Calcium in PDB 1sds: Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Protein crystallography data
The structure of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna, PDB code: 1sds
was solved by
T.Hamma,
A.Ferre-D'amare,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.48 /
1.80
|
Space group
|
F 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.970,
141.300,
162.870,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.7 /
22.5
|
Other elements in 1sds:
The structure of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
(pdb code 1sds). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna, PDB code: 1sds:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 1sds
Go back to
Calcium Binding Sites List in 1sds
Calcium binding site 1 out
of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca755
b:36.5
occ:1.00
|
O
|
D:HOH987
|
2.3
|
41.2
|
1.0
|
OP2
|
D:U206
|
2.3
|
33.0
|
1.0
|
O6
|
D:G208
|
2.3
|
31.5
|
1.0
|
O
|
D:HOH886
|
2.4
|
31.4
|
1.0
|
O
|
D:HOH986
|
2.4
|
40.8
|
1.0
|
O
|
D:HOH1030
|
2.4
|
54.9
|
1.0
|
C6
|
D:G208
|
3.4
|
27.9
|
1.0
|
P
|
D:U206
|
3.7
|
31.4
|
1.0
|
CA
|
D:CA756
|
3.9
|
34.7
|
1.0
|
N7
|
D:G208
|
4.1
|
27.4
|
1.0
|
C5
|
D:G208
|
4.1
|
27.6
|
1.0
|
O
|
A:HOH950
|
4.3
|
31.8
|
1.0
|
OP2
|
D:U207
|
4.4
|
33.5
|
1.0
|
O5'
|
D:U206
|
4.4
|
31.6
|
1.0
|
O
|
D:HOH1031
|
4.4
|
52.9
|
1.0
|
C5'
|
D:U206
|
4.4
|
31.2
|
1.0
|
O3'
|
D:A205
|
4.5
|
28.8
|
1.0
|
N1
|
D:G208
|
4.6
|
28.2
|
1.0
|
C5
|
D:U207
|
4.6
|
25.8
|
1.0
|
OP1
|
D:U206
|
4.6
|
31.0
|
1.0
|
O4
|
D:U207
|
4.9
|
27.6
|
1.0
|
|
Calcium binding site 2 out
of 10 in 1sds
Go back to
Calcium Binding Sites List in 1sds
Calcium binding site 2 out
of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca756
b:34.7
occ:1.00
|
O2'
|
D:A205
|
2.6
|
29.8
|
1.0
|
O4
|
D:U207
|
2.8
|
27.6
|
1.0
|
O
|
D:HOH987
|
3.0
|
41.2
|
1.0
|
O
|
D:HOH1033
|
3.0
|
59.5
|
1.0
|
O6
|
D:G208
|
3.1
|
31.5
|
1.0
|
OP2
|
D:U206
|
3.2
|
33.0
|
1.0
|
O3'
|
D:A205
|
3.2
|
28.8
|
1.0
|
O
|
D:HOH996
|
3.3
|
39.8
|
1.0
|
P
|
D:U206
|
3.7
|
31.4
|
1.0
|
C4
|
D:U207
|
3.7
|
28.3
|
1.0
|
C2'
|
D:A205
|
3.7
|
28.5
|
1.0
|
C6
|
D:G208
|
3.7
|
27.9
|
1.0
|
CA
|
D:CA755
|
3.9
|
36.5
|
1.0
|
N1
|
D:G208
