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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

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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

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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

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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

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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

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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

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