Calcium in PDB 8wm1: Dhs Dehydratase
Protein crystallography data
The structure of Dhs Dehydratase, PDB code: 8wm1
was solved by
M.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.28 /
2.74
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
143.56,
97.67,
132.82,
90,
90,
90
|
|
R / Rfree (%)
|
22.4 /
25.5
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Dhs Dehydratase
(pdb code 8wm1). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Dhs Dehydratase, PDB code: 8wm1:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 8wm1
Go back to
Calcium Binding Sites List in 8wm1
Calcium binding site 1 out
of 8 in the Dhs Dehydratase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Dhs Dehydratase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:27.4
occ:1.00
|
OE1
|
A:GLU210
|
2.1
|
30.2
|
1.0
|
|
O
|
A:THR120
|
2.2
|
35.9
|
1.0
|
|
OD2
|
A:ASP207
|
2.4
|
21.1
|
1.0
|
|
O
|
A:GLY173
|
2.4
|
28.9
|
1.0
|
|
CD
|
A:GLU210
|
3.3
|
25.5
|
1.0
|
|
OG1
|
A:THR120
|
3.4
|
35.3
|
1.0
|
|
C
|
A:THR120
|
3.4
|
34.3
|
1.0
|
|
CG
|
A:ASP207
|
3.5
|
21.0
|
1.0
|
|
C
|
A:GLY173
|
3.5
|
29.1
|
1.0
|
|
CA
|
A:CA502
|
3.9
|
20.7
|
1.0
|
|
OE2
|
A:GLU210
|
3.9
|
24.6
|
1.0
|
|
CA
|
A:GLY173
|
4.0
|
29.7
|
1.0
|
|
CB
|
A:ASP207
|
4.1
|
20.8
|
1.0
|
|
CA
|
A:THR120
|
4.2
|
34.2
|
1.0
|
|
CG
|
A:GLU210
|
4.3
|
23.5
|
1.0
|
|
CB
|
A:THR120
|
4.4
|
35.4
|
1.0
|
|
OE2
|
A:GLU239
|
4.4
|
22.6
|
1.0
|
|
N
|
A:ASN121
|
4.5
|
33.1
|
1.0
|
|
OD1
|
A:ASP207
|
4.5
|
20.7
|
1.0
|
|
CA
|
A:ASN121
|
4.6
|
33.1
|
1.0
|
|
N
|
A:ALA174
|
4.7
|
26.9
|
1.0
|
|
CE
|
A:MET177
|
4.7
|
23.6
|
1.0
|
|
O
|
A:VAL122
|
4.7
|
32.3
|
1.0
|
|
OD1
|
A:ASN121
|
4.8
|
36.7
|
1.0
|
|
O
|
A:GLY172
|
4.8
|
29.1
|
1.0
|
|
CB
|
A:ALA174
|
4.9
|
26.0
|
1.0
|
|
N
|
A:VAL122
|
5.0
|
32.0
|
1.0
|
|
Calcium binding site 2 out
of 8 in 8wm1
Go back to
Calcium Binding Sites List in 8wm1
Calcium binding site 2 out
of 8 in the Dhs Dehydratase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Dhs Dehydratase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:20.7
occ:1.00
|
OE2
|
A:GLU239
|
2.0
|
22.6
|
1.0
|
|
OD1
|
A:ASN121
|
2.3
|
36.7
|
1.0
|
|
OE1
|
A:GLN236
|
2.3
|
23.4
|
1.0
|
|
OD2
|
A:ASP207
|
2.4
|
21.1
|
1.0
|
|
OD1
|
A:ASP207
|
2.6
|
20.7
|
1.0
|
|
CG
|
A:ASP207
|
2.9
|
21.0
|
