Calcium in PDB 5oyh: Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
Protein crystallography data
The structure of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas, PDB code: 5oyh
was solved by
M.Broser,
U.Scheib,
P.Hegemann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
45.90 /
2.25
|
|
Space group
|
I 41 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
193.283,
193.283,
225.501,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18.2 /
22.4
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
(pdb code 5oyh). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the
Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas, PDB code: 5oyh:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 16 in 5oyh
Go back to
Calcium Binding Sites List in 5oyh
Calcium binding site 1 out
of 16 in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca702
b:34.0
occ:1.00
|
OD2
|
A:ASP457
|
2.2
|
36.8
|
1.0
|
|
O2B
|
A:T99701
|
2.4
|
33.3
|
1.0
|
|
O
|
A:ILE458
|
2.4
|
22.6
|
1.0
|
|
O3G
|
A:T99701
|
2.4
|
54.8
|
1.0
|
|
OD2
|
A:ASP501
|
2.4
|
35.7
|
1.0
|
|
O
|
A:HOH803
|
2.7
|
41.2
|
1.0
|
|
CG
|
A:ASP457
|
3.3
|
33.9
|
1.0
|
|
PB
|
A:T99701
|
3.5
|
33.5
|
1.0
|
|
C
|
A:ILE458
|
3.6
|
27.1
|
1.0
|
|
PG
|
A:T99701
|
3.6
|
44.0
|
1.0
|
|
CG
|
A:ASP501
|
3.6
|
30.8
|
1.0
|
|
O3B
|
A:T99701
|
3.7
|
40.4
|
1.0
|
|
CB
|
A:PHE461
|
3.9
|
18.7
|
1.0
|
|
CB
|
A:ASP457
|
4.0
|
28.0
|
1.0
|
|
N
|
A:ILE458
|
4.1
|
31.5
|
1.0
|
|
NH1
|
A:ARG545
|
4.1
|
46.0
|
1.0
|
|
O1A
|
A:T99701
|
4.2
|
38.1
|
1.0
|
|
O2A
|
A:T99701
|
4.2
|
59.6
|
1.0
|
|
O
|
A:HOH809
|
4.2
|
50.2
|
1.0
|
|
OD1
|
A:ASP501
|
4.3
|
37.6
|
1.0
|
|
OD1
|
A:ASP457
|
4.3
|
39.0
|
1.0
|
|
O3A
|
A:T99701
|
4.3
|
51.3
|
1.0
|
|
N
|
A:PHE461
|
4.4
|
27.5
|
1.0
|
|
CA
|
A:ILE458
|
4.4
|
28.5
|
1.0
|
|
N
|
A:THR459
|
4.4
|
29.5
|
1.0
|
|
CA
|
A:THR459
|
4.5
|
31.3
|
1.0
|
|
C
|
A:ASP457
|
4.5
|
28.6
|
1.0
|
|
PA
|
A:T99701
|
4.7
|
59.0
|
1.0
|
|
CB
|
A:ASP501
|
4.8
|
22.8
|
1.0
|
|
N
|
A:ASN460
|
4.8
|
30.8
|
1.0
|
|
O1B
|
A:T99701
|
4.8
|
34.8
|
1.0
|
|
O5'
|
A:T99701
|
4.8
|
56.2
|
1.0
|
|
CA
|
A:PHE461
|
4.8
|
23.4
|
1.0
|
|
C
|
A:THR459
|
4.8
|
35.9
|
1.0
|
|
CA
|
A:ASP457
|
4.9
|
26.1
|
1.0
|
|
O2G
