Sodium in PDB 1ph3: Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg
Protein crystallography data
The structure of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg, PDB code: 1ph3
was solved by
D.L.Theobald,
S.C.Schultz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.82 /
2.30
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.636,
93.636,
423.111,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23 /
26.3
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg
(pdb code 1ph3). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg, PDB code: 1ph3:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 1ph3
Go back to
Sodium Binding Sites List in 1ph3
Sodium binding site 1 out
of 4 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg
![](/pictures/NA/pdb/ph/1ph3-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/ph/1ph3-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na1001
b:48.4
occ:1.00
|
O6
|
G:DG9
|
2.5
|
52.0
|
1.0
|
O6
|
G:DG4
|
2.5
|
44.4
|
1.0
|
O
|
G:HOH500
|
2.5
|
63.4
|
1.0
|
O2
|
G:DT7
|
2.5
|
47.8
|
1.0
|
O6
|
H:DG12
|
2.5
|
42.6
|
1.0
|
O6
|
H:DG1
|
2.8
|
43.5
|
1.0
|
C6
|
G:DG4
|
3.3
|
42.5
|
1.0
|
C6
|
G:DG9
|
3.4
|
51.1
|
1.0
|
C2
|
G:DT7
|
3.4
|
46.0
|
1.0
|
O2
|
G:DT5
|
3.5
|
38.2
|
1.0
|
C6
|
H:DG12
|
3.5
|
44.1
|
1.0
|
N1
|
G:DG4
|
3.5
|
42.2
|
1.0
|
C6
|
H:DG1
|
3.6
|
44.2
|
1.0
|
N1
|
G:DG9
|
3.7
|
48.9
|
1.0
|
N3
|
G:DT7
|
3.7
|
44.2
|
1.0
|
N1
|
H:DG12
|
3.8
|
45.2
|
1.0
|
N1
|
H:DG1
|
3.9
|
46.1
|
1.0
|
NA
|
H:NA1002
|
3.9
|
45.6
|
1.0
|
N3
|
G:DT5
|
4.1
|
38.9
|
1.0
|
C2
|
G:DT5
|
4.2
|
39.1
|
1.0
|
O6
|
H:DG11
|
4.3
|
45.4
|
1.0
|
C5
|
G:DG4
|
4.5
|
40.8
|
1.0
|
N1
|
G:DT7
|
4.7
|
46.4
|
1.0
|
O2
|
G:DT6
|
4.7
|
41.5
|
1.0
|
C5
|
G:DG9
|
4.7
|
52.0
|
1.0
|
C5
|
H:DG1
|
4.7
|
46.1
|
1.0
|
C2
|
G:DG4
|
4.8
|
41.8
|
1.0
|
C5
|
H:DG12
|
4.8
|
46.3
|
1.0
|
C6
|
H:DG11
|
4.8
|
45.6
|
1.0
|
O
|
G:HOH499
|
4.9
|
48.6
|
1.0
|
O6
|
G:DG3
|
4.9
|
40.0
|
1.0
|
O6
|
G:DG10
|
4.9
|
51.5
|
1.0
|
C2
|
G:DG9
|
5.0
|
48.6
|
1.0
|
|
Sodium binding site 2 out
of 4 in 1ph3
Go back to
Sodium Binding Sites List in 1ph3
Sodium binding site 2 out
of 4 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg
![](/pictures/NA/pdb/ph/1ph3-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/ph/1ph3-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na1002