1.0
|
|
CD
|
A:GLU239
|
3.2
|
22.8
|
1.0
|
|
CG
|
A:ASN121
|
3.5
|
35.4
|
1.0
|
|
CD
|
A:GLN236
|
3.5
|
23.1
|
1.0
|
|
OE1
|
A:GLU239
|
3.8
|
23.7
|
1.0
|
|
CA
|
A:CA501
|
3.9
|
27.4
|
1.0
|
|
O
|
A:THR120
|
4.0
|
35.9
|
1.0
|
|
CA
|
A:ASN121
|
4.2
|
33.1
|
1.0
|
|
CB
|
A:ASN121
|
4.2
|
34.1
|
1.0
|
|
CG
|
A:GLN236
|
4.3
|
22.7
|
1.0
|
|
CB
|
A:SER235
|
4.3
|
27.6
|
1.0
|
|
CG
|
A:GLU239
|
4.4
|
22.0
|
1.0
|
|
NE2
|
A:GLN236
|
4.4
|
23.7
|
1.0
|
|
CB
|
A:ASP207
|
4.4
|
20.8
|
1.0
|
|
ND2
|
A:ASN121
|
4.5
|
35.1
|
1.0
|
|
C
|
A:THR120
|
4.6
|
34.3
|
1.0
|
|
CB
|
A:GLN236
|
4.6
|
21.8
|
1.0
|
|
CB
|
A:GLU239
|
4.6
|
21.3
|
1.0
|
|
N
|
A:ASN121
|
4.7
|
33.1
|
1.0
|
|
CG2
|
A:THR120
|
4.8
|
35.5
|
1.0
|
|
OG1
|
A:THR120
|
4.8
|
35.3
|
1.0
|
|
CB
|
A:ALA334
|
4.9
|
25.4
|
1.0
|
|
OE1
|
A:GLN261
|
4.9
|
17.8
|
1.0
|
|
OG
|
A:SER235
|
4.9
|
28.9
|
1.0
|
|
N
|
A:GLN236
|
5.0
|
23.6
|
1.0
|
|
OE1
|
A:GLU210
|
5.0
|
30.2
|
1.0
|
|
Calcium binding site 3 out
of 8 in 8wm1
Go back to
Calcium Binding Sites List in 8wm1
Calcium binding site 3 out
of 8 in the Dhs Dehydratase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Dhs Dehydratase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca501
b:20.7
occ:1.00
|
OE1
|
B:GLN236
|
2.0
|
26.0
|
1.0
|
|
OD1
|
B:ASN121
|
2.1
|
28.6
|
1.0
|
|
OE2
|
B:GLU239
|
2.2
|
17.6
|
1.0
|
|
OD2
|
B:ASP207
|
2.6
|
19.4
|
1.0
|
|
OD1
|
B:ASP207
|
2.6
|
17.7
|
1.0
|
|
CG
|
B:ASP207
|
2.9
|
18.4
|
1.0
|
|
CD
|
B:GLN236
|
3.2
|
25.7
|
1.0
|
|
CG
|
B:ASN121
|
3.4
|
26.6
|
1.0
|
|
CD
|
B:GLU239
|
3.4
|
16.7
|
1.0
|
|
OE1
|
B:GLU239
|
4.0
|
16.9
|
1.0
|
|
CA
|
B:CA502
|
4.0
|
24.9
|
1.0
|
|
CB
|
B:SER235
|
4.1
|
22.4
|
1.0
|
|
O
|
B:THR120
|
4.1
|
27.7
|
1.0
|
|
CG
|
B:GLN236
|
4.2
|
23.7
|
1.0
|
|
NE2
|
B:GLN236
|
4.2
|
27.1
|
1.0
|
|
CB
|
B:ASN121
|
4.2
|
26.7
|
1.0
|
|
CA
|
B:ASN121
|
4.3
|
27.2
|
1.0
|
|
ND2
|
B:ASN121
|
4.3
|
26.0
|
1.0
|
|
CB
|
B:GLN236
|
4.5
|
22.2
|
1.0
|
|
CB
|
B:ASP207
|
4.5
|
18.5
|
1.0
|
|
CG
|
B:GLU239
|
4.5
|
16.1
|
1.0
|
|
C
|
B:THR120
|
4.7
|
28.1
|
1.0
|
|
CB
|
B:GLU239
|
4.7
|
15.6
|
1.0
|
|
OG
|
B:SER235
|
4.7
|
23.6
|
1.0
|
|
CB
|
B:ALA334
|
4.8
|
24.7
|
1.0
|
|
N
|
B:GLN236
|
4.8
|
21.6
|
1.0
|
|
CG2
|
B:THR120
|
4.8
|
29.7
|
1.0
|
|
N
|
B:ASN121
|
4.8
|
27.7
|
1.0
|
|
OE1
|
B:GLN261
