16.0
|
1.0
|
CA
|
C:GLU351
|
4.9
|
17.1
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6bum
Go back to
Calcium Binding Sites List in 6bum
Calcium binding site 4 out
of 4 in the Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca402
b:27.7
occ:0.56
|
O
|
D:GLN353
|
2.4
|
26.1
|
1.0
|
OE1
|
D:GLU301
|
2.4
|
23.1
|
1.0
|
O
|
D:ALA350
|
2.4
|
23.5
|
1.0
|
HO3
|
D:PDO405
|
2.4
|
59.0
|
1.0
|
O
|
D:PRO355
|
2.5
|
23.9
|
1.0
|
O
|
D:GLY358
|
2.7
|
24.3
|
1.0
|
H32
|
D:PDO405
|
2.8
|
58.6
|
1.0
|
HB3
|
D:ALA350
|
2.9
|
26.4
|
1.0
|
HB1
|
D:ALA350
|
2.9
|
26.4
|
1.0
|
O3
|
D:PDO405
|
2.9
|
49.2
|
1.0
|
O
|
D:GLY354
|
3.2
|
29.1
|
1.0
|
CD
|
D:GLU301
|
3.2
|
23.0
|
1.0
|
CB
|
D:ALA350
|
3.3
|
22.0
|
1.0
|
H
|
D:GLN353
|
3.3
|
32.5
|
1.0
|
C3
|
D:PDO405
|
3.3
|
48.8
|
1.0
|
C
|
D:GLN353
|
3.4
|
27.3
|
1.0
|
C
|
D:PRO355
|
3.4
|
24.2
|
1.0
|
H
|
D:GLY358
|
3.4
|
26.9
|
1.0
|
C
|
D:ALA350
|
3.4
|
23.9
|
1.0
|
C
|
D:GLY354
|
3.5
|
27.3
|
1.0
|
H
|
D:GLY357
|
3.7
|
26.4
|
1.0
|
C
|
D:GLY358
|
3.7
|
23.6
|
1.0
|
HA
|
D:ASP356
|
3.7
|
28.9
|
1.0
|
H21
|
D:PDO405
|
3.8
|
57.9
|
1.0
|
OE2
|
D:GLU301
|
3.8
|
24.0
|
1.0
|
HG2
|
D:GLU301
|
3.8
|
26.7
|
1.0
|
CA
|
D:ALA350
|
4.0
|
23.0
|
1.0
|
N
|
D:GLN353
|
4.0
|
27.1
|
1.0
|
HA2
|
D:GLY359
|
4.0
|
28.4
|
1.0
|
HB2
|
D:GLN353
|
4.0
|
31.6
|
1.0
|
N
|
D:GLY358
|
4.1
|
22.4
|
1.0
|
HA3
|
D:GLY354
|
4.1
|
33.8
|
1.0
|
N
|
D:PRO355
|
4.1
|
26.6
|
1.0
|
H31
|
D:PDO405
|
4.1
|
58.6
|
1.0
|
C2
|
D:PDO405
|
4.2
|
48.2
|
1.0
|
HB2
|
D:ALA350
|
4.2
|
26.4
|
1.0
|
CG
|
D:GLU301
|
4.2
|
22.2
|
1.0
|
N
|
D:ASP356
|
4.2
|
24.2
|
1.0
|
CA
|
D:GLY354
|
4.2
|
28.2
|
1.0
|
N
|
D:GLY354
|
4.2
|
27.7
|
1.0
|
N
|
D:GLY357
|
4.2
|
22.0
|
1.0
|
CA
|
D:GLN353
|
4.2
|
26.7
|
1.0
|
CA
|
D:PRO355
|
4.3
|
25.7
|
1.0
|
CA
|
D:ASP356
|
4.3
|
24.1
|
1.0
|
H
|
D:HIS352
|
4.4
|
31.4
|
1.0
|
O
|
D:HOH560
|
4.5
|
33.7
|
1.0
|
CA
|
D:GLY358
|
4.5
|
22.3
|
1.0
|
HA
|
D:GLU351
|
4.5
|
30.4
|
1.0
|
N
|
D:GLU351
|
4.5
|
24.6
|
1.0
|
N
|
D:GLY359
|
4.5
|
24.0
|
1.0
|
HA
|
D:ALA350
|
4.6
|
27.6
|
1.0
|
CA
|
D:GLY359
|
4.6
|
23.7
|
1.0
|
CB
|
D:GLN353
|
4.7
|
26.3
|
1.0
|
HA
|
D:PRO355
|
4.7
|
30.9
|
1.0
|
N
|
D:HIS352
|
4.7
|
26.2
|
1.0
|
C
|
D:ASP356
|
4.7
|
23.1
|
1.0
|
H11
|
D:PDO405
|
4.8
|
59.8
|
1.0
|
HG3
|
D:GLU301
|
4.8
|
26.7
|
1.0
|
H
|
D:ALA350
|
4.8
|
28.4
|
1.0
|
HA3
|
D:GLY359
|
4.8
|
28.4
|
1.0
|
H22
|
D:PDO405
|
4.8
|
57.9
|
1.0
|
HA3
|
D:GLY358
|
4.9
|
26.8
|
1.0
|
HD2
|
D:PRO355
|
4.9
|
32.6
|
1.0
|
CA
|
D:GLU351
|
4.9
|
25.3
|
1.0
|
H
|
D:ASP356
|
4.9
|
29.0
|
1.0
|
N
|
D:ALA350
|
5.0
|
23.7
|
1.0
|
C
|
D:GLY357
|
5.0
|
20.6
|
1.0
|
HB3
|
D:GLU301
|
5.0
|
26.9
|
1.0
|
H
|
D:GLY354
|
5.0
|
33.2
|
1.0
|
|
Reference:
K.Shi,
S.Cho,
A.Bera,
J.L.Seffernick,
L.P.Wackett,
H.Aihara.
Crystal Structures of Cyanuric Acid Hydrolase From Moorella Thermoacetica To Be Published.
Page generated: Mon Jul 15 17:07:06 2024
|