|
A:T99701
|
4.9
|
42.4
|
1.0
|
|
CG
|
A:PHE461
|
4.9
|
19.6
|
1.0
|
|
C3'
|
A:T99701
|
4.9
|
40.9
|
1.0
|
|
Calcium binding site 2 out
of 16 in 5oyh
Go back to
Calcium Binding Sites List in 5oyh
Calcium binding site 2 out
of 16 in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca702
b:38.2
occ:1.00
|
OD2
|
B:ASP457
|
2.1
|
42.3
|
1.0
|
|
O3G
|
B:T99701
|
2.3
|
52.6
|
1.0
|
|
O
|
B:ILE458
|
2.3
|
23.6
|
1.0
|
|
O1B
|
B:T99701
|
2.4
|
39.5
|
1.0
|
|
OD2
|
B:ASP501
|
2.5
|
40.0
|
1.0
|
|
O
|
B:HOH804
|
2.5
|
42.4
|
1.0
|
|
CG
|
B:ASP457
|
3.4
|
33.3
|
1.0
|
|
C
|
B:ILE458
|
3.5
|
23.3
|
1.0
|
|
PB
|
B:T99701
|
3.6
|
42.8
|
1.0
|
|
PG
|
B:T99701
|
3.6
|
48.2
|
1.0
|
|
CG
|
B:ASP501
|
3.6
|
40.0
|
1.0
|
|
O3B
|
B:T99701
|
3.8
|
45.5
|
1.0
|
|
CB
|
B:PHE461
|
3.9
|
30.4
|
1.0
|
|
O
|
B:HOH843
|
4.0
|
57.2
|
1.0
|
|
N
|
B:ILE458
|
4.0
|
22.3
|
1.0
|
|
NH1
|
B:ARG545
|
4.1
|
40.5
|
1.0
|
|
CB
|
B:ASP457
|
4.1
|
19.5
|
1.0
|
|
OD1
|
B:ASP501
|
4.2
|
42.2
|
1.0
|
|
O2G
|
B:T99701
|
4.2
|
44.4
|
1.0
|
|
OD1
|
B:ASP457
|
4.2
|
40.5
|
1.0
|
|
O2A
|
B:T99701
|
4.2
|
72.4
|
1.0
|
|
CA
|
B:ILE458
|
4.3
|
21.7
|
1.0
|
|
N
|
B:THR459
|
4.4
|
23.2
|
1.0
|
|
N
|
B:PHE461
|
4.4
|
29.2
|
1.0
|
|
CA
|
B:THR459
|
4.4
|
25.2
|
1.0
|
|
O3A
|
B:T99701
|
4.5
|
62.1
|
1.0
|
|
C
|
B:ASP457
|
4.5
|
22.0
|
1.0
|
|
O2B
|
B:T99701
|
4.7
|
43.2
|
1.0
|
|
N
|
B:ASN460
|
4.7
|
33.0
|
1.0
|
|
C
|
B:THR459
|
4.8
|
32.2
|
1.0
|
|
O1A
|
B:T99701
|
4.8
|
47.7
|
1.0
|
|
CA
|
B:PHE461
|
4.8
|
29.1
|
1.0
|
|
CB
|
B:ASP501
|
4.8
|
36.0
|
1.0
|
|
PA
|
B:T99701
|
4.8
|
69.2
|
1.0
|
|
O3'
|
B:T99701
|
4.9
|
59.6
|
1.0
|
|
CG
|
B:PHE461
|
4.9
|
32.0
|
1.0
|
|
C3'
|
B:T99701
|
4.9
|
56.4
|
1.0
|
|
CB
|
B:ILE458
|
4.9
|
22.2
|
1.0
|
|
CA
|
B:ASP457
|
5.0
|
19.9
|
1.0
|
|
Calcium binding site 3 out
of 16 in 5oyh
Go back to
Calcium Binding Sites List in 5oyh
Calcium binding site 3 out
of 16 in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca703
b:37.5
occ:1.00
|
OD1
|
C:ASP457
|
2.2
|
47.0
|
1.0
|
|
O3G
|
C:T99702
|
2.3
|
54.2
|
1.0
|
|
O
|
C:ILE458
|
2.5
|
21.4
|
1.0
|
|
O1B
|
C:T99702
|
2.5
|
53.1
|
1.0
|
|
OD2
|
C:ASP501
|
2.5
|
38.1
|
1.0
|
|
O
|
C:HOH883
|
3.0
|
61.5
|
1.0
|
|
CG
|
C:ASP457
|
3.3
|
36.5
|
1.0
|
|
C
|
C:ILE458
|
3.6
|
21.1
|
1.0
|
|
PB
|
C:T99702
|
3.6
|
45.9
|
1.0
|
|
PG
|
C:T99702
|
3.6
|
55.3
|
1.0
|
|
CG
|
C:ASP501
|
3.8
|
35.4
|
1.0
|
|
O3B
|
C:T99702
|
3.8
|
48.2
|
1.0
|
|
CB
|
C:PHE461
|
3.8
|
19.9
|
1.0
|
|
O
|
C:HOH823
|
3.9
|
65.2
|
1.0
|
|
CB
|
C:ASP457
|
4.0
|
24.8
|
1.0
|
|
N
|
C:ILE458
|
4.1
|
22.2
|
1.0
|
|
OD2
|
C:ASP457
|
4.2
|
41.7
|
1.0
|
|
O2G
|
C:T99702
|
4.3
|
48.1
|
1.0
|
|
N
|
C:PHE461
|
4.4
|
24.6
|
1.0
|
|
OD1
|
C:ASP501
|
4.4
|
42.9
|
1.0
|
|
CA
|
C:ILE458
|
4.4
|
20.3
|
1.0
|
|
N
|
C:THR459
|
4.5
|
23.1
|
1.0
|
|
CA
|
C:THR459
|
4.5
|
26.8
|
1.0
|
|
O3A
|
C:T99702
|
4.5
|
69.2
|
1.0
|
|
C
|
C:ASP457
|
4.5
|
21.8
|
1.0
|
|
O2A
|
C:T99702
|
4.6
|
80.7
|
1.0
|
|
NH1
|
C:ARG545
|
4.6
|
56.9
|
1.0
|
|
O2B
|
C:T99702
|
4.7
|
34.4
|
1.0
|
|
CA
|
C:PHE461
|
4.7
|
21.4
|
1.0
|
|
O1A
|
C:T99702
|
4.8
|
64.5
|
1.0
|
|
CG
|
C:PHE461
|
4.8
|
19.6
|
1.0
|
|
N
|
C:ASN460
|
4.8
|
24.5
|
1.0
|
|
CB
|
C:ASP501
|
4.9
|
27.6
|
1.0
|
|
C
|
C:THR459
|
4.9
|
28.0
|
1.0
|
|
O5'
|
C:T99702
|
4.9
|
67.7
|
1.0
|
|
PA
|
C:T99702
|
4.9
|
78.9
|
1.0
|
|
O3'
|
C:T99702
|
4.9
|
51.9
|
1.0
|
|
CA
|
C:ASP457
|
4.9
|
21.0
|
1.0
|
|
Calcium binding site 4 out
of 16 in 5oyh
Go back to
Calcium Binding Sites List in 5oyh
Calcium binding site 4 out
of 16 in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca703
b:27.9
occ:1.00
|
OD2
|
D:ASP457
|
2.2
|
35.4
|
1.0
|
|
O
|
D:ILE458
|
2.3
|
19.4
|
1.0
|
|
O3G
|
D:T99701
|
2.4
|
52.9
|
1.0
|
|
OD2
|
D:ASP501
|
2.4
|
26.6
|
1.0
|
|
O
|
D:HOH806
|
2.4
|
44.7
|
1.0
|
|
O2B
|
D:T99701
|
2.5
|
39.5
|
1.0
|
|
CG
|
D:ASP457
|
3.4
|
32.2
|
1.0
|
|
C
|
D:ILE458
|
3.5
|
18.4
|
1.0
|
|
CG
|
D:ASP501
|
3.6
|
24.0
|
1.0
|
|
PB
|
D:T99701
|
3.6
|
39.0
|
1.0
|
|
PG
|
D:T99701
|
3.7
|
47.0
|
1.0
|
|
CB
|
D:PHE461
|
3.9
|
20.2
|
1.0
|
|
O3B
|
D:T99701
|
3.9
|
42.1
|
1.0
|
|
CB
|
D:ASP457
|
4.0
|
21.2
|
1.0
|
|
N
|
D:ILE458
|
4.0
|
16.3
|
1.0
|
|
OD1
|
D:ASP501
|
4.1
|
27.8
|
1.0
|
|
O
|
D:HOH875
|
4.1
|
41.9
|
1.0
|
|
O2A
|
D:T99701
|
4.2
|
69.5
|
1.0
|
|
CA
|
D:ILE458
|
4.3
|
16.9
|
1.0
|
|
OD1
|
D:ASP457
|
4.4
|
41.9
|
1.0
|
|
NH1
|
D:ARG545
|
4.4
|
41.8
|
1.0
|
|
N
|
D:THR459
|
4.4
|
17.8
|
1.0
|
|
CA
|