|
3.9
|
28.2
|
1.0
|
C3'
|
D:A205
|
4.0
|
27.3
|
1.0
|
C5
|
D:U207
|
4.1
|
25.8
|
1.0
|
OP1
|
D:U206
|
4.2
|
31.0
|
1.0
|
C1'
|
D:A205
|
4.6
|
25.6
|
1.0
|
O
|
D:HOH1034
|
4.7
|
47.1
|
1.0
|
C5
|
D:G208
|
4.9
|
27.6
|
1.0
|
N3
|
D:U207
|
5.0
|
25.5
|
1.0
|
|
Calcium binding site 3 out
of 10 in 1sds
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Calcium Binding Sites List in 1sds
Calcium binding site 3 out
of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca757
b:30.1
occ:0.90
|
OP2
|
D:A212
|
2.3
|
26.4
|
1.0
|
O
|
D:HOH852
|
2.3
|
19.9
|
0.9
|
O
|
D:HOH910
|
2.3
|
29.2
|
0.9
|
O
|
D:HOH957
|
2.4
|
38.9
|
0.9
|
O
|
D:HOH956
|
2.5
|
35.8
|
0.9
|
O
|
D:HOH1036
|
2.7
|
50.9
|
1.0
|
O
|
D:HOH1017
|
3.6
|
42.1
|
1.0
|
P
|
D:A212
|
3.6
|
25.2
|
1.0
|
O2'
|
D:G211
|
4.1
|
25.4
|
1.0
|
O5'
|
D:A212
|
4.2
|
23.7
|
1.0
|
O6
|
D:G214
|
4.3
|
26.7
|
1.0
|
O
|
D:HOH1109
|
4.3
|
40.3
|
1.0
|
OP1
|
D:A212
|
4.5
|
24.4
|
1.0
|
N7
|
D:G213
|
4.6
|
20.5
|
1.0
|
O3'
|
D:G211
|
4.8
|
24.2
|
1.0
|
O6
|
D:G213
|
4.8
|
22.7
|
1.0
|
O
|
D:HOH1037
|
4.8
|
35.0
|
1.0
|
OP2
|
D:G213
|
4.8
|
23.8
|
1.0
|
O
|
D:HOH1038
|
5.0
|
46.4
|
1.0
|
|
Calcium binding site 4 out
of 10 in 1sds
Go back to
Calcium Binding Sites List in 1sds
Calcium binding site 4 out
of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca752
b:32.0
occ:1.00
|
OP2
|
E:U206
|
2.3
|
26.8
|
1.0
|
O
|
E:HOH1013
|
2.3
|
38.2
|
1.0
|
O
|
E:HOH1026
|
2.3
|
48.6
|
1.0
|
O
|
E:HOH899
|
2.3
|
37.5
|
1.0
|
O6
|
E:G208
|
2.4
|
29.4
|
1.0
|
O
|
E:HOH1020
|
2.5
|
45.7
|
1.0
|
C6
|
E:G208
|
3.5
|
30.0
|
1.0
|
P
|
E:U206
|
3.7
|
27.0
|
1.0
|
CA
|
E:CA754
|
3.9
|
33.9
|
1.0
|
N7
|
E:G208
|
4.1
|
28.0
|
1.0
|
C5
|
E:G208
|
4.1
|
26.7
|
1.0
|
C5'
|
E:U206
|
4.4
|
27.3
|
1.0
|
OP2
|
E:U207
|
4.4
|
28.7
|
1.0
|
O5'
|
E:U206
|
4.4
|
29.1
|
1.0
|
O
|
B:HOH1029
|
4.5
|
44.3
|
1.0
|
OP1
|
E:U206
|
4.6
|
28.9
|
1.0
|
C5
|
E:U207
|
4.6
|
27.0
|
1.0
|
O3'
|
E:A205
|
4.6
|
25.0
|
1.0
|
N1
|
E:G208
|
4.6
|
27.3
|
1.0
|
O4
|
E:U207
|
4.9
|
26.2
|
1.0
|
|
Calcium binding site 5 out
of 10 in 1sds
Go back to
Calcium Binding Sites List in 1sds
Calcium binding site 5 out
of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca754
b:33.9
