Sodium in PDB 1u8r: Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions
Protein crystallography data
The structure of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions, PDB code: 1u8r
was solved by
G.Wisedchaisri,
R.K.Holmes,
W.G.J.Hol,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.75 /
2.75
|
Space group
|
P 31
|
Cell size a, b, c (Å), α, β, γ (°)
|
107.959,
107.959,
215.124,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23 /
26.5
|
Other elements in 1u8r:
The structure of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions
(pdb code 1u8r). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the
Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions, PDB code: 1u8r:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 1u8r
Go back to
Sodium Binding Sites List in 1u8r
Sodium binding site 1 out
of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1101
b:65.0
occ:1.00
|
OP1
|
F:DC19
|
2.2
|
47.7
|
1.0
|
O
|
A:ASP35
|
2.3
|
55.8
|
1.0
|
O
|
A:HOH1103
|
2.5
|
39.2
|
1.0
|
O
|
F:HOH37
|
2.6
|
45.3
|
1.0
|
OD1
|
A:ASP35
|
2.9
|
0.6
|
1.0
|
C
|
A:ASP35
|
3.5
|
56.8
|
1.0
|
P
|
F:DC19
|
3.7
|
42.0
|
1.0
|
CG
|
A:ASP35
|
4.0
|
0.3
|
1.0
|
CA
|
A:GLN36
|
4.1
|
62.2
|
1.0
|
N
|
A:GLN36
|
4.3
|
63.7
|
1.0
|
O5'
|
F:DC19
|
4.3
|
41.4
|
1.0
|
O3'
|
F:DC18
|
4.4
|
41.9
|
1.0
|
CB
|
A:ASP35
|
4.5
|
0.5
|
1.0
|
CA
|
A:ASP35
|
4.6
|
57.6
|
1.0
|
OP2
|
F:DC19
|
4.7
|
44.4
|
1.0
|
C
|
A:GLN36
|
5.0
|
62.4
|
1.0
|
|
Sodium binding site 2 out
of 8 in 1u8r
Go back to
Sodium Binding Sites List in 1u8r
Sodium binding site 2 out
of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na2102
b:41.1
occ:1.00
|
OP1
|
E:DC21
|
2.4
|
62.8
|
1.0
|
O
|
B:ASP35
|
2.6
|
66.0
|
1.0
|
OD1
|
B:ASP35
|
3.1
|
0.7
|
1.0
|
P
|
E:DC21
|
3.8
|
59.0
|
1.0
|
C
|
B:ASP35
|
3.8
|
64.9
|
1.0
|
O3'
|
E:DC20
|
4.1
|
60.4
|
1.0
|
CG
|
B:ASP35
|
4.2
|
0.5
|
1.0
|
CA
|
B:GLN36
|
4.3
|
67.4
|
1.0
|
N
|
B:GLN36
|
4.5
|
67.2
|
1.0
|
CB
|
B:ASP35
|
4.6
|
0.1
|
1.0
|
OP2
|
E:DC21
|
4.7
|
61.0
|
1.0
|
O5'
|
E:DC21
|
4.8
|
58.9
|
1.0
|
CA
|
B:ASP35
|
4.9
|
67.1
|
1.0
|
|
Sodium binding site 3 out
of 8 in 1u8r
Go back to
Sodium Binding Sites List in 1u8r
Sodium binding site 3 out
of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na3103
b:58.8
occ:1.00
|
OP1
|
E:DC16
|
2.6
|
58.7
|
1.0
|
O
|
C:ASP35
|
2.7
|
57.1
|
1.0
|
OD1
|
C:ASP35
|
3.4
|
0.3
|
1.0
|
C
|
C:ASP35
|
3.9
|
59.4
|
1.0
|
P
|
E:DC16
|
3.9
|
49.5
|
1.0
|
O3'
|
E:DG15
|
4.2
|
56.2
|
1.0
|
CG
|
C:ASP35
|
4.4
|
0.5
|
1.0
|
CA
|
C:GLN36
|
4.5
|
57.5
|
1.0
|
N
|
C:GLN36
|
4.6
|
59.6
|
1.0
|
CB
|
C:ASP35
|
4.7
|
0.5
|
1.0
|
OP2
|
E:DC16
|
4.7
|
56.0
|
1.0
|
CA
|
C:ASP35
|
5.0
|
61.4
|
1.0
|
O5'
|
E:DC16
|
5.0
|
47.7
|
1.0
|
|
Sodium binding site 4 out
of 8 in 1u8r
Go back to
Sodium Binding Sites List in 1u8r
Sodium binding site 4 out
of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na4104
b:50.9
occ:1.00
|
O
|
D:HOH4111
|
2.3
|
46.1
|
1.0
|
OP1
|
F:DC24
|
2.5
|
51.0
|
1.0
|
O
|
D:ASP35
|
2.6
|
70.0
|
1.0
|
OD1
|
D:ASP35
|
3.0
|
0.8
|
1.0
|
C
|
D:ASP35
|
3.7
|
69.6
|
1.0
|
P
|
F:DC24
|