D:THR459
|
4.4
|
25.6
|
1.0
|
|
O1A
|
D:T99701
|
4.4
|
43.2
|
1.0
|
|
N
|
D:PHE461
|
4.5
|
21.4
|
1.0
|
|
C
|
D:ASP457
|
4.5
|
16.5
|
1.0
|
|
O3A
|
D:T99701
|
4.5
|
57.9
|
1.0
|
|
O5'
|
D:T99701
|
4.7
|
59.6
|
1.0
|
|
CB
|
D:ASP501
|
4.7
|
22.2
|
1.0
|
|
PA
|
D:T99701
|
4.7
|
65.9
|
1.0
|
|
N
|
D:ASN460
|
4.8
|
25.4
|
1.0
|
|
O1B
|
D:T99701
|
4.8
|
40.6
|
1.0
|
|
C
|
D:THR459
|
4.8
|
25.6
|
1.0
|
|
CA
|
D:PHE461
|
4.8
|
20.6
|
1.0
|
|
O2G
|
D:T99701
|
4.9
|
49.1
|
1.0
|
|
CG
|
D:PHE461
|
4.9
|
22.7
|
1.0
|
|
CA
|
D:ASP457
|
4.9
|
16.5
|
1.0
|
|
C3'
|
D:T99701
|
4.9
|
46.7
|
1.0
|
|
CB
|
D:ILE458
|
4.9
|
19.7
|
1.0
|
|
Calcium binding site 5 out
of 16 in 5oyh
Go back to
Calcium Binding Sites List in 5oyh
Calcium binding site 5 out
of 16 in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca702
b:38.8
occ:1.00
|
OD1
|
E:ASP457
|
2.1
|
44.5
|
1.0
|
|
O3G
|
E:T99701
|
2.2
|
58.2
|
1.0
|
|
O1B
|
E:T99701
|
2.4
|
45.8
|
1.0
|
|
OD2
|
E:ASP501
|
2.5
|
45.0
|
1.0
|
|
O
|
E:ILE458
|
2.5
|
26.2
|
1.0
|
|
O
|
E:HOH851
|
2.8
|
56.8
|
1.0
|
|
CG
|
E:ASP457
|
3.2
|
35.6
|
1.0
|
|
PB
|
E:T99701
|
3.5
|
43.7
|
1.0
|
|
PG
|
E:T99701
|
3.6
|
54.9
|
1.0
|
|
C
|
E:ILE458
|
3.6
|
25.6
|
1.0
|
|
O3B
|
E:T99701
|
3.6
|
45.1
|
1.0
|
|
CG
|
E:ASP501
|
3.7
|
42.8
|
1.0
|
|
CB
|
E:PHE461
|
4.0
|
25.0
|
1.0
|
|
CB
|
E:ASP457
|
4.0
|
24.1
|
1.0
|
|
N
|
E:ILE458
|
4.1
|
23.8
|
1.0
|
|
OD2
|
E:ASP457
|
4.1
|
43.4
|
1.0
|
|
O
|
E:HOH844
|
4.2
|
61.0
|
1.0
|
|
O2A
|
E:T99701
|
4.3
|
76.3
|
1.0
|
|
NH1
|
E:ARG545
|
4.3
|
51.0
|
1.0
|
|
O2G
|
E:T99701
|
4.3
|
46.0
|
1.0
|
|
OD1
|
E:ASP501
|
4.3
|
49.6
|
1.0
|
|
O3A
|
E:T99701
|
4.4
|
64.4
|
1.0
|
|
CA
|
E:ILE458
|
4.5
|
22.5
|
1.0
|
|
N
|
E:PHE461
|
4.5
|
27.3
|
1.0
|
|
N
|
E:THR459
|
4.5
|
27.6
|
1.0
|
|
CA
|
E:THR459
|
4.5
|
34.3
|
1.0
|
|
C
|
E:ASP457
|
4.6
|
24.2
|
1.0
|
|
O2B
|
E:T99701
|
4.6
|
40.0
|
1.0
|
|
O1A
|
E:T99701
|
4.7
|
61.8
|
1.0
|
|
PA
|
E:T99701
|
4.7
|
71.1
|
1.0
|
|
O5'
|
E:T99701
|
4.8
|
67.4
|
1.0
|
|
CB
|
E:ASP501
|
4.8
|
32.7
|
1.0
|
|
N
|
E:ASN460
|
4.8
|
31.0
|
1.0
|
|
O3'
|
E:T99701
|
4.9
|
42.7
|
1.0
|
|
CA
|
E:PHE461
|
4.9
|
25.2
|
1.0
|
|
CA
|
E:ASP457
|
4.9
|
23.3
|
1.0
|
|
C3'
|
E:T99701
|
4.9
|
47.3
|
