Calcium in PDB 8a29: Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
Enzymatic activity of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
All present enzymatic activity of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa:
2.2.1.7;
Protein crystallography data
The structure of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa, PDB code: 8a29
was solved by
R.Hamid,
S.Adam,
A.Lacour,
L.Monjas,
A.Hirsch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.59 /
2.10
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.444,
137.631,
232.082,
90,
90,
90
|
|
R / Rfree (%)
|
17.1 /
22.4
|
Other elements in 8a29:
The structure of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
(pdb code 8a29). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa, PDB code: 8a29:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 8a29
Go back to
Calcium Binding Sites List in 8a29
Calcium binding site 1 out
of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca706
b:61.8
occ:1.00
|
HH12
|
A:ARG145
|
2.2
|
33.4
|
1.0
|
|
NH1
|
A:ARG145
|
3.0
|
27.8
|
1.0
|
|
HA
|
A:THR152
|
3.1
|
27.1
|
1.0
|
|
HH11
|
A:ARG145
|
3.3
|
33.4
|
1.0
|
|
HG22
|
A:THR152
|
3.4
|
34.0
|
1.0
|
|
HH22
|
A:ARG145
|
3.7
|
32.7
|
1.0
|
|
HD2
|
A:ARG108
|
3.8
|
27.6
|
1.0
|
|
HB3
|
E:CYS382
|
3.9
|
27.1
|
1.0
|
|
HB
|
A:THR152
|
3.9
|
35.3
|
1.0
|
|
CA
|
A:THR152
|
4.0
|
22.5
|
1.0
|
|
CZ
|
A:ARG145
|
4.0
|
24.0
|
1.0
|
|
NE
|
A:ARG108
|
4.1
|
27.1
|
1.0
|
|
CZ
|
A:ARG108
|
4.1
|
28.9
|
1.0
|
|
HE
|
A:ARG108
|
4.2
|
32.5
|
1.0
|
|
CG2
|
A:THR152
|
4.2
|
28.3
|
1.0
|
|
NH2
|
A:ARG145
|
4.2
|
27.3
|
1.0
|
|
O
|
A:THR152
|
4.2
|
19.0
|
1.0
|
|
CB
|
A:THR152
|
4.2
|
29.4
|
1.0
|
|
O
|
E:CYS382
|
4.3
|
26.3
|
1.0
|
|
NH2
|
A:ARG108
|
4.4
|
23.6
|
1.0
|
|
HH21
|
A:ARG108
|
4.4
|
28.4
|
1.0
|
|
OE2
|
E:GLU383
|
4.4
|
31.8
|
1.0
|
|
HE2
|
A:MET168
|
4.5
|
25.6
|
1.0
|
|
CD
|
A:ARG108
|
4.5
|
23.0
|
1.0
|
|
NH1
|
A:ARG108
|
4.6
|
24.1
|
1.0
|
|
C
|
A:THR152
|
4.6
|
22.6
|
1.0
|
|
O
|
A:HOH939
|
4.6
|
27.9
|
1.0
|
|
O
|
A:HOH841
|
4.7
|
27.9
|
1.0
|
|
HG21
|
A:THR152
|
4.7
|
34.0
|
1.0
|
|
HH22
|