b:45.6
occ:1.00
|
O6
|
H:DG2
|
2.3
|
45.8
|
1.0
|
O6
|
H:DG11
|
2.3
|
45.4
|
1.0
|
O6
|
G:DG10
|
2.4
|
51.5
|
1.0
|
O6
|
G:DG3
|
2.5
|
40.0
|
1.0
|
O6
|
H:DG1
|
2.7
|
43.5
|
1.0
|
C6
|
H:DG2
|
3.2
|
45.1
|
1.0
|
C6
|
G:DG10
|
3.2
|
49.9
|
1.0
|
N1
|
G:DG10
|
3.3
|
49.5
|
1.0
|
C6
|
H:DG11
|
3.4
|
45.6
|
1.0
|
C6
|
H:DG1
|
3.5
|
44.2
|
1.0
|
O6
|
G:DG9
|
3.6
|
52.0
|
1.0
|
O6
|
G:DG2
|
3.6
|
44.8
|
1.0
|
N1
|
H:DG2
|
3.6
|
44.3
|
1.0
|
C6
|
G:DG3
|
3.6
|
41.3
|
1.0
|
O6
|
G:DG4
|
3.8
|
44.4
|
1.0
|
N1
|
H:DG11
|
3.8
|
45.8
|
1.0
|
NA
|
G:NA1001
|
3.9
|
48.4
|
1.0
|
N1
|
H:DG1
|
3.9
|
46.1
|
1.0
|
N1
|
G:DG3
|
4.0
|
39.8
|
1.0
|
N1
|
G:DG4
|
4.1
|
42.2
|
1.0
|
NA
|
H:NA1003
|
4.2
|
55.0
|
1.0
|
C6
|
G:DG2
|
4.2
|
46.7
|
1.0
|
C6
|
G:DG4
|
4.3
|
42.5
|
1.0
|
C6
|
G:DG9
|
4.4
|
51.1
|
1.0
|
N1
|
H:DG10
|
4.5
|
48.4
|
1.0
|
O6
|
H:DG10
|
4.5
|
48.8
|
1.0
|
O6
|
H:DG12
|
4.5
|
42.6
|
1.0
|
C5
|
H:DG2
|
4.5
|
46.1
|
1.0
|
C5
|
G:DG10
|
4.6
|
52.1
|
1.0
|
C2
|
G:DG10
|
4.6
|
47.7
|
1.0
|
C5
|
H:DG1
|
4.6
|
46.1
|
1.0
|
O6
|
H:DG3
|
4.7
|
46.8
|
1.0
|
N1
|
G:DG2
|
4.7
|
45.9
|
1.0
|
C5
|
H:DG11
|
4.7
|
46.6
|
1.0
|
C6
|
H:DG10
|
4.7
|
49.4
|
1.0
|
C5
|
G:DG3
|
4.8
|
40.7
|
1.0
|
N1
|
G:DG9
|
4.9
|
48.9
|
1.0
|
C2
|
H:DG2
|
4.9
|
44.3
|
1.0
|
|
Sodium binding site 3 out
of 4 in 1ph3
Go back to
Sodium Binding Sites List in 1ph3
Sodium binding site 3 out
of 4 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg
![](/pictures/NA/pdb/ph/1ph3-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/ph/1ph3-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na1003
b:55.0
occ:1.00
|
O6
|
H:DG3
|
2.2
|
46.8
|
1.0
|
O6
|
G:DG11
|
2.2
|
55.4
|
1.0
|
O6
|
H:DG10
|
2.3
|
48.8
|
1.0
|
O6
|
G:DG2
|
2.5
|
44.8
|
1.0
|
O6
|
G:DG1
|
2.9
|
50.8
|
1.0
|
C6
|
H:DG3
|
3.2
|
47.7
|
1.0
|
C6
|
H:DG10
|
3.2
|
49.4
|
1.0
|
C6
|
G:DG11
|
3.2
|
54.8
|
1.0
|
O6
|
H:DG2
|
3.3
|
45.8
|
1.0
|
N1
|
H:DG10
|
3.5
|
48.4
|
1.0
|
C6
|
G:DG2
|
3.5
|
46.7
|
1.0
|
N1
|
H:DG3
|
3.5
|
44.6
|
1.0
|
N1
|
G:DG11
|
3.5
|
55.6
|
1.0
|
C6
|
G:DG1
|
3.7
|
51.4
|
1.0
|
N1
|
G:DG2
|
3.8
|
45.9
|
1.0
|
O6
|
H:DG4
|
3.8
|
45.8
|
1.0
|
O6
|
H:DG9
|
3.8
|
52.4
|
1.0
|
C6
|
H:DG2
|
3.9
|
45.1
|
1.0
|
NA
|
H:NA1004
|
4.0
|
58.4
|
1.0
|
N1
|
G:DG1
|
4.1
|
50.5
|
1.0
|
NA
|
H:NA1002
|
4.2
|
45.6