|
4.8
|
18.2
|
1.0
|
|
OG1
|
B:THR120
|
4.9
|
29.4
|
1.0
|
|
Calcium binding site 4 out
of 8 in 8wm1
Go back to
Calcium Binding Sites List in 8wm1
Calcium binding site 4 out
of 8 in the Dhs Dehydratase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Dhs Dehydratase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca502
b:24.9
occ:1.00
|
OE1
|
B:GLU210
|
2.1
|
18.1
|
1.0
|
|
OD2
|
B:ASP207
|
2.2
|
19.4
|
1.0
|
|
O
|
B:THR120
|
2.3
|
27.7
|
1.0
|
|
O
|
B:GLY173
|
2.4
|
20.9
|
1.0
|
|
O
|
B:HOH613
|
2.4
|
9.7
|
1.0
|
|
CD
|
B:GLU210
|
3.3
|
18.5
|
1.0
|
|
OG1
|
B:THR120
|
3.3
|
29.4
|
1.0
|
|
CG
|
B:ASP207
|
3.3
|
18.4
|
1.0
|
|
C
|
B:THR120
|
3.5
|
28.1
|
1.0
|
|
C
|
B:GLY173
|
3.5
|
20.0
|
1.0
|
|
CB
|
B:ASP207
|
3.9
|
18.5
|
1.0
|
|
OE2
|
B:GLU210
|
4.0
|
19.9
|
1.0
|
|
CA
|
B:CA501
|
4.0
|
20.7
|
1.0
|
|
CA
|
B:GLY173
|
4.1
|
19.6
|
1.0
|
|
CA
|
B:THR120
|
4.2
|
28.9
|
1.0
|
|
CG
|
B:GLU210
|
4.3
|
17.9
|
1.0
|
|
OE2
|
B:GLU239
|
4.3
|
17.6
|
1.0
|
|
CB
|
B:THR120
|
4.3
|
29.8
|
1.0
|
|
OD1
|
B:ASP207
|
4.3
|
17.7
|
1.0
|
|
N
|
B:ASN121
|
4.5
|
27.7
|
1.0
|
|
N
|
B:ALA174
|
4.7
|
19.5
|
1.0
|
|
CA
|
B:ASN121
|
4.7
|
27.2
|
1.0
|
|
OD1
|
B:ASN121
|
4.8
|
28.6
|
1.0
|
|
CB
|
B:ALA174
|
4.8
|
19.4
|
1.0
|
|
O
|
B:GLY172
|
4.8
|
18.3
|
1.0
|
|
CE
|
B:MET177
|
4.9
|
18.7
|
1.0
|
|
CD
|
B:GLU239
|
4.9
|
16.7
|
1.0
|
|
CG2
|
B:THR120
|
5.0
|
29.7
|
1.0
|
|
Calcium binding site 5 out
of 8 in 8wm1
Go back to
Calcium Binding Sites List in 8wm1
Calcium binding site 5 out
of 8 in the Dhs Dehydratase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Dhs Dehydratase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca501
b:21.9
occ:1.00
|
OE1
|
C:GLU210
|
2.0
|
23.6
|
1.0
|
|
OD2
|
C:ASP207
|
2.2
|
24.8
|
1.0
|
|
O
|
C:THR120
|
2.3
|
29.0
|
1.0
|
|
O
|
C:HOH612
|
2.3
|
15.3
|
1.0
|
|
O
|
C:GLY173
|
2.6
|
21.4
|
1.0
|
|
CD
|
C:GLU210
|
3.2
|
22.1
|
1.0
|
|
CG
|
C:ASP207
|
3.4
|
23.6
|
1.0
|
|
OG1
|
C:THR120
|
3.5
|
32.5
|
1.0
|
|
C
|
C:THR120
|
3.5
|
30.4
|
1.0
|
|
C
|
C:GLY173
|
3.7
|
21.3
|
1.0
|
|
CA
|
C:CA502
|
3.8
|
27.0
|
1.0
|
|
OE2
|
C:GLU210
|
3.9
|
20.2
|
1.0
|
|
CB
|
C:ASP207
|
4.0
|
23.7
|
1.0
|
|
CG
|
C:GLU210
|
4.1
|
21.5
|
1.0
|
|
OE2
|
C:GLU239
|
4.2
|
20.1
|
1.0
|
|
CA
|
C:GLY173
|
4.2
|
21.5
|
1.0
|
|
CA
|
C:THR120
|
4.3
