Atomistry » Sodium » PDB 7oa7-7p0j » 7ozq
Atomistry »
  Sodium »
    PDB 7oa7-7p0j »
      7ozq »

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:

Chlorine (Cl) 1 atom
Calcium (Ca) 3 atoms

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: Mon Aug 18 11:18:01 2025

Last articles

Cd in 9J00
Cd in 9J01
Ca in 9VAK
Ca in 9O9V
Ca in 9U8G
Ca in 9UD8
Ca in 9R0Q
Ca in 9QDT
Ca in 9O4Q
Ca in 9O4O
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy