Sodium in PDB 7ozq: Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop
Protein crystallography data
The structure of Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop, PDB code: 7ozq
was solved by
S.Hoefler,
P.Lukat,
T.Carlomagno,
W.Blankenfeldt,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
54.50 /
1.91
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
109.391,
61.598,
138.611,
90,
108.36,
90
|
R / Rfree (%)
|
17.3 /
21.9
|
Other elements in 7ozq:
The structure of Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop
(pdb code 7ozq). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop, PDB code: 7ozq:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 7ozq
Go back to
Sodium Binding Sites List in 7ozq
Sodium binding site 1 out
of 6 in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop
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 Archaeal L7AE Bound to Eukaryotic Kink-Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na201
b:60.7
occ:1.00
|
O
|
D:HOH306
|
2.3
|
60.4
|
1.0
|
OP2
|
E:U22
|
2.3
|
34.7
|
1.0
|
O
|
E:HOH274
|
2.3
|
38.2
|
1.0
|
O
|
E:HOH237
|
2.5
|
43.6
|
1.0
|
OE2
|
D:GLU14
|
2.7
|
43.9
|
0.5
|
CD
|
D:GLU14
|
3.4
|
45.6
|
0.5
|
OE1
|
D:GLU14
|
3.5
|
44.7
|
0.5
|
P
|
E:U22
|
3.7
|
36.3
|
1.0
|
H3'
|
E:C21
|
4.1
|
40.4
|
1.0
|
H5
|
E:U22
|
4.2
|
36.2
|
1.0
|
HG2
|
D:GLU14
|
4.3
|
46.9
|
0.5
|
OP1
|
E:U22
|
4.3
|
39.9
|
1.0
|
HB3
|
D:GLU14
|
4.3
|
40.2
|
0.5
|
HB2
|
D:GLU14
|
4.4
|
40.2
|
0.5
|
O5'
|
E:C21
|
4.5
|
35.1
|
1.0
|
O3'
|
E:C21
|
4.5
|
37.0
|
1.0
|
OP1
|
E:C21
|
4.6
|
45.8
|
1.0
|
OP2
|
E:C21
|
4.6
|
32.0
|
1.0
|
O5'
|
E:U22
|
4.7
|
28.9
|
1.0
|
CG
|
D:GLU14
|
4.7
|
44.8
|
0.5
|
C3'
|
E:C21
|
4.8
|
33.6
|
1.0
|
P
|
E:C21
|
4.8
|
39.9
|
1.0
|
H5''
|
E:C21
|
4.8
|
36.7
|
1.0
|
HG3
|
D:GLU14
|
4.9
|
53.8
|
0.5
|
O
|
E:HOH265
|
5.0
|
44.8
|
1.0
|
C5
|
E:U22
|
5.0
|
30.2
|
1.0
|
|
Sodium binding site 2 out
of 6 in 7ozq
Go back to
Sodium Binding Sites List in 7ozq
Sodium binding site 2 out
of 6 in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop
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 Archaeal L7AE Bound to Eukaryotic Kink-Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na102
b:50.1
occ:1.00
|
O6
|
F:G12
|
2.1
|
28.0
|
1.0
|
O
|
F:HOH219
|
2.6
|
39.8
|
1.0
|
O
|
F:HOH205
|
2.7
|
45.4
|
1.0
|
O
|
F:ACT101
|
2.7
|
56.5
|
1.0
|
O4
|
F:U13
|
2.9
|
31.2
|
1.0
|
C6
|
F:G12
|
3.2
|
31.1
|
1.0
|
C
|
F:ACT101
|
3.2
|
56.4
|
1.0
|
H42
|
F:C21
|
3.2
|
36.9
|
1.0
|
O
|
F:HOH207
|
3.5
|
34.9
|
1.0
|
C4
|
F:U13
|
3.7
|
27.6
|
1.0
|
OXT
|
F:ACT101
|
3.7
|
38.9
|
1.0
|
N7
|
F:G12
|
3.7
|
34.6
|
1.0
|
O
|
F:HOH243
|
3.8
|
34.1
|
1.0
|
H1
|
F:ACT101
|
3.8
|
57.7