A:ARG108
|
4.7
|
28.4
|
1.0
|
|
HH11
|
A:ARG108
|
4.7
|
28.9
|
1.0
|
|
HG23
|
A:THR152
|
4.8
|
34.0
|
1.0
|
|
O
|
A:ASP151
|
4.8
|
25.6
|
1.0
|
|
CB
|
E:CYS382
|
4.8
|
22.6
|
1.0
|
|
HG2
|
A:ARG145
|
4.9
|
24.4
|
1.0
|
|
HH12
|
A:ARG108
|
4.9
|
28.9
|
1.0
|
|
Calcium binding site 2 out
of 12 in 8a29
Go back to
Calcium Binding Sites List in 8a29
Calcium binding site 2 out
of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca707
b:66.2
occ:1.00
|
O
|
A:HOH1024
|
2.8
|
41.2
|
1.0
|
|
HE22
|
A:GLN327
|
2.8
|
38.4
|
1.0
|
|
HH12
|
A:ARG358
|
2.9
|
48.6
|
1.0
|
|
HH22
|
A:ARG358
|
3.0
|
53.4
|
1.0
|
|
O
|
B:HOH1161
|
3.2
|
37.8
|
1.0
|
|
NE2
|
A:GLN327
|
3.6
|
32.0
|
1.0
|
|
NH1
|
A:ARG358
|
3.7
|
40.5
|
1.0
|
|
NH2
|
A:ARG358
|
3.7
|
44.5
|
1.0
|
|
HE21
|
A:GLN327
|
4.1
|
38.4
|
1.0
|
|
CZ
|
A:ARG358
|
4.2
|
48.2
|
1.0
|
|
OE1
|
A:GLN327
|
4.2
|
30.5
|
1.0
|
|
HH11
|
A:ARG358
|
4.3
|
48.6
|
1.0
|
|
CD
|
A:GLN327
|
4.3
|
32.5
|
1.0
|
|
HH21
|
A:ARG358
|
4.4
|
53.4
|
1.0
|
|
O
|
A:HOH982
|
4.6
|
27.4
|
1.0
|
|
OD1
|
A:ASP331
|
4.9
|
21.6
|
1.0
|
|
Calcium binding site 3 out
of 12 in 8a29
Go back to
Calcium Binding Sites List in 8a29
Calcium binding site 3 out
of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca706
b:63.3
occ:1.00
|
O
|
B:HOH1172
|
2.7
|
43.3
|
1.0
|
|
OD1
|
B:ASP526
|
2.8
|
31.0
|
1.0
|
|
O
|
B:HOH1109
|
2.9
|
44.9
|
1.0
|
|
OD2
|
B:ASP526
|
2.9
|
40.2
|
1.0
|
|
CG
|
B:ASP526
|
3.2
|
33.1
|
1.0
|
|
HA2
|
B:GLY503
|
3.9
|
32.4
|
1.0
|
|
HH22
|
B:ARG501
|
4.0
|
40.0
|
1.0
|
|
O
|
B:HOH1097
|
4.3
|
45.1
|
1.0
|
|
HH12
|
B:ARG501
|
4.3
|
39.1
|
1.0
|
|
O
|
B:ARG502
|
4.5
|
31.0
|
1.0
|
|
CB
|
B:ASP526
|
4.7
|
31.3
|
1.0
|
|
NH2
|
B:ARG501
|
4.7
|
33.4
|
1.0
|
|
CA
|
B:GLY503
|
4.9
|
27.0
|
1.0
|
|
Calcium binding site 4 out
of 12 in 8a29
Go back to
Calcium Binding Sites List in 8a29
Calcium binding site 4 out
of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca704
b:67.5
occ:1.00
|
HH12
|
C:ARG145
|
2.6
|
28.2
|
1.0
|
|
HH22
|
C:ARG145
|
3.1
|
40.0
|
1.0
|
|
O
|
C:HOH1060
|
3.1
|
29.6
|
1.0
|
|
NH1
|
C:ARG145
|
3.4
|
23.5
|
1.0
|
|
NH2
|
C:ARG145