|
31.8
|
1.0
|
|
OD1
|
C:ASP207
|
4.4
|
22.8
|
1.0
|
|
CB
|
C:THR120
|
4.4
|
32.5
|
1.0
|
|
N
|
C:ASN121
|
4.5
|
30.1
|
1.0
|
|
CA
|
C:ASN121
|
4.6
|
30.2
|
1.0
|
|
OD1
|
C:ASN121
|
4.7
|
29.2
|
1.0
|
|
CD
|
C:GLU239
|
4.8
|
19.3
|
1.0
|
|
N
|
C:ALA174
|
4.8
|
21.3
|
1.0
|
|
CE
|
C:MET177
|
4.8
|
23.7
|
1.0
|
|
O
|
C:VAL122
|
4.9
|
31.8
|
1.0
|
|
CB
|
C:ALA174
|
4.9
|
21.8
|
1.0
|
|
O
|
C:GLY172
|
5.0
|
21.0
|
1.0
|
|
Calcium binding site 6 out
of 8 in 8wm1
Go back to
Calcium Binding Sites List in 8wm1
Calcium binding site 6 out
of 8 in the Dhs Dehydratase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Dhs Dehydratase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca502
b:27.0
occ:1.00
|
OE2
|
C:GLU239
|
2.0
|
20.1
|
1.0
|
|
OD1
|
C:ASN121
|
2.2
|
29.2
|
1.0
|
|
OE1
|
C:GLN236
|
2.2
|
29.3
|
1.0
|
|
OD2
|
C:ASP207
|
2.5
|
24.8
|
1.0
|
|
OD1
|
C:ASP207
|
2.7
|
22.8
|
1.0
|
|
CG
|
C:ASP207
|
3.0
|
23.6
|
1.0
|
|
CD
|
C:GLU239
|
3.2
|
19.3
|
1.0
|
|
CG
|
C:ASN121
|
3.4
|
29.0
|
1.0
|
|
CD
|
C:GLN236
|
3.4
|
28.2
|
1.0
|
|
OE1
|
C:GLU239
|
3.7
|
19.7
|
1.0
|
|
CA
|
C:CA501
|
3.8
|
21.9
|
1.0
|
|
O
|
C:THR120
|
4.0
|
29.0
|
1.0
|
|
CB
|
C:ASN121
|
4.1
|
29.1
|
1.0
|
|
CA
|
C:ASN121
|
4.1
|
30.2
|
1.0
|
|
CG
|
C:GLN236
|
4.3
|
26.6
|
1.0
|
|
CB
|
C:SER235
|
4.3
|
26.5
|
1.0
|
|
NE2
|
C:GLN236
|
4.4
|
29.2
|
1.0
|
|
CG
|
C:GLU239
|
4.4
|
19.1
|
1.0
|
|
ND2
|
C:ASN121
|
4.4
|
28.6
|
1.0
|
|
CB
|
C:ASP207
|
4.5
|
23.7
|
1.0
|
|
CB
|
C:GLU239
|
4.6
|
18.6
|
1.0
|
|
C
|
C:THR120
|
4.6
|
30.4
|
1.0
|
|
CB
|
C:GLN236
|
4.6
|
25.5
|
1.0
|
|
N
|
C:ASN121
|
4.7
|
30.1
|
1.0
|
|
CB
|
C:ALA334
|
4.8
|
24.1
|
1.0
|
|
OE1
|
C:GLN261
|
4.8
|
19.3
|
1.0
|
|
CG2
|
C:THR120
|
4.9
|
32.7
|
1.0
|
|
OG1
|
C:THR120
|
4.9
|
32.5
|
1.0
|
|
OG
|
C:SER235
|
5.0
|
27.7
|
1.0
|
|
N
|
C:GLN236
|
5.0
|
25.8
|
1.0
|
|
Calcium binding site 7 out
of 8 in 8wm1
Go back to
Calcium Binding Sites List in 8wm1
Calcium binding site 7 out
of 8 in the Dhs Dehydratase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Dhs Dehydratase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca501
b:35.0
occ:1.00
|
OE1
|
D:GLU210
|
2.1
|
36.3
|
1.0
|
|
O
|
D:THR120
|
2.2
|
50.0
|
1.0
|
|
OD2
|
D:ASP207
|
2.3
|
24.6
|
1.0
|
|
O
|
D:GLY173
|
2.3
|
30.2
|
1.0
|
|
OG1
|
D:THR120
|
3.3
|
52.9
|
1.0
|
|
CD
|
D:GLU210
|
3.3
|
33.5
|
1.0
|
|
C
|
D:THR120
|
3.4
|
47.7
|
1.0
|
|
CG
|
D:ASP207
|
3.4
|
25.7
|
1.0
|
|
C
|
D:GLY173
|
3.4
|
32.4
|
1.0
|
|
CA
|
D:CA502
|
3.9
|
43.5
|
1.0
|
|
CB
|
D:ASP207
|
4.0
|
26.3
|
1.0
|
|
CA
|
D:GLY173
|
4.0
|
34.6
|
1.0
|
|
OE2
|
D:GLU210
|
4.0
|
36.6
|
1.0
|
|
CA
|
D:THR120
|
4.1
|
49.1
|
1.0
|
|
CB
|
D:THR120
|
4.3
|
50.6
|
1.0
|
|
CG
|
D:GLU210
|
4.3
|
31.1
|
1.0
|
|
OD1
|
D:ASP207
|
4.4
|
25.9
|
1.0
|
|
N
|
D:ASN121
|
4.4
|
43.7
|
1.0
|
|
OE2
|
D:GLU239
|
4.5
|
30.7
|
1.0
|
|
N
|
D:ALA174
|
4.6
|
30.9
|
1.0
|
|
CA
|
D:ASN121
|
4.6
|
40.5
|
1.0
|
|
O
|
D:GLY172
|
4.7
|
32.0
|
1.0
|
|
CE
|
D:MET177
|
4.7
|
33.9
|
1.0
|
|
CB
|
D:ALA174
|
4.8
|
30.7
|
1.0
|
|
O
|
D:VAL122
|
4.8
|
36.0
|
1.0
|
|
OD1
|
D:ASN121
|
4.8
|
43.4
|
1.0
|
|
CG2
|
D:THR120
|
5.0
|
50.6
|
1.0
|
|
Calcium binding site 8 out
of 8 in 8wm1
Go back to
Calcium Binding Sites List in 8wm1
Calcium binding site 8 out
of 8 in the Dhs Dehydratase
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Dhs Dehydratase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca502
b:43.5
occ:1.00
|
OE2
|
D:GLU239
|
2.0
|
30.7
|
1.0
|
|
OD1
|
D:ASN121
|
2.3
|
43.4
|
1.0
|
|
OE1
|
D:GLN236
|
2.3
|
32.1
|
1.0
|
|
OD2
|
D:ASP207
|
2.4
|
24.6
|
1.0
|
|
OD1
|
D:ASP207
|
2.7
|
25.9
|
1.0
|
|
CG
|
D:ASP207
|
2.9
|
25.7
|
1.0
|
|
CD
|
D:GLU239
|
3.2
|
31.3
|
1.0
|
|
CG
|
D:ASN121
|
3.4
|
40.1
|
1.0
|
|
CD
|
D:GLN236
|
3.5
|
31.2
|
1.0
|
|
OE1
|
D:GLU239
|
3.7
|
31.9
|
1.0
|
|
CA
|
D:CA501
|
3.9
|
35.0
|
1.0
|
|
O
|
D:THR120
|
4.0
|
50.0
|
1.0
|
|
CA
|
D:ASN121
|
4.2
|
40.5
|
1.0
|
|
CB
|
D:ASN121
|
4.2
|
40.2
|
1.0
|
|
CG
|
D:GLN236
|
4.3
|
30.8
|
1.0
|
|
CG
|
D:GLU239
|
4.4
|
32.0
|
1.0
|
|
CB
|
D:SER235
|
4.4
|
38.7
|
1.0
|
|
NE2
|
D:GLN236
|
4.4
|
30.4
|
1.0
|
|
ND2
|
D:ASN121
|
4.5
|
39.4
|
1.0
|
|
CB
|
D:ASP207
|
4.5
|
26.3
|
1.0
|
|
C
|
D:THR120
|
4.6
|
47.7
|
1.0
|
|
CB
|
D:GLU239
|
4.6
|
30.6
|
1.0
|
|
CB
|
D:GLN236
|
4.6
|
30.6
|
1.0
|
|
N
|
D:ASN121
|
4.7
|
43.7
|
1.0
|
|
CG2
|
D:THR120
|
4.9
|
50.6
|
1.0
|
|
OG1
|
D:THR120
|
4.9
|
52.9
|
1.0
|
|
CB
|
D:ALA334
|
4.9
|
40.2
|
1.0
|
|
OE1
|
D:GLN261
|
4.9
|
24.7
|
1.0
|
|
N
|
D:GLN236
|
5.0
|
31.5
|
1.0
|
|
Reference:
M.Wang,
M.Wang.
N/A N/A.
Page generated: Thu Jul 10 08:12:43 2025
|
