Calcium in PDB 1pjg: Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg
Protein crystallography data
The structure of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg, PDB code: 1pjg
was solved by
M.L.Kopka,
L.Lavelle,
G.W.Han,
H.-L.Ng,
R.E.Dickerson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
1.15
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
25.701,
41.073,
46.116,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
13.2 /
16.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg
(pdb code 1pjg). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg, PDB code: 1pjg:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 1pjg
Go back to
Calcium Binding Sites List in 1pjg
Calcium binding site 1 out
of 5 in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca32
b:22.8
occ:0.50
|
CA
|
A:CA32
|
0.0
|
22.8
|
0.5
|
O
|
A:HOH140
|
2.0
|
17.4
|
1.0
|
O
|
A:HOH139
|
2.1
|
20.6
|
1.0
|
O
|
A:HOH141
|
2.1
|
21.3
|
0.5
|
O
|
A:HOH143
|
2.2
|
24.4
|
1.0
|
O
|
A:HOH138
|
2.2
|
24.3
|
0.5
|
CA
|
A:CA32
|
2.3
|
19.2
|
0.5
|
OP2
|
A:G5
|
2.3
|
18.2
|
1.0
|
O
|
A:HOH142
|
2.5
|
25.3
|
0.5
|
O
|
A:HOH84
|
3.3
|
29.7
|
1.0
|
H3'
|
A:A4
|
3.6
|
13.5
|
1.0
|
P
|
A:G5
|
3.7
|
14.3
|
1.0
|
O
|
A:HOH142
|
3.9
|
24.7
|
0.5
|
O
|
A:HOH138
|
3.9
|
13.6
|
0.5
|
N7
|
A:G5
|
4.0
|
10.0
|
1.0
|
O5'
|
A:G5
|
4.1
|
12.6
|
1.0
|
O
|
A:HOH141
|
4.2
|
32.0
|
0.5
|
OP2
|
A:A6
|
4.3
|
15.9
|
1.0
|
H8
|
A:G5
|
4.3
|
12.6
|
1.0
|
N7
|
A:A6
|
4.4
|
10.2
|
1.0
|
H2'
|
A:A4
|
4.4
|
12.5
|
1.0
|
C8
|
A:G5
|
4.4
|
10.5
|
1.0
|
O
|
A:HOH78
|
4.4
|
24.6
|
1.0
|
C3'
|
A:A4
|
4.5
|
11.2
|
1.0
|
H3'
|
A:G5
|
4.5
|
13.4
|
1.0
|
H62
|
A:A6
|
4.5
|
11.0
|
1.0
|
O
|
A:HOH71
|
4.6
|
29.1
|
1.0
|
O3'
|
A:A4
|
4.6
|
14.5
|
1.0
|
OP1
|
A:G5
|
4.7
|
17.9
|
1.0
|
C5
|
A:G5
|
4.9
|
8.7
|
1.0
|
H8
|
A:A6
|
4.9
|
12.6
|
1.0
|
C2'
|
A:A4
|
5.0
|
10.4
|
1.0
|
|
Calcium binding site 2 out
of 5 in 1pjg
Go back to
Calcium Binding Sites List in 1pjg
Calcium binding site 2 out
of 5 in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca32
b:19.2
occ:0.50
|
CA
|
A:CA32
|
0.0
|
19.2
|
0.5
|
O
|
A:HOH142
|
1.9
|
24.7
|
0.5
|
CA
|
A:CA32
|
2.3
|
22.8
|
0.5
|
O
|
A:HOH140
|
2.3
|
17.4
|
1.0
|
O
|
A:HOH139
|
2.3
|
20.6
|
1.0
|
O
|
A:HOH142
|
2.3
|
25.3
|
0.5
|
O
|
A:HOH143
|
2.4
|
24.4
|
1.0
|
O
|
A:HOH138
|
2.5
|
13.6
|
0.5
|
O
|
A:HOH141
|
2.6
|
32.0
|
0.5
|
H62
|
A:A6
|
3.7
|
11.0
|
1.0
|
O
|
A:HOH141
|
3.8
|
21.3
|
0.5
|
O
|
A:HOH138
|
4.1
|
24.3
|
0.5
|
OP2
|
A:G5
|
4.2
|
18.2
|
1.0
|
O
|
A:HOH84
|
4.3
|
29.7
|
1.0
|
N7
|
A:A4
|
4.3
|
9.1
|
1.0
|
O
|
A:HOH65
|
4.3
|
23.9
|
1.0
|
O
|
B:HOH30
|
4.3
|
19.6
|
1.0
|
O
|
B:HOH26
|
4.5
|
12.6
|
1.0
|
H3'
|
A:A4
|
4.5
|
13.5
|
1.0
|
N6
|
A:A6
|
4.6
|
9.1
|
1.0
|
C8
|
A:A4
|
4.6
|
8.9
|
1.0
|
H8
|
A:A4
|
4.6
|
10.7
|
1.0
|
O
|
A:HOH78
|
4.6
|
24.6
|
1.0
|
OP2
|
A:A4
|
4.7
|
21.4
|
1.0
|
N7
|
A:G5
|
4.8
|
10.0
|
1.0
|
H61
|
A:A6
|
4.9
|
11.0
|
1.0
|
H62
|
A:A7
|
4.9
|
11.9
|
1.0
|
O6
|
A:G5
|
4.9
|
8.9
|
1.0
|
C5
|
A:A4
|
4.9
|
7.7
|
1.0
|
|
Calcium binding site 3 out