|
3.8
|
33.3
|
1.0
|
|
HH11
|
C:ARG145
|
4.0
|
28.2
|
1.0
|
|
HA
|
C:THR152
|
4.0
|
28.1
|
1.0
|
|
CZ
|
C:ARG108
|
4.0
|
30.9
|
1.0
|
|
CZ
|
C:ARG145
|
4.0
|
22.7
|
1.0
|
|
HG22
|
C:THR152
|
4.1
|
31.3
|
1.0
|
|
NH2
|
C:ARG108
|
4.1
|
29.8
|
1.0
|
|
HH21
|
C:ARG108
|
4.3
|
35.8
|
1.0
|
|
HH22
|
C:ARG108
|
4.3
|
35.8
|
1.0
|
|
NH1
|
C:ARG108
|
4.3
|
25.1
|
1.0
|
|
NE
|
C:ARG108
|
4.3
|
28.0
|
1.0
|
|
HD2
|
C:ARG108
|
4.4
|
28.0
|
1.0
|
|
HH12
|
C:ARG108
|
4.5
|
30.2
|
1.0
|
|
HE
|
C:ARG108
|
4.5
|
33.6
|
1.0
|
|
HH21
|
C:ARG145
|
4.5
|
40.0
|
1.0
|
|
HH11
|
C:ARG108
|
4.6
|
30.2
|
1.0
|
|
O
|
C:HOH930
|
4.8
|
33.6
|
1.0
|
|
HB
|
C:THR152
|
4.9
|
28.6
|
1.0
|
|
O
|
C:HOH943
|
4.9
|
23.4
|
1.0
|
|
O
|
C:HOH1018
|
4.9
|
39.7
|
1.0
|
|
CA
|
C:THR152
|
4.9
|
23.4
|
1.0
|
|
CD
|
C:ARG108
|
4.9
|
23.3
|
1.0
|
|
CG2
|
C:THR152
|
5.0
|
26.1
|
1.0
|
|
Calcium binding site 5 out
of 12 in 8a29
Go back to
Calcium Binding Sites List in 8a29
Calcium binding site 5 out
of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca704
b:54.1
occ:1.00
|
O
|
D:HOH989
|
2.2
|
34.1
|
1.0
|
|
O
|
D:PHE467
|
2.3
|
24.1
|
1.0
|
|
O
|
D:HOH999
|
2.4
|
30.7
|
1.0
|
|
O
|
D:GLY464
|
2.4
|
18.7
|
1.0
|
|
OD1
|
D:ASP413
|
2.4
|
27.1
|
1.0
|
|
O
|
D:TYR465
|
2.6
|
23.3
|
1.0
|
|
O
|
D:GLY469
|
3.3
|
20.9
|
1.0
|
|
HA
|
D:TYR465
|
3.3
|
27.0
|
1.0
|
|
C
|
D:TYR465
|
3.3
|
22.2
|
1.0
|
|
C
|
D:PHE467
|
3.4
|
21.2
|
1.0
|
|
H
|
D:GLY469
|
3.5
|
26.1
|
1.0
|
|
C
|
D:GLY464
|
3.5
|
22.5
|
1.0
|
|
HB3
|
D:PHE467
|
3.5
|
24.7
|
1.0
|
|
CG
|
D:ASP413
|
3.6
|
24.6
|
1.0
|
|
H
|
D:PHE467
|
3.6
|
27.2
|
1.0
|
|
HZ2
|
D:LYS386
|
3.6
|
33.4
|
1.0
|
|
N
|
D:PHE467
|
3.7
|
22.7
|
1.0
|
|
CA
|
D:TYR465
|
3.7
|
22.5
|
1.0
|
|
HZ1
|
D:LYS386
|
3.8
|
33.4
|
1.0
|
|
HD2
|
D:PHE467
|
3.9
|
21.8
|
1.0
|
|
CA
|
D:PHE467
|
4.0
|
21.4
|
1.0
|
|
N
|
D:TYR465
|
4.1
|
20.8
|
1.0
|
|
OD2
|
D:ASP413
|
4.1
|
27.8
|
1.0
|
|
NZ
|
D:LYS386
|
4.1
|
27.9
|
1.0
|
|
HA
|
D:ASP413
|
4.2
|
24.9
|
1.0
|
|
CB
|
D:PHE467
|
4.2
|
20.6
|
1.0
|
|
HB2
|
D:LEU415
|
4.2
|
24.0
|
1.0
|
|
C
|
D:LEU466
|
4.2
|
22.4
|
1.0
|
|
HE3
|
D:LYS386
|