3.9
|
51.9
|
1.0
|
CG
|
D:ASP35
|
4.1
|
99.0
|
1.0
|
CA
|
D:GLN36
|
4.3
|
48.3
|
1.0
|
O3'
|
F:DG23
|
4.3
|
53.1
|
1.0
|
N
|
D:GLN36
|
4.4
|
50.6
|
1.0
|
CB
|
D:ASP35
|
4.5
|
92.1
|
1.0
|
CA
|
D:ASP35
|
4.7
|
70.4
|
1.0
|
O5'
|
F:DC24
|
4.8
|
52.4
|
1.0
|
OP2
|
F:DC24
|
4.9
|
55.0
|
1.0
|
|
Sodium binding site 5 out
of 8 in 1u8r
Go back to
Sodium Binding Sites List in 1u8r
Sodium binding site 5 out
of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na5105
b:51.5
occ:1.00
|
OP1
|
L:DC19
|
2.3
|
51.0
|
1.0
|
O
|
L:HOH42
|
2.3
|
44.1
|
1.0
|
O
|
L:HOH35
|
2.5
|
33.2
|
1.0
|
O
|
G:ASP35
|
2.9
|
76.7
|
1.0
|
OD1
|
G:ASP35
|
3.2
|
0.3
|
1.0
|
P
|
L:DC19
|
3.7
|
48.3
|
1.0
|
C
|
G:ASP35
|
4.0
|
77.2
|
1.0
|
O5'
|
L:DC19
|
4.2
|
48.2
|
1.0
|
O3'
|
L:DC18
|
4.3
|
48.2
|
1.0
|
CG
|
G:ASP35
|
4.3
|
1.0
|
1.0
|
CA
|
G:GLN36
|
4.6
|
55.0
|
1.0
|
O
|
L:HOH38
|
4.7
|
45.8
|
1.0
|
N
|
G:GLN36
|
4.8
|
56.5
|
1.0
|
CB
|
G:ASP35
|
4.8
|
0.4
|
1.0
|
OP2
|
L:DC19
|
4.9
|
48.6
|
1.0
|
|
Sodium binding site 6 out
of 8 in 1u8r
Go back to
Sodium Binding Sites List in 1u8r
Sodium binding site 6 out
of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na6106
b:59.2
occ:1.00
|
OP1
|
K:DC21
|
2.7
|
57.5
|
1.0
|
O
|
H:ASP35
|
2.9
|
67.9
|
1.0
|
O
|
H:HOH6109
|
3.0
|
43.5
|
1.0
|
OD1
|
H:ASP35
|
3.4
|
0.7
|
1.0
|
P
|
K:DC21
|
4.0
|
58.6
|
1.0
|
C
|
H:ASP35
|
4.1
|
68.0
|
1.0
|
O3'
|
K:DC20
|
4.4
|
64.6
|
1.0
|
CG
|
H:ASP35
|
4.5
|
0.9
|
1.0
|
CA
|
H:GLN36
|
4.6
|
49.4
|
1.0
|
N
|
H:GLN36
|
4.8
|
52.2
|
1.0
|
CB
|
H:ASP35
|
4.9
|
0.9
|
1.0
|
OP2
|
K:DC21
|
5.0
|
55.8
|
1.0
|
|
Sodium binding site 7 out
of 8 in 1u8r
Go back to
Sodium Binding Sites List in 1u8r
Sodium binding site 7 out
of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na7107
b:50.3
occ:1.00
|
O
|
I:ASP35
|
2.4
|
78.6
|
1.0
|
OP1
|
K:DC16
|
2.5
|
50.3
|
1.0
|
OD1
|
I:ASP35
|
3.0
|
0.6
|
1.0
|
O
|
I:HOH7109
|
3.1
|
33.8
|
1.0
|
C
|
I:ASP35
|
3.6
|
77.4
|
1.0
|
P
|
K:DC16
|
3.9
|
51.7
|
1.0
|
CG
|
I:ASP35
|
4.1
|
0.9
|
1.0
|
CA
|
I:GLN36
|
4.3
|
64.2
|
1.0
|
N
|
I:GLN36
|
4.4
|
65.3
|
1.0
|
CB
|
I:ASP35
|
4.4
|
0.1
|
1.0
|
O3'
|
K:DG15
|
4.4
|
48.0
|
1.0
|
CA
|
I:ASP35
|
4.7
|
78.2
|
1.0
|
OP2
|
K:DC16
|
4.8
|
51.5
|
1.0
|
O5'
|
K:DC16
|
4.9
|
48.4
|
1.0
|
|
Sodium binding site 8 out
of 8 in 1u8r
Go back to
Sodium Binding Sites List in 1u8r
Sodium binding site 8 out
of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Na8108
b:50.8
occ:1.00
|
O
|
L:HOH36
|
2.5
|
34.4
|
1.0
|
OP1
|
L:DC24
|
2.7
|
64.1
|
1.0
|
O
|
J:ASP35
|
2.7
|
73.2
|
1.0
|
OD1
|
J:ASP35
|
3.6
|
0.1
|
1.0
|
P
|
L:DC24
|
3.9
|
63.1
|
1.0
|
C
|
J:ASP35
|
4.0
|
71.9
|
1.0
|
O3'
|
L:DG23
|
4.1
|
55.0
|
1.0
|
CA
|
J:GLN36
|
4.4
|
53.8
|
1.0
|
CG
|
J:ASP35
|
4.6
|
0.8
|
1.0
|
N
|
J:GLN36
|
4.7
|
55.0
|
1.0
|
CB
|
J:ASP35
|
4.8
|
0.3
|
1.0
|
OP2
|
L:DC24
|
4.8
|
62.3
|
1.0
|
|
Reference:
G.Wisedchaisri,
R.K.Holmes,
W.G.J.Hol.
Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions. J.Mol.Biol. V. 342 1155 2004.
ISSN: ISSN 0022-2836
PubMed: 15351642
DOI: 10.1016/J.JMB.2004.07.083
Page generated: Sun Oct 6 22:43:10 2024
|