1.0
|
|
C
|
E:THR459
|
4.9
|
39.0
|
1.0
|
|
Calcium binding site 6 out
of 16 in 5oyh
Go back to
Calcium Binding Sites List in 5oyh
Calcium binding site 6 out
of 16 in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca704
b:40.8
occ:1.00
|
OD2
|
F:ASP457
|
2.1
|
41.6
|
1.0
|
|
O2G
|
F:T99702
|
2.2
|
61.3
|
1.0
|
|
OD2
|
F:ASP501
|
2.4
|
36.2
|
1.0
|
|
O
|
F:ILE458
|
2.4
|
31.1
|
1.0
|
|
O2B
|
F:T99702
|
2.4
|
47.8
|
1.0
|
|
O
|
F:HOH806
|
2.6
|
62.9
|
1.0
|
|
CG
|
F:ASP457
|
3.4
|
32.7
|
1.0
|
|
C
|
F:ILE458
|
3.6
|
25.3
|
1.0
|
|
PG
|
F:T99702
|
3.6
|
60.2
|
1.0
|
|
CG
|
F:ASP501
|
3.6
|
32.0
|
1.0
|
|
PB
|
F:T99702
|
3.6
|
53.6
|
1.0
|
|
CB
|
F:PHE461
|
3.9
|
30.6
|
1.0
|
|
O3B
|
F:T99702
|
3.9
|
56.3
|
1.0
|
|
N
|
F:ILE458
|
4.1
|
28.4
|
1.0
|
|
O
|
F:HOH834
|
4.1
|
48.2
|
1.0
|
|
OD1
|
F:ASP501
|
4.1
|
38.1
|
1.0
|
|
CB
|
F:ASP457
|
4.1
|
23.3
|
1.0
|
|
O2A
|
F:T99702
|
4.2
|
77.3
|
1.0
|
|
OD1
|
F:ASP457
|
4.3
|
35.6
|
1.0
|
|
NH1
|
F:ARG545
|
4.3
|
52.5
|
1.0
|
|
O1A
|
F:T99702
|
4.3
|
54.7
|
1.0
|
|
CA
|
F:ILE458
|
4.4
|
27.8
|
1.0
|
|
O3A
|
F:T99702
|
4.4
|
71.3
|
1.0
|
|
N
|
F:PHE461
|
4.4
|
29.6
|
1.0
|
|
N
|
F:THR459
|
4.5
|
30.9
|
1.0
|
|
CA
|
F:THR459
|
4.5
|
35.5
|
1.0
|
|
C
|
F:ASP457
|
4.6
|
28.2
|
1.0
|
|
PA
|
F:T99702
|
4.6
|
74.3
|
1.0
|
|
O3G
|
F:T99702
|
4.7
|
63.8
|
1.0
|
|
O5'
|
F:T99702
|
4.7
|
69.0
|
1.0
|
|
O3'
|
F:T99702
|
4.8
|
49.5
|
1.0
|
|
CB
|
F:ASP501
|
4.8
|
26.5
|
1.0
|
|
N
|
F:ASN460
|
4.8
|
35.3
|
1.0
|
|
CA
|
F:PHE461
|
4.8
|
29.9
|
1.0
|
|
O1B
|
F:T99702
|
4.8
|
53.5
|
1.0
|
|
C3'
|
F:T99702
|
4.9
|
56.7
|
1.0
|
|
CG
|
F:PHE461
|
4.9
|
32.2
|
1.0
|
|
C
|
F:THR459
|
4.9
|
38.6
|
1.0
|
|
CB
|
F:ILE458
|
5.0
|
26.8
|
1.0
|
|
CA
|
F:ASP457
|
5.0
|
22.9
|
1.0
|
|
Calcium binding site 7 out
of 16 in 5oyh
Go back to
Calcium Binding Sites List in 5oyh
Calcium binding site 7 out
of 16 in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca702
b:35.7
occ:1.00
|
O3G
|
G:T99701
|
2.2
|
65.7
|
1.0
|
|
OD1
|
G:ASP457
|
2.2
|
44.8
|
1.0
|
|
O2B
|
G:T99701
|
2.4
|
52.3
|
1.0
|
|
O
|
G:ILE458
|
2.4
|
29.6
|
1.0
|
|
OD2
|
G:ASP501
|
2.5
|
32.4
|
1.0
|
|
O
|
G:HOH817
|
2.8
|
43.5
|
1.0
|
|
CG
|
G:ASP457
|
3.3
|
38.4
|
1.0
|
|
PG
|