4.3
|
33.0
|
1.0
|
|
N
|
D:LEU466
|
4.3
|
21.5
|
1.0
|
|
N
|
D:GLY469
|
4.3
|
21.8
|
1.0
|
|
HB3
|
D:ALA471
|
4.3
|
21.8
|
1.0
|
|
HA
|
D:ASP468
|
4.4
|
30.8
|
1.0
|
|
C
|
D:GLY469
|
4.4
|
19.0
|
1.0
|
|
HB2
|
D:ALA471
|
4.4
|
21.8
|
1.0
|
|
N
|
D:ASP468
|
4.5
|
22.7
|
1.0
|
|
O
|
D:HOH846
|
4.5
|
23.9
|
1.0
|
|
H
|
D:VAL414
|
4.6
|
26.5
|
1.0
|
|
CD2
|
D:PHE467
|
4.6
|
18.1
|
1.0
|
|
N
|
D:VAL414
|
4.6
|
22.1
|
1.0
|
|
C
|
D:ASP413
|
4.7
|
21.0
|
1.0
|
|
CA
|
D:ASP413
|
4.7
|
20.7
|
1.0
|
|
CA
|
D:LEU466
|
4.7
|
18.9
|
1.0
|
|
HA2
|
D:GLY464
|
4.7
|
25.4
|
1.0
|
|
CB
|
D:ASP413
|
4.7
|
24.8
|
1.0
|
|
CE
|
D:LYS386
|
4.8
|
27.5
|
1.0
|
|
O
|
D:LEU466
|
4.8
|
21.3
|
1.0
|
|
CA
|
D:GLY464
|
4.8
|
21.1
|
1.0
|
|
CB
|
D:ALA471
|
4.8
|
18.2
|
1.0
|
|
HZ3
|
D:LYS386
|
4.9
|
33.4
|
1.0
|
|
CA
|
D:ASP468
|
4.9
|
25.7
|
1.0
|
|
HA
|
D:LEU466
|
4.9
|
22.7
|
1.0
|
|
H
|
D:LEU466
|
4.9
|
25.8
|
1.0
|
|
C
|
D:VAL414
|
4.9
|
23.1
|
1.0
|
|
HA
|
D:PHE467
|
4.9
|
25.6
|
1.0
|
|
CG
|
D:PHE467
|
4.9
|
19.2
|
1.0
|
|
H
|
D:TYR465
|
4.9
|
24.9
|
1.0
|
|
O
|
D:VAL414
|
5.0
|
16.9
|
1.0
|
|
HB2
|
D:PHE467
|
5.0
|
24.7
|
1.0
|
|
CA
|
D:GLY469
|
5.0
|
21.1
|
1.0
|
|
HA
|
D:LEU415
|
5.0
|
22.9
|
1.0
|
|
Calcium binding site 6 out
of 12 in 8a29
Go back to
Calcium Binding Sites List in 8a29
Calcium binding site 6 out
of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca705
b:49.6
occ:1.00
|
OE2
|
D:GLU456
|
2.4
|
21.1
|
1.0
|
|
OD2
|
D:ASP455
|
2.7
|
27.1
|
1.0
|
|
HG2
|
D:GLU456
|
2.8
|
26.0
|
1.0
|
|
HH22
|
D:ARG500
|
3.0
|
34.6
|
1.0
|
|
O
|
D:HOH835
|
3.0
|
25.6
|
1.0
|
|
O
|
D:HOH984
|
3.0
|
31.3
|
1.0
|
|
HB3
|
D:ASP455
|
3.2
|
32.8
|
1.0
|
|
CD
|
D:GLU456
|
3.3
|
23.9
|
1.0
|
|
CG
|
D:GLU456
|
3.5
|
21.7
|
1.0
|
|
CG
|
D:ASP455
|
3.7
|
27.3
|
1.0
|
|
HD2
|
D:LYS459
|
3.7
|
27.8
|
1.0
|
|
NH2
|
D:ARG500
|
3.7
|
28.9
|
1.0
|
|
HZ3
|
D:LYS459
|
3.9
|
41.5
|
1.0
|
|
CB
|
D:ASP455
|
3.9
|
27.3
|
1.0
|
|
HH21
|
D:ARG533
|
3.9
|
26.9
|
1.0
|
|
HH12
|
D:ARG500
|
3.9
|
34.5
|
1.0
|
|
H
|
D:GLU456
|
4.0
|
23.7
|
1.0
|
|
HG3
|
D:GLU456
|
4.1
|
26.0
|
1.0
|
|
N
|
D:GLU456
|
4.1
|
19.7
|
1.0