occ:1.00
|
O2'
|
E:A205
|
2.7
|
25.9
|
1.0
|
O4
|
E:U207
|
2.7
|
26.2
|
1.0
|
O6
|
E:G208
|
3.0
|
29.4
|
1.0
|
OP2
|
E:U206
|
3.1
|
26.8
|
1.0
|
O
|
E:HOH975
|
3.1
|
38.7
|
1.0
|
O
|
E:HOH1020
|
3.1
|
45.7
|
1.0
|
O3'
|
E:A205
|
3.2
|
25.0
|
1.0
|
O
|
E:HOH895
|
3.5
|
32.8
|
1.0
|
P
|
E:U206
|
3.6
|
27.0
|
1.0
|
C4
|
E:U207
|
3.7
|
27.1
|
1.0
|
C6
|
E:G208
|
3.7
|
30.0
|
1.0
|
C2'
|
E:A205
|
3.8
|
23.0
|
1.0
|
N1
|
E:G208
|
3.9
|
27.3
|
1.0
|
CA
|
E:CA752
|
3.9
|
32.0
|
1.0
|
C3'
|
E:A205
|
4.0
|
24.6
|
1.0
|
C5
|
E:U207
|
4.1
|
27.0
|
1.0
|
OP1
|
E:U206
|
4.2
|
28.9
|
1.0
|
C1'
|
E:A205
|
4.7
|
23.6
|
1.0
|
C5
|
E:G208
|
4.9
|
26.7
|
1.0
|
N3
|
E:U207
|
4.9
|
23.8
|
1.0
|
|
Calcium binding site 6 out
of 10 in 1sds
Go back to
Calcium Binding Sites List in 1sds
Calcium binding site 6 out
of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca759
b:56.2
occ:0.90
|
O
|
E:HOH1039
|
2.3
|
31.1
|
0.9
|
O2
|
E:U210
|
4.4
|
28.5
|
1.0
|
O2'
|
E:U210
|
4.5
|
24.5
|
1.0
|
O
|
E:HOH927
|
4.7
|
35.9
|
1.0
|
|
Calcium binding site 7 out
of 10 in 1sds
Go back to
Calcium Binding Sites List in 1sds
Calcium binding site 7 out
of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca751
b:29.6
occ:1.00
|
OP2
|
F:U206
|
2.2
|
24.9
|
1.0
|
O
|
F:HOH874
|
2.3
|
32.9
|
1.0
|
O
|
F:HOH995
|
2.3
|
41.0
|
1.0
|
O6
|
F:G208
|
2.3
|
28.6
|
1.0
|
O
|
F:HOH1024
|
2.4
|
45.3
|
1.0
|
O
|
F:HOH953
|
2.5
|
39.9
|
1.0
|
O
|
F:HOH1023
|
2.5
|
47.5
|
1.0
|
C6
|
F:G208
|
3.5
|
28.4
|
1.0
|
P
|
F:U206
|
3.7
|
25.4
|
1.0
|
CA
|
F:CA753
|
3.9
|
29.1
|
1.0
|
N7
|
F:G208
|
4.1
|
27.1
|
1.0
|
C5
|
F:G208
|
4.1
|
26.8
|
1.0
|
O5'
|
F:U206
|
4.4
|
26.6
|
1.0
|
C5'
|
F:U206
|
4.4
|
25.3
|
1.0
|
OP2
|
F:U207
|
4.5
|
27.3
|
1.0
|
O
|
C:HOH936
|
4.5
|
33.3
|
1.0
|
O
|
F:HOH1025
|
4.5
|
44.2
|
1.0
|
OP1
|
F:U206
|
4.5
|
23.9
|
1.0
|
C5
|
F:U207
|
4.5
|
24.6
|
1.0
|
O3'
|
F:A205
|
4.5
|
22.6
|
1.0
|
N1
|
F:G208
|
4.6
|
28.8
|
1.0
|
O
|
F:HOH1077
|
4.7
|
52.3
|
1.0
|
O4
|
F:U207
|
4.9
|
25.7
|
1.0
|
O
|
C:HOH1005
|
4.9
|
34.8
|
1.0
|
|
Calcium binding site 8 out
of 10 in 1sds
Go back to
Calcium Binding Sites List in 1sds
Calcium binding site 8 out
of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca753
b:29.1
occ:1.00
|
O2'
|
F:A205
|
2.6
|
27.3
|
1.0
|
O4
|
F:U207
|
2.7
|
25.7
|
1.0
|
O
|
F:HOH979
|
2.9
|
37.5
|
1.0
|
O6
|
F:G208
|
3.0
|
28.6
|
1.0
|
OP2
|
F:U206
|
3.1
|
24.9
|
1.0
|
O
|
F:HOH995
|
3.1
|
41.0
|
1.0
|
O3'
|
F:A205
|
3.2
|
22.6
|
1.0
|
O
|
F:HOH893
|
3.3
|
33.4
|
1.0
|
P
|
F:U206
|
3.6
|
25.4
|
1.0
|
C4
|
F:U207
|
3.7
|
25.6
|
1.0
|
C6
|
F:G208
|
3.7
|
28.4
|
1.0
|
C2'
|
F:A205
|
3.8
|
24.8
|
1.0
|
CA
|
F:CA751
|
3.9
|
29.6
|
1.0
|
N1
|
F:G208
|
3.9
|
28.8
|
1.0
|
C3'
|
F:A205
|
4.0
|
25.4
|
1.0
|
C5
|
F:U207
|
4.0
|
24.6
|
1.0
|
OP1
|
F:U206
|
4.1
|
23.9
|
1.0
|
C1'
|
F:A205
|
4.7
|
24.7
|
1.0
|
C5
|
F:G208
|
4.9
|
26.8
|
1.0
|
N3
|
F:U207
|
4.9
|
24.1
|
1.0
|
|
Calcium binding site 9 out
of 10 in 1sds
Go back to
Calcium Binding Sites List in 1sds
Calcium binding site 9 out
of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca758
b:31.0
occ:0.90
|
O
|
F:HOH1007
|
2.2
|
34.4
|
0.9
|
OP2
|
F:A212
|
2.3
|
27.9
|
1.0
|
O
|
F:HOH1021
|
2.3
|
31.9
|
0.9
|
O
|
F:HOH885
|
2.4
|
24.7
|
0.9
|
O
|
F:HOH851
|
2.4
|
18.5
|
0.9
|
P
|
F:A212
|
3.7
|
26.6
|
1.0
|
O2'
|
F:G211
|
4.1
|
27.4
|
1.0
|
O5'
|
F:A212
|
4.3
|
25.3
|
1.0
|
O
|
F:HOH932
|
4.3
|
36.2
|
1.0
|
O6
|
F:G214
|
4.3
|
20.7
|
1.0
|
O
|
F:HOH1022
|
4.4
|
35.2
|
0.5
|
OP1
|
F:A212
|
4.4
|
26.8
|
1.0
|
N7
|
F:G213
|
4.7
|
20.4
|
1.0
|
O3'
|
F:G211
|
4.8
|
26.0
|
1.0
|
O6
|
F:G213
|
4.8
|
21.9
|
1.0
|
|
Calcium binding site 10 out
of 10 in 1sds
Go back to
Calcium Binding Sites List in 1sds
Calcium binding site 10 out
of 10 in the Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca760
b:47.8
occ:0.90
|
O
|
F:HOH1078
|
2.2
|
39.2
|
0.9
|
O
|
F:HOH1041
|
2.2
|
33.4
|
0.9
|
O
|
F:HOH1043
|
2.3
|
38.6
|
0.9
|
O
|
F:HOH1042
|
2.6
|
35.5
|
0.9
|
O
|
F:HOH1040
|
2.7
|
47.9
|
0.9
|
O2
|
F:U210
|
4.5
|
23.1
|
1.0
|
O2'
|
F:U210
|
4.6
|
22.6
|
1.0
|
O
|
F:HOH919
|
4.7
|
35.1
|
1.0
|
O3'
|
F:U210
|
5.0
|
24.8
|
1.0
|
|
Reference:
T.Hamma,
A.Ferre-D'amare.
Structure of Protein L7AE Bound to A K-Turn Derived From An Archaeal Box H/Aca Srna at 1.8 A Resolution. Structure V. 12 893 2004.
ISSN: ISSN 0969-2126
PubMed: 15130481
DOI: 10.1016/J.STR.2004.03.015
Page generated: Thu Jul 11 22:36:07 2024
|