of 5 in 1pjg
Go back to
Calcium Binding Sites List in 1pjg
Calcium binding site 3 out
of 5 in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca33
b:11.9
occ:1.00
|
OP2
|
A:A9
|
2.0
|
8.6
|
1.0
|
O
|
A:HOH147
|
2.0
|
12.3
|
1.0
|
O
|
A:HOH144
|
2.0
|
13.7
|
1.0
|
O
|
A:HOH146
|
2.1
|
10.3
|
1.0
|
O
|
A:HOH145
|
2.1
|
10.0
|
1.0
|
O
|
A:HOH148
|
2.1
|
10.8
|
1.0
|
P
|
A:A9
|
3.5
|
7.4
|
1.0
|
H3'
|
A:A8
|
3.5
|
10.3
|
1.0
|
O
|
A:HOH66
|
4.0
|
19.6
|
1.0
|
O5'
|
A:A9
|
4.1
|
7.5
|
1.0
|
H8
|
A:A9
|
4.2
|
9.8
|
1.0
|
O
|
A:HOH44
|
4.2
|
9.6
|
1.0
|
N7
|
A:A9
|
4.2
|
8.0
|
1.0
|
OP2
|
A:G10
|
4.3
|
7.4
|
1.0
|
C3'
|
A:A8
|
4.3
|
8.6
|
1.0
|
O3'
|
A:A8
|
4.4
|
7.6
|
1.0
|
OP1
|
A:A9
|
4.4
|
8.2
|
1.0
|
C8
|
A:A9
|
4.5
|
8.2
|
1.0
|
H3'
|
A:A9
|
4.6
|
9.1
|
1.0
|
O
|
A:HOH60
|
4.7
|
27.6
|
1.0
|
O
|
A:HOH41
|
4.8
|
13.8
|
1.0
|
N7
|
A:G10
|
4.8
|
7.2
|
1.0
|
H5'
|
A:A8
|
4.8
|
15.0
|
1.0
|
H2'
|
A:A8
|
4.8
|
11.5
|
1.0
|
H5''
|
A:A8
|
5.0
|
15.0
|
1.0
|
|
Calcium binding site 4 out
of 5 in 1pjg
Go back to
Calcium Binding Sites List in 1pjg
Calcium binding site 4 out
of 5 in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca31
b:8.7
occ:1.00
|
OP2
|
B:DT18
|
2.2
|
8.3
|
1.0
|
O
|
B:HOH136
|
2.3
|
11.8
|
1.0
|
O
|
B:HOH137
|
2.3
|
10.3
|
1.0
|
O
|
B:HOH134
|
2.3
|
10.5
|
1.0
|
O
|
B:HOH135
|
2.3
|
13.1
|
1.0
|
P
|
B:DT18
|
3.5
|
7.5
|
1.0
|
H3'
|
B:DT17
|
3.8
|
8.2
|
1.0
|
H72
|
B:DT18
|
4.0
|
14.3
|
1.0
|
OP1
|
B:DT18
|
4.1
|
9.1
|
1.0
|
H73
|
B:DT18
|
4.2
|
14.3
|
1.0
|
O3'
|
B:DT17
|
4.2
|
7.2
|
1.0
|
O5'
|
B:DT17
|
4.3
|
7.4
|
1.0
|
H5''
|
B:DT17
|
4.4
|
9.4
|
1.0
|
O
|
B:HOH38
|
4.4
|
26.0
|
1.0
|
OP2
|
B:DT17
|
4.4
|
9.1
|
1.0
|
OP1
|
B:DT17
|
4.5
|
9.8
|
1.0
|
C3'
|
B:DT17
|
4.5
|
6.9
|
1.0
|
C7
|
B:DT18
|
4.6
|
9.5
|
1.0
|
P
|
B:DT17
|
4.6
|
8.6
|
1.0
|
O5'
|
B:DT18
|
4.7
|
7.1
|
1.0
|
C5'
|
B:DT17
|
4.8
|
7.8
|
1.0
|
H71
|
B:DT18
|
5.0
|
14.3
|
1.0
|
|
Calcium binding site 5 out
of 5 in 1pjg
Go back to
Calcium Binding Sites List in 1pjg
Calcium binding site 5 out
of 5 in the Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Rna/Dna Hybrid Decamer of Caaagaaaag/Cttttctttg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca34
b:12.6
occ:1.00
|
O
|
B:HOH150
|
2.0
|
26.2
|
1.0
|
OP1
|
B:DT18
|
2.2
|
9.1
|
1.0
|
O
|
B:HOH149
|
2.4
|
22.7
|
1.0
|
O
|
B:HOH151
|
2.5
|
20.0
|
1.0
|
O
|
B:HOH152
|
2.5
|
12.9
|
1.0
|
H5''
|
B:DT18
|
3.4
|
8.4
|
1.0
|
P
|
B:DT18
|
3.7
|
7.5
|
1.0
|
O
|
B:HOH50
|
4.0
|
19.3
|
1.0
|
C5'
|
B:DT18
|
4.2
|
7.0
|
1.0
|
H5'
|
B:DT18
|
4.3
|
8.4
|
1.0
|
O5'
|
B:DT18
|
4.3
|
7.1
|
1.0
|
O
|
B:HOH136
|
4.4
|
11.8
|
1.0
|
O3'
|
B:DT17
|
4.5
|
7.2
|
1.0
|
OP2
|
B:DT18
|
4.6
|
8.3
|
1.0
|
O
|
B:HOH91
|
4.8
|
37.1
|
1.0
|
|
Reference:
M.L.Kopka,
L.Lavelle,
G.W.Han,
H.L.Ng,
R.E.Dickerson.
An Unusual Sugar Conformation in the Structure of An Rna/Dna Decamer of the Polypurine Tract May Affect Recognition By Rnase H. J.Mol.Biol. V. 334 653 2003.
ISSN: ISSN 0022-2836
PubMed: 14636594
DOI: 10.1016/J.JMB.2003.09.057
Page generated: Thu Jul 11 13:48:09 2024
|