|
|
HA
|
D:GLU456
|
4.1
|
29.0
|
1.0
|
|
HH21
|
D:ARG500
|
4.1
|
34.6
|
1.0
|
|
HE2
|
D:LYS459
|
4.2
|
39.6
|
1.0
|
|
OD1
|
D:ASP453
|
4.3
|
17.1
|
1.0
|
|
C
|
D:ASP455
|
4.4
|
21.4
|
1.0
|
|
CD
|
D:LYS459
|
4.4
|
23.2
|
1.0
|
|
CA
|
D:GLU456
|
4.5
|
24.2
|
1.0
|
|
HD3
|
D:LYS459
|
4.5
|
27.8
|
1.0
|
|
OE1
|
D:GLU456
|
4.5
|
24.0
|
1.0
|
|
NH1
|
D:ARG500
|
4.5
|
28.7
|
1.0
|
|
CB
|
D:GLU456
|
4.6
|
24.6
|
1.0
|
|
CZ
|
D:ARG500
|
4.6
|
30.4
|
1.0
|
|
HB2
|
D:ASP455
|
4.6
|
32.8
|
1.0
|
|
NZ
|
D:LYS459
|
4.6
|
34.5
|
1.0
|
|
O
|
D:HOH871
|
4.6
|
28.0
|
1.0
|
|
CE
|
D:LYS459
|
4.6
|
33.0
|
1.0
|
|
NH2
|
D:ARG533
|
4.7
|
22.4
|
1.0
|
|
OD2
|
D:ASP453
|
4.7
|
22.6
|
1.0
|
|
O
|
D:HOH1043
|
4.7
|
32.1
|
1.0
|
|
HH22
|
D:ARG533
|
4.8
|
26.9
|
1.0
|
|
CA
|
D:ASP455
|
4.8
|
20.0
|
1.0
|
|
O
|
D:HOH1104
|
4.8
|
38.9
|
1.0
|
|
OD1
|
D:ASP455
|
4.8
|
24.8
|
1.0
|
|
O
|
D:ASP455
|
4.9
|
19.9
|
1.0
|
|
CG
|
D:ASP453
|
4.9
|
21.4
|
1.0
|
|
Calcium binding site 7 out
of 12 in 8a29
Go back to
Calcium Binding Sites List in 8a29
Calcium binding site 7 out
of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca706
b:69.8
occ:1.00
|
O
|
D:HOH1064
|
2.5
|
52.0
|
1.0
|
|
O
|
D:HIS550
|
2.9
|
23.6
|
1.0
|
|
O
|
D:HOH1112
|
2.9
|
40.7
|
1.0
|
|
O
|
D:ALA547
|
3.0
|
32.1
|
1.0
|
|
HA2
|
D:GLY548
|
3.7
|
30.9
|
1.0
|
|
HG23
|
D:VAL580
|
3.8
|
40.1
|
1.0
|
|
HA
|
D:GLU551
|
3.9
|
25.1
|
1.0
|
|
C
|
D:HIS550
|
3.9
|
21.8
|
1.0
|
|
H
|
D:HIS550
|
4.0
|
26.7
|
1.0
|
|
O
|
D:GLY548
|
4.0
|
31.1
|
1.0
|
|
C
|
D:GLY548
|
4.1
|
29.2
|
1.0
|
|
HB
|
D:VAL580
|
4.1
|
31.4
|
1.0
|
|
C
|
D:ALA547
|
4.1
|
24.4
|
1.0
|
|
CA
|
D:GLY548
|
4.3
|
25.7
|
1.0
|
|
HG21
|
D:VAL580
|
4.3
|
40.1
|
1.0
|
|
N
|
D:HIS550
|
4.4
|
22.2
|
1.0
|
|
CG2
|
D:VAL580
|
4.5
|
33.4
|
1.0
|
|
N
|
D:SER549
|
4.5
|
26.3
|
1.0
|
|
OE2
|
D:GLU551
|
4.5
|
47.4
|
1.0
|
|
N
|
D:GLY548
|
4.7
|
24.1
|
1.0
|
|
CB
|
D:VAL580
|
4.8
|
26.2
|
1.0
|
|
CA
|
D:GLU551
|
4.8
|
20.9
|
1.0
|
|
N
|
D:GLU551
|
4.8
|
22.8
|
1.0
|
|
CA
|
D:HIS550
|
4.8
|
21.0
|
1.0
|
|
HA
|
D:VAL580
|
4.8
|
36.8
|
1.0
|
|
H
|
D:SER549
|
4.8
|
31.5
|
1.0
|
|
OE1
|
D:GLU551
|
4.9
|
40.1
|
1.0
|
|
CD
|
D:GLU551
|
4.9
|
34.0
|
1.0
|
|
C
|
D:SER549
|
5.0
|
27.5
|
1.0
|
|
HA
|
D:SER549
|
5.0
|
33.4
|
1.0
|
|
Calcium binding site 8 out
of 12 in 8a29
Go back to
Calcium Binding Sites List in 8a29
Calcium binding site 8 out
of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca707
b:38.0
occ:1.00
|
O
|
D:HOH1012
|
2.3
|
29.6
|
1.0
|
|
O
|
D:ASP620
|
2.4
|
30.4
|
1.0
|
|
O
|
D:HOH1128
|
2.6
|
39.3
|
1.0
|
|
O
|
D:HOH1088
|
2.8
|
43.7
|
1.0
|
|
O
|
D:HOH880
|
2.8
|
38.0
|
1.0
|
|
C
|
D:ASP620
|
3.5
|
32.1
|
1.0
|
|
HA
|
D:ASP620
|
3.8
|
32.2
|
1.0
|
|
HB3
|
D:ASP620
|
4.1
|
30.6
|
1.0
|
|
HA
|
D:ARG621
|
4.1
|
43.9
|
1.0
|
|
CA
|
D:ASP620
|
4.2
|
26.8
|
1.0
|
|
N
|
D:ARG621
|
4.6
|
33.6
|
1.0
|
|
CB
|
D:ASP620
|
4.6
|
25.5
|
1.0
|
|
O
|
D:GLN622
|
4.7
|
45.7
|
1.0
|
|
CA
|
D:ARG621
|
4.8
|
36.6
|
1.0
|
|
O
|
D:HOH1101
|
4.9
|
36.6
|
1.0
|
|
Calcium binding site 9 out
of 12 in 8a29
Go back to
Calcium Binding Sites List in 8a29
Calcium binding site 9 out
of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca706
b:49.3
occ:1.00
|
HH
|
E:TYR363
|
2.1
|
34.2
|
1.0
|
|
O
|
E:HOH1095
|
2.6
|
43.3
|
1.0
|
|
OD2
|
E:ASP365
|
2.6
|
28.4
|
1.0
|
|
HE2
|
E:TYR363
|
2.8
|
31.0
|
1.0
|
|
HB2
|
E:ASP365
|
2.8
|
27.0
|
1.0
|
|
O
|
E:HOH1149
|
2.9
|
36.6
|
1.0
|
|
OH
|
E:TYR363
|
3.0
|
28.5
|
1.0
|
|
HD3
|
E:LYS347
|
3.1
|
43.7
|
1.0
|
|
HB3
|
E:ASP365
|
3.2
|
27.0
|
1.0
|
|
HZ3
|
E:LYS347
|
3.3
|
53.9
|
1.0
|
|
CB
|
E:ASP365
|
3.3
|
22.5
|
1.0
|
|
CG
|
E:ASP365
|
3.4
|
29.5
|
1.0
|
|
CE2
|
E:TYR363
|
3.5
|
25.9
|
1.0
|
|
HB2
|
E:LYS347
|
3.7
|
41.5
|
1.0
|
|
CZ
|
E:TYR363
|
3.7
|
25.7
|
1.0
|
|
O
|
E:HOH960
|
3.9
|
35.7
|
1.0
|
|
CD
|
E:LYS347
|
4.1
|
36.4
|
1.0
|
|
NZ
|
E:LYS347
|
4.1
|
44.9
|
1.0
|
|
HZ2
|
E:LYS347
|
4.3
|
53.9
|
1.0
|
|
O
|
E:HOH947
|
4.4
|
45.4
|
1.0
|
|
HB3
|
E:LYS347
|
4.4
|
41.5
|
1.0
|
|
CB
|
E:LYS347
|
4.5
|
34.6
|
1.0
|
|
HD2
|
E:LYS347
|
4.5
|
43.7
|
1.0
|
|
OD1
|
E:ASP365
|
4.6
|
27.3
|
1.0
|
|
CE
|
E:LYS347
|
4.7
|
35.1
|
1.0
|
|
HZ1
|
E:LYS347
|
4.7
|
53.9
|
1.0
|
|
CA
|
E:ASP365
|
4.8
|
18.7
|
1.0
|
|
CD2
|
E:TYR363
|
4.8
|
27.2
|
1.0
|
|
HE2
|
E:LYS347
|
4.8
|
42.1
|
1.0
|
|
CG
|
E:LYS347
|
4.9
|
31.6
|
1.0
|
|
Calcium binding site 10 out
of 12 in 8a29
Go back to
Calcium Binding Sites List in 8a29
Calcium binding site 10 out
of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca707
b:47.8
occ:1.00
|
OD2
|
E:ASP455
|
2.5
|
24.4
|
1.0
|
|
O
|
E:HOH1069
|
2.6
|
29.2
|
1.0
|
|
OE2
|
E:GLU456
|
2.7
|
22.4
|
1.0
|
|
O
|
E:HOH844
|
2.9
|
20.4
|
1.0
|
|
HG2
|
E:GLU456
|
3.1
|
21.2
|
1.0
|
|
HB3
|
E:ASP455
|
3.2
|
29.0
|
1.0
|
|
HZ2
|
E:LYS459
|
3.2
|
32.6
|
1.0
|
|
HH22
|
E:ARG500
|
3.3
|
32.0
|
1.0
|
|
HZ3
|
E:LYS459
|
3.5
|
32.6
|
1.0
|
|
CG
|
E:ASP455
|
3.5
|
25.1
|
1.0
|
|
CD
|
E:GLU456
|
3.6
|
22.6
|
1.0
|
|
NZ
|
E:LYS459
|
3.8
|
27.1
|
1.0
|
|
CG
|
E:GLU456
|
3.8
|
17.7
|
1.0
|
|
CB
|
E:ASP455
|
3.8
|
24.2
|
1.0
|
|
HD2
|
E:LYS459
|
3.8
|
25.7
|
1.0
|
|
HH21
|
E:ARG533
|
3.9
|
25.1
|
1.0
|
|
HH12
|
E:ARG500
|
3.9
|
30.4
|
1.0
|
|
NH2
|
E:ARG500
|
4.0
|
26.7
|
1.0
|
|
HZ1
|
E:LYS459
|
4.3
|
32.6
|
1.0
|
|
H
|
E:GLU456
|
4.3
|
26.8
|
1.0
|
|
OD1
|
E:ASP453
|
4.3
|
20.4
|
1.0
|
|
HG3
|
E:GLU456
|
4.4
|
21.2
|
1.0
|
|
HA
|
E:GLU456
|
4.4
|
26.2
|
1.0
|
|
N
|
E:GLU456
|
4.4
|
22.3
|
1.0
|
|
HB2
|
E:ASP455
|
4.4
|
29.0
|
1.0
|
|
HH21
|
E:ARG500
|
4.5
|
32.0
|
1.0
|
|
O
|
E:HOH850
|
4.5
|
20.4
|
1.0
|
|
NH1
|
E:ARG500
|
4.6
|
25.4
|
1.0
|
|
NH2
|
E:ARG533
|
4.6
|
20.9
|
1.0
|
|
C
|
E:ASP455
|
4.6
|
18.1
|
1.0
|
|
CD
|
E:LYS459
|
4.7
|
21.4
|
1.0
|
|
HH22
|
E:ARG533
|
4.7
|
25.1
|
1.0
|
|
OD2
|
E:ASP453
|
4.7
|
27.0
|
1.0
|
|
OD1
|
E:ASP455
|
4.7
|
26.6
|
1.0
|
|
CZ
|
E:ARG500
|
4.7
|
33.5
|
1.0
|
|
O
|
E:HOH1067
|
4.7
|
37.3
|
1.0
|
|
CA
|
E:GLU456
|
4.8
|
21.9
|
1.0
|
|
OE1
|
E:GLU456
|
4.8
|
24.6
|
1.0
|
|
CE
|
E:LYS459
|
4.9
|
24.4
|
1.0
|
|
HD3
|
E:LYS459
|
4.9
|
25.7
|
1.0
|
|
CB
|
E:GLU456
|
4.9
|
19.7
|
1.0
|
|
CA
|
E:ASP455
|
4.9
|
20.8
|
1.0
|
|
CG
|
E:ASP453
|
5.0
|
27.5
|
1.0
|
|
Reference:
R.Hamid,
S.Adam,
A.Lacour,
L.Monjas,
A.Hirsch.
Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding To Be Published.
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