|
1.0
|
C5
|
F:G12
|
3.8
|
38.1
|
1.0
|
N4
|
F:C21
|
3.9
|
30.7
|
1.0
|
H3
|
F:U13
|
3.9
|
31.1
|
1.0
|
H41
|
F:C21
|
4.0
|
36.9
|
1.0
|
CH3
|
F:ACT101
|
4.1
|
48.1
|
1.0
|
O6
|
F:G20
|
4.1
|
29.1
|
1.0
|
N3
|
F:U13
|
4.2
|
25.9
|
1.0
|
N1
|
F:G12
|
4.4
|
31.6
|
1.0
|
H1
|
F:G12
|
4.5
|
37.9
|
1.0
|
H2
|
F:ACT101
|
4.7
|
57.7
|
1.0
|
C5
|
F:U13
|
4.7
|
35.7
|
1.0
|
H3
|
F:ACT101
|
4.8
|
57.7
|
1.0
|
O6
|
F:G11
|
4.8
|
29.8
|
1.0
|
H5
|
F:U13
|
4.9
|
42.8
|
1.0
|
O
|
F:HOH271
|
5.0
|
48.1
|
1.0
|
C8
|
F:G12
|
5.0
|
33.9
|
1.0
|
O
|
F:HOH217
|
5.0
|
42.6
|
1.0
|
|
Sodium binding site 3 out
of 6 in 7ozq
Go back to
Sodium Binding Sites List in 7ozq
Sodium binding site 3 out
of 6 in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop
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 Archaeal L7AE Bound to Eukaryotic Kink-Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na103
b:45.0
occ:1.00
|
O
|
F:HOH250
|
2.2
|
39.0
|
1.0
|
OP2
|
F:G15
|
2.6
|
36.5
|
1.0
|
O
|
F:HOH239
|
2.6
|
36.8
|
1.0
|
H8
|
F:G15
|
3.8
|
37.2
|
1.0
|
P
|
F:G15
|
3.8
|
33.3
|
1.0
|
NA
|
F:NA104
|
3.9
|
50.8
|
1.0
|
O5'
|
F:G15
|
4.0
|
29.8
|
1.0
|
O
|
F:HOH234
|
4.2
|
44.9
|
1.0
|
N7
|
F:G15
|
4.2
|
29.2
|
1.0
|
H3'
|
F:C14
|
4.2
|
37.0
|
1.0
|
C8
|
F:G15
|
4.2
|
31.0
|
1.0
|
OP2
|
F:A16
|
4.4
|
32.0
|
1.0
|
H3'
|
F:G15
|
4.5
|
32.7
|
1.0
|
OP1
|
F:G15
|
4.7
|
33.2
|
1.0
|
OP2
|
F:C14
|
4.9
|
26.5
|
1.0
|
O3'
|
F:C14
|
5.0
|
35.7
|
1.0
|
O
|
F:HOH261
|
5.0
|
42.9
|
1.0
|
|
Sodium binding site 4 out
of 6 in 7ozq
Go back to
Sodium Binding Sites List in 7ozq
Sodium binding site 4 out
of 6 in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop
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 Archaeal L7AE Bound to Eukaryotic Kink-Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na104
b:50.8
occ:1.00
|
O
|
F:HOH250
|
2.2
|
39.0
|
1.0
|
OP2
|
F:A17
|
2.4
|
30.9
|
1.0
|
H5''
|
F:A16
|
2.5
|
50.0
|
1.0
|
O
|
F:HOH261
|
2.8
|
42.9
|
1.0
|
N7
|
F:G15
|
3.3
|
29.2
|
1.0
|
P
|
F:A17
|
3.3
|
37.8
|
1.0
|
C5'
|
F:A16
|
3.4
|
41.6
|
1.0
|
C5
|
F:G15
|
3.5
|
26.1
|
1.0
|
O3'
|
F:A16
|
3.5
|
35.2
|
1.0
|
O5'
|
F:A16
|
3.6
|
31.6
|
1.0
|
C8
|
F:G15
|
3.7
|
31.0
|
1.0
|
H3'
|
F:G15
|
3.7
|
32.7
|
1.0
|
H2'
|
F:G15
|
3.7
|
32.3
|
1.0
|
O
|
F:HOH239
|
3.8
|
36.8
|
1.0
|
H3'
|
F:A16
|
3.8
|
39.8
|
1.0
|
OP1
|
F:A17
|
3.9
|
44.5
|
1.0
|
C4
|
F:G15
|
3.9
|
24.9
|
1.0
|
NA
|
F:NA103
|
3.9
|
45.0
|
1.0
|
C6
|
F:G15
|
3.9
|
31.7
|
1.0
|
H8
|
F:G15
|
4.0
|
37.2
|
1.0
|
C3'
|
F:A16
|
4.0
|
33.2
|
1.0
|
N9
|
F:G15
|
4.0
|
29.0
|
1.0
|
H5'
|
F:A16
|
4.0
|
50.0
|
1.0
|
C4'
|
F:A16
|
4.2
|
27.6
|
1.0
|
O6
|
F:G15
|
4.2
|
29.8
|
1.0
|
OP2
|
F:A16
|
4.2
|
32.0
|
1.0
|
C2'
|
F:G15
|
4.4
|
26.9
|
1.0
|
H4'
|
F:A16
|
4.4
|
33.2
|
1.0
|
C3'
|
F:G15
|
4.4
|
27.2
|
1.0
|
P
|
F:A16
|
4.6
|
32.1
|
1.0
|
N1
|
F:G15
|
4.6
|
30.4
|
1.0
|
N3
|
F:G15
|
4.7
|
32.9
|
1.0
|
O5'
|
F:A17
|
4.8
|
41.7
|
1.0
|
C1'
|
F:G15
|
4.9
|
29.8
|
1.0
|
O
|
F:HOH234
|
4.9
|
44.9
|
1.0
|
C2
|
F:G15
|
5.0
|
28.6
|
1.0
|
O3'
|
F:G15
|
5.0
|
28.9
|
1.0
|
|
Sodium binding site 5 out
of 6 in 7ozq
Go back to
Sodium Binding Sites List in 7ozq
Sodium binding site 5 out
of 6 in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop
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 Archaeal L7AE Bound to Eukaryotic Kink-Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na105
b:57.7
occ:1.00
|
OP2
|
F:U22
|
2.3
|
31.6
|
1.0
|
O
|
F:HOH259
|
2.6
|
36.4
|
1.0
|
P
|
F:U22
|
3.7
|
34.9
|
1.0
|
H3'
|
F:C21
|
4.1
|
35.4
|
1.0
|
H5
|
F:U22
|
4.1
|
38.8
|
1.0
|
OP1
|
F:U22
|
4.3
|
38.4
|
1.0
|
O3'
|
F:C21
|
4.6
|
32.4
|
1.0
|
O5'
|
F:C21
|
4.6
|
36.2
|
1.0
|
O5'
|
F:U22
|
4.7
|
35.3
|
1.0
|
OP1
|
F:C21
|
4.7
|
39.5
|
1.0
|
OP2
|
F:C21
|
4.7
|
30.9
|
1.0
|
C3'
|
F:C21
|
4.8
|
29.5
|
1.0
|
P
|
F:C21
|
4.9
|
38.0
|
1.0
|
H6
|
F:U22
|
4.9
|
41.5
|
1.0
|
C5
|
F:U22
|
4.9
|
32.3
|
1.0
|
H5''
|
F:C21
|
4.9
|
41.9
|
1.0
|
|
Sodium binding site 6 out
of 6 in 7ozq
Go back to
Sodium Binding Sites List in 7ozq
Sodium binding site 6 out
of 6 in the Crystal Structure of Archaeal L7AE Bound to Eukaryotic Kink-Loop
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 Archaeal L7AE Bound to Eukaryotic Kink-Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na102
b:40.4
occ:1.00
|
O
|
G:HOH272
|
2.5
|
43.8
|
1.0
|
O2'
|
G:G20
|
2.5
|
35.3
|
1.0
|
O
|
G:HOH244
|
2.8
|
38.5
|
1.0
|
H5'
|
G:C21
|
3.2
|
39.6
|
1.0
|
O4'
|
G:C21
|
3.4
|
34.5
|
1.0
|
H2'
|
G:G20
|
3.4
|
42.0
|
1.0
|
H4'
|
G:C21
|
3.5
|
42.6
|
1.0
|
C2'
|
G:G20
|
3.5
|
35.0
|
1.0
|
O
|
G:HOH257
|
3.7
|
39.2
|
1.0
|
C4'
|
G:C21
|
3.8
|
35.5
|
1.0
|
H1'
|
G:G20
|
3.8
|
39.5
|
1.0
|
C5'
|
G:C21
|
3.9
|
33.0
|
1.0
|
H22
|
G:G20
|
4.1
|
37.4
|
1.0
|
N3
|
G:G20
|
4.1
|
33.9
|
1.0
|
C1'
|
G:G20
|
4.2
|
32.9
|
1.0
|
H1'
|
G:C21
|
4.4
|
43.1
|
1.0
|
H5''
|
G:C21
|
4.4
|
39.6
|
1.0
|
O
|
G:HOH274
|
4.4
|
49.6
|
1.0
|
C1'
|
G:C21
|
4.5
|
35.9
|
1.0
|
N2
|
G:G20
|
4.8
|
31.2
|
1.0
|
C3'
|
G:G20
|
4.8
|
30.9
|
1.0
|
O5'
|
G:C21
|
4.9
|
31.0
|
1.0
|
C2
|
G:G20
|
5.0
|
34.4
|
1.0
|
O3'
|
G:G20
|
5.0
|
33.4
|
1.0
|
|
Reference:
S.Hofler,
P.Lukat,
W.Blankenfeldt,
T.Carlomagno.
Eukaryotic Box C/D Methylation Machinery Has Two Non-Symmetric Protein Assembly Sites. Sci Rep V. 11 17561 2021.
ISSN: ESSN 2045-2322
PubMed: 34475498
DOI: 10.1038/S41598-021-97030-Y
Page generated: Tue Oct 8 18:24:20 2024
|