G:T99701
|
3.5
|
57.1
|
1.0
|
|
C
|
G:ILE458
|
3.6
|
26.9
|
1.0
|
|
PB
|
G:T99701
|
3.6
|
49.1
|
1.0
|
|
CG
|
G:ASP501
|
3.7
|
29.7
|
1.0
|
|
O3B
|
G:T99701
|
3.8
|
50.8
|
1.0
|
|
CB
|
G:PHE461
|
3.8
|
22.6
|
1.0
|
|
O
|
G:HOH815
|
3.9
|
59.7
|
1.0
|
|
CB
|
G:ASP457
|
4.0
|
26.3
|
1.0
|
|
N
|
G:ILE458
|
4.1
|
26.4
|
1.0
|
|
NH1
|
G:ARG545
|
4.2
|
56.6
|
1.0
|
|
OD2
|
G:ASP457
|
4.3
|
42.4
|
1.0
|
|
OD1
|
G:ASP501
|
4.3
|
34.2
|
1.0
|
|
O1A
|
G:T99701
|
4.3
|
43.6
|
1.0
|
|
N
|
G:PHE461
|
4.3
|
31.6
|
1.0
|
|
CA
|
G:ILE458
|
4.4
|
24.2
|
1.0
|
|
O3A
|
G:T99701
|
4.4
|
70.1
|
1.0
|
|
N
|
G:THR459
|
4.4
|
26.3
|
1.0
|
|
O2A
|
G:T99701
|
4.5
|
83.4
|
1.0
|
|
CA
|
G:THR459
|
4.5
|
28.3
|
1.0
|
|
C
|
G:ASP457
|
4.6
|
21.9
|
1.0
|
|
O2G
|
G:T99701
|
4.6
|
62.4
|
1.0
|
|
N
|
G:ASN460
|
4.7
|
26.6
|
1.0
|
|
CA
|
G:PHE461
|
4.7
|
26.9
|
1.0
|
|
O1B
|
G:T99701
|
4.8
|
41.6
|
1.0
|
|
PA
|
G:T99701
|
4.8
|
78.7
|
1.0
|
|
O5'
|
G:T99701
|
4.8
|
65.7
|
1.0
|
|
CG
|
G:PHE461
|
4.8
|
21.8
|
1.0
|
|
C
|
G:THR459
|
4.8
|
32.0
|
1.0
|
|
CA
|
G:ASP457
|
4.9
|
21.3
|
1.0
|
|
O3'
|
G:T99701
|
4.9
|
57.5
|
1.0
|
|
CB
|
G:ASP501
|
4.9
|
24.6
|
1.0
|
|
Calcium binding site 8 out
of 16 in 5oyh
Go back to
Calcium Binding Sites List in 5oyh
Calcium binding site 8 out
of 16 in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca702
b:29.5
occ:1.00
|
OD2
|
H:ASP457
|
2.2
|
29.6
|
1.0
|
|
O2G
|
H:T99701
|
2.3
|
54.2
|
1.0
|
|
O
|
H:ILE458
|
2.3
|
20.0
|
1.0
|
|
O1B
|
H:T99701
|
2.4
|
45.1
|
1.0
|
|
O
|
H:HOH804
|
2.6
|
46.8
|
1.0
|
|
OD2
|
H:ASP501
|
2.6
|
33.1
|
1.0
|
|
CG
|
H:ASP457
|
3.4
|
23.5
|
1.0
|
|
C
|
H:ILE458
|
3.5
|
17.2
|
1.0
|
|
PB
|
H:T99701
|
3.5
|
39.1
|
1.0
|
|
PG
|
H:T99701
|
3.5
|
48.7
|
1.0
|
|
CG
|
H:ASP501
|
3.7
|
28.8
|
1.0
|
|
O3B
|
H:T99701
|
3.8
|
41.4
|
1.0
|
|
CB
|
H:PHE461
|
3.9
|
28.6
|
1.0
|
|
N
|
H:ILE458
|
4.0
|
17.7
|
1.0
|
|
O
|
H:HOH809
|
4.0
|
51.1
|
1.0
|
|
CB
|
H:ASP457
|
4.1
|
18.0
|
1.0
|
|
O2A
|
H:T99701
|
4.1
|
85.8
|
1.0
|
|
NH1
|
H:ARG545
|
4.2
|
48.4
|
1.0
|
|
OD1
|
H:ASP501
|
4.2
|
34.1
|
1.0
|
|
OD1
|
H:ASP457
|
4.3
|
30.6
|
1.0
|
|
O3G
|
H:T99701
|
4.3
|
33.4
|
1.0
|
|
CA
|
H:ILE458
|
4.3
|
16.2
|
1.0
|
|
O3A
|
H:T99701
|
4.4
|
66.3
|
1.0