|
1.0
|
N1
|
G:DG10
|
4.2
|
49.5
|
1.0
|
O6
|
G:DG10
|
4.3
|
51.5
|
1.0
|
N1
|
H:DG4
|
4.4
|
46.1
|
1.0
|
N1
|
H:DG2
|
4.5
|
44.3
|
1.0
|
O6
|
G:DG12
|
4.5
|
49.6
|
1.0
|
C6
|
H:DG4
|
4.5
|
46.5
|
1.0
|
C6
|
G:DG10
|
4.5
|
49.9
|
1.0
|
C5
|
H:DG3
|
4.6
|
45.6
|
1.0
|
C5
|
H:DG10
|
4.6
|
50.1
|
1.0
|
C5
|
G:DG11
|
4.6
|
55.3
|
1.0
|
C5
|
H:DG2
|
4.7
|
46.1
|
1.0
|
C6
|
H:DG9
|
4.7
|
51.8
|
1.0
|
C5
|
G:DG1
|
4.7
|
51.1
|
1.0
|
C5
|
G:DG2
|
4.8
|
45.6
|
1.0
|
C2
|
H:DG10
|
4.8
|
49.2
|
1.0
|
O6
|
G:DG3
|
4.8
|
40.0
|
1.0
|
C2
|
H:DG3
|
4.8
|
45.0
|
1.0
|
C2
|
G:DG11
|
4.9
|
55.4
|
1.0
|
C2
|
G:DG10
|
5.0
|
47.7
|
1.0
|
|
Sodium binding site 4 out
of 4 in 1ph3
Go back to
Sodium Binding Sites List in 1ph3
Sodium binding site 4 out
of 4 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg
![](/pictures/NA/pdb/ph/1ph3-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/ph/1ph3-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na1004
b:58.4
occ:1.00
|
O6
|
G:DG12
|
2.2
|
49.6
|
1.0
|
O6
|
H:DG9
|
2.4
|
52.4
|
1.0
|
O6
|
H:DG4
|
2.5
|
45.8
|
1.0
|
O6
|
G:DG1
|
2.7
|
50.8
|
1.0
|
O2
|
H:DT7
|
2.8
|
50.3
|
1.0
|
O
|
H:HOH501
|
2.9
|
53.1
|
1.0
|
C6
|
G:DG12
|
3.2
|
52.8
|
1.0
|
C6
|
H:DG9
|
3.4
|
51.8
|
1.0
|
C6
|
H:DG4
|
3.4
|
46.5
|
1.0
|
N1
|
G:DG12
|
3.5
|
52.3
|
1.0
|
C6
|
G:DG1
|
3.6
|
51.4
|
1.0
|
O2
|
H:DT5
|
3.6
|
56.1
|
1.0
|
C2
|
H:DT7
|
3.7
|
50.8
|
1.0
|
N1
|
H:DG9
|
3.8
|
52.6
|
1.0
|
N1
|
G:DG1
|
3.9
|
50.5
|
1.0
|
N1
|
H:DG4
|
3.9
|
46.1
|
1.0
|
N3
|
H:DT7
|
4.0
|
49.7
|
1.0
|
NA
|
H:NA1003
|
4.0
|
55.0
|
1.0
|
O6
|
G:DG11
|
4.1
|
55.4
|
1.0
|
N3
|
H:DT5
|
4.2
|
55.4
|
1.0
|
C2
|
H:DT5
|
4.3
|
54.5
|
1.0
|
C5
|
G:DG12
|
4.5
|
52.5
|
1.0
|
C6
|
G:DG11
|
4.5
|
54.8
|
1.0
|
O
|
H:HOH502
|
4.6
|
58.2
|
1.0
|
C5
|
H:DG4
|
4.6
|
47.9
|
1.0
|
C5
|
H:DG9
|
4.7
|
53.8
|
1.0
|
O6
|
H:DG10
|
4.7
|
48.8
|
1.0
|
C5
|
G:DG1
|
4.8
|
51.1
|
1.0
|
N1
|
G:DG11
|
4.8
|
55.6
|
1.0
|
O2
|
H:DT6
|
4.8
|
56.4
|
1.0
|
O6
|
H:DG3
|
4.9
|
46.8
|
1.0
|
C2
|
G:DG12
|
4.9
|
53.0
|
1.0
|
N1
|
H:DT7
|
4.9
|
51.8
|
1.0
|
|
Reference:
D.L.Theobald,
S.C.Schultz.
Nucleotide Shuffling and Ssdna Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes Embo J. V. 22 4314 2003.
ISSN: ISSN 0261-4189
PubMed: 12912928
DOI: 10.1093/EMBOJ/CDG415
Page generated: Tue Dec 15 05:32:46 2020
|