|
|
N
|
H:PHE461
|
4.4
|
23.4
|
1.0
|
|
O
|
H:HOH820
|
4.4
|
58.3
|
1.0
|
|
N
|
H:THR459
|
4.4
|
19.5
|
1.0
|
|
CA
|
H:THR459
|
4.5
|
23.2
|
1.0
|
|
C
|
H:ASP457
|
4.5
|
19.3
|
1.0
|
|
PA
|
H:T99701
|
4.7
|
76.5
|
1.0
|
|
O1A
|
H:T99701
|
4.7
|
60.9
|
1.0
|
|
N
|
H:ASN460
|
4.7
|
22.4
|
1.0
|
|
O2B
|
H:T99701
|
4.8
|
32.6
|
1.0
|
|
O5'
|
H:T99701
|
4.8
|
60.9
|
1.0
|
|
C
|
H:THR459
|
4.8
|
26.5
|
1.0
|
|
CA
|
H:PHE461
|
4.8
|
27.2
|
1.0
|
|
C3'
|
H:T99701
|
4.8
|
57.9
|
1.0
|
|
O3'
|
H:T99701
|
4.9
|
61.4
|
1.0
|
|
CG
|
H:PHE461
|
4.9
|
28.8
|
1.0
|
|
CA
|
H:ASP457
|
4.9
|
17.2
|
1.0
|
|
CB
|
H:ILE458
|
5.0
|
18.4
|
1.0
|
|
CB
|
H:ASP501
|
5.0
|
22.1
|
1.0
|
|
Calcium binding site 9 out
of 16 in 5oyh
Go back to
Calcium Binding Sites List in 5oyh
Calcium binding site 9 out
of 16 in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca703
b:46.6
occ:1.00
|
OD2
|
I:ASP457
|
2.2
|
43.0
|
1.0
|
|
O3G
|
I:T99702
|
2.2
|
76.4
|
1.0
|
|
O1B
|
I:T99702
|
2.3
|
54.9
|
1.0
|
|
OD2
|
I:ASP501
|
2.5
|
48.9
|
1.0
|
|
O
|
I:ILE458
|
2.5
|
28.7
|
1.0
|
|
O
|
I:HOH825
|
3.1
|
59.2
|
1.0
|
|
CG
|
I:ASP457
|
3.3
|
38.2
|
1.0
|
|
CG
|
I:ASP501
|
3.6
|
41.4
|
1.0
|
|
PB
|
I:T99702
|
3.6
|
59.8
|
1.0
|
|
C
|
I:ILE458
|
3.6
|
30.0
|
1.0
|
|
PG
|
I:T99702
|
3.7
|
70.5
|
1.0
|
|
CB
|
I:PHE461
|
3.8
|
29.1
|
1.0
|
|
O3B
|
I:T99702
|
4.0
|
61.6
|
1.0
|
|
CB
|
I:ASP457
|
4.0
|
28.4
|
1.0
|
|
N
|
I:ILE458
|
4.0
|
33.4
|
1.0
|
|
OD1
|
I:ASP501
|
4.1
|
45.0
|
1.0
|
|
NH2
|
I:ARG545
|
4.1
|
69.9
|
1.0
|
|
OD1
|
I:ASP457
|
4.3
|
46.0
|
1.0
|
|
O3A
|
I:T99702
|
4.4
|
81.6
|
1.0
|
|
CA
|
I:ILE458
|
4.4
|
30.1
|
1.0
|
|
N
|
I:PHE461
|
4.4
|
29.1
|
1.0
|
|
O2G
|
I:T99702
|
4.5
|
64.1
|
1.0
|
|
N
|
I:THR459
|
4.5
|
33.2
|
1.0
|
|
O2A
|
I:T99702
|
4.5
|
90.2
|
1.0
|
|
C
|
I:ASP457
|
4.5
|
33.6
|
1.0
|
|
CA
|
I:THR459
|
4.6
|
37.6
|
1.0
|
|
O1A
|
I:T99702
|
4.7
|
74.2
|
1.0
|
|
O2B
|
I:T99702
|
4.8
|
54.4
|
1.0
|
|
CG
|
I:PHE461
|
4.8
|
30.1
|
1.0
|
|
CA
|
I:PHE461
|
4.8
|
29.5
|
1.0
|
|
PA
|
I:T99702
|
4.8
|
88.2
|
1.0
|
|
O5'
|
I:T99702
|
4.8
|
81.9
|
1.0
|
|
CB
|
I:ASP501
|
4.8
|
32.3
|
1.0
|
|
N
|
I:ASN460
|
4.9
|
37.8
|
1.0
|
|
O3'
|
I:T99702
|
4.9
|
68.6
|
1.0
|
|
CA
|
I:ASP457
|
4.9
|
30.1
|
1.0
|
|
CZ
|
I:ARG545
|
5.0
|
66.2
|
1.0
|
|
Calcium binding site 10 out
of 16 in 5oyh
Go back to
Calcium Binding Sites List in 5oyh
Calcium binding site 10 out
of 16 in the Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of the Catalytic Core of A Rhodopsin-Guanylyl Cyclase with Converted Specificity in Complex with Atpalphas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Ca704
b:39.0
occ:1.00
|
OD2
|
J:ASP457
|
2.2
|
38.9
|
1.0
|
|
O3G
|
J:T99703
|
2.3
|
57.8
|
1.0
|
|
O2B
|
J:T99703
|
2.4
|
57.7
|
1.0
|
|
O
|
J:ILE458
|
2.5
|
29.0
|
1.0
|
|
OD2
|
J:ASP501
|
2.6
|
49.1
|
1.0
|
|
O
|
J:HOH833
|
3.2
|
64.4
|
1.0
|
|
CG
|
J:ASP457
|
3.3
|
40.0
|
1.0
|
|
C
|
J:ILE458
|
3.6
|
25.3
|
1.0
|
|
PB
|
J:T99703
|
3.7
|
58.7
|
1.0
|
|
PG
|
J:T99703
|
3.7
|
54.8
|
1.0
|
|
CG
|
J:ASP501
|
3.8
|
42.7
|
1.0
|
|
CB
|
J:PHE461
|
3.8
|
31.6
|
1.0
|
|
O3B
|
J:T99703
|
4.0
|
51.1
|
1.0
|
|
CB
|
J:ASP457
|
4.0
|
28.9
|
1.0
|
|
OD1
|
J:ASP501
|
4.2
|
45.5
|
1.0
|
|
N
|
J:ILE458
|
4.2
|
24.3
|
1.0
|
|
O3A
|
J:T99703
|
4.3
|
80.1
|
1.0
|
|
OD1
|
J:ASP457
|
4.3
|
47.4
|
1.0
|
|
O2A
|
J:T99703
|
4.4
|
94.5
|
1.0
|
|
N
|
J:PHE461
|
4.4
|
32.5
|
1.0
|
|
CA
|
J:ILE458
|
4.5
|
22.7
|
1.0
|
|
O5'
|
J:T99703
|
4.5
|
90.4
|
1.0
|
|
O1A
|
J:T99703
|
4.5
|
48.5
|
1.0
|
|
N
|
J:THR459
|
4.6
|
27.5
|
1.0
|
|
C
|
J:ASP457
|
4.6
|
24.1
|
1.0
|
|
NH2
|
J:ARG545
|
4.6
|
64.3
|
1.0
|
|
CA
|
J:THR459
|
4.6
|
32.4
|
1.0
|
|
PA
|
J:T99703
|
4.6
|
92.8
|
1.0
|
|
C3'
|
J:T99703
|
4.8
|
87.0
|
1.0
|
|
CA
|
J:PHE461
|
4.8
|
31.5
|
1.0
|
|
O2G
|
J:T99703
|
4.8
|
58.2
|
1.0
|
|
CG
|
J:PHE461
|
4.8
|
32.4
|
1.0
|
|
NH1
|
J:ARG545
|
4.9
|
61.5
|
1.0
|
|
O3'
|
J:T99703
|
4.9
|
87.3
|
1.0
|
|
N
|
J:ASN460
|
4.9
|
33.8
|
1.0
|
|
O1B
|
J:T99703
|
4.9
|
54.2
|
1.0
|
|
CA
|
J:ASP457
|
4.9
|
25.6
|
1.0
|
|
C
|
J:THR459
|
5.0
|
33.6
|
1.0
|
|
Reference:
U.Scheib,
M.Broser,
O.M.Constantin,
S.Yang,
S.Gao,
S.Mukherjee,
K.Stehfest,
G.Nagel,
C.E.Gee,
P.Hegemann.
Rhodopsin-Cyclases For Photocontrol of Cgmp/Camp and 2.3 Angstrom Structure of the Adenylyl Cyclase Domain. Nat Commun V. 9 2046 2018.
ISSN: ESSN 2041-1723
PubMed: 29799525
DOI: 10.1038/S41467-018-04428-W
Page generated: Sat Dec 12 05:42:01 2020
|
