Potassium in PDB 8x0s: Crystal Structure of R(G4C2)2

Protein crystallography data

The structure of Crystal Structure of R(G4C2)2, PDB code: 8x0s was solved by Y.Geng, C.Liu, Q.Cai, G.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.71 / 2.96
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.971, 62.971, 129.227, 90, 90, 120
R / Rfree (%) 26.1 / 30

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of R(G4C2)2 (pdb code 8x0s). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Crystal Structure of R(G4C2)2, PDB code: 8x0s:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 8x0s

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Potassium binding site 1 out of 9 in the Crystal Structure of R(G4C2)2


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of R(G4C2)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K101

b:54.0
occ:0.50
 O6 A:G7 2.7 64.3 1.0
O6 A:G8 2.8 52.7 1.0
O6 A:G2 2.8 54.0 1.0
O6 A:G1 2.9 54.5 1.0
K A:K104 3.3 67.1 0.5
K A:K102 3.4 59.5 0.5
C6 A:G7 3.6 66.3 1.0
C6 A:G8 3.7 56.6 1.0
C6 A:G2 3.7 58.6 1.0
C6 A:G1 3.8 55.3 1.0
N1 A:G7 4.0 64.6 1.0
N1 A:G8 4.1 58.7 1.0
N1 A:G2 4.1 61.5 1.0
N1 A:G1 4.2 59.7 1.0
C5 A:G2 4.9 56.1 1.0
C5 A:G7 4.9 61.2 1.0
C5 A:G8 4.9 56.2 1.0

Potassium binding site 2 out of 9 in 8x0s

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Potassium binding site 2 out of 9 in the Crystal Structure of R(G4C2)2


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of R(G4C2)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K102

b:59.5
occ:0.50
 O6 A:G2 2.7 54.0 1.0
O6 A:G8 2.7 52.7 1.0
O6 A:G9 2.8 49.0 1.0
O6 A:G3 2.9 62.3 1.0
K A:K103 3.3 57.0 0.5
K A:K101 3.4 54.0 0.5
C6 A:G2 3.6 58.6 1.0
C6 A:G8 3.7 56.6 1.0
C6 A:G9 3.8 61.4 1.0
C6 A:G3 3.8 64.7 1.0
N1 A:G2 3.9 61.5 1.0
N1 A:G8 4.0 58.7 1.0
N1 A:G3 4.2 68.3 1.0
N1 A:G9 4.2 63.9 1.0
C5 A:G2 4.9 56.1 1.0
C5 A:G8 4.9 56.2 1.0
C5 A:G9 5.0 62.3 1.0

Potassium binding site 3 out of 9 in 8x0s

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Potassium binding site 3 out of 9 in the Crystal Structure of R(G4C2)2


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of R(G4C2)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:57.0
occ:0.50
 O6 A:G10 2.8 62.2 1.0
O6 A:G9 2.8 49.0 1.0
O6 A:G3 2.8 62.3 1.0
O6 A:G4 2.9 60.9 1.0
K A:K102 3.3 59.5 0.5
C6 A:G3 3.7 64.7 1.0
C6 A:G9 3.7 61.4 1.0
C6 A:G10 3.7 62.0 1.0
C6 A:G4 3.8 62.7 1.0
K A:K105 4.0 85.8 0.5
N1 A:G3 4.0 68.3 1.0
N1 A:G4 4.1 62.4 1.0
N1 A:G9 4.1 63.9 1.0
N1 A:G10 4.2 65.4 1.0
C5 A:G9 4.9 62.3 1.0
C5 A:G3 4.9 61.2 1.0
C5 A:G10 4.9 55.3 1.0
C5 A:G4 5.0 58.6 1.0

Potassium binding site 4 out of 9 in 8x0s

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Potassium binding site 4 out of 9 in the Crystal Structure of R(G4C2)2


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of R(G4C2)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K104

b:67.1
occ:0.50
 O6 B:G7 2.9 58.4 1.0
O6 A:G7 2.9 64.3 1.0
O6 B:G1 3.0 53.6 1.0
O6 A:G1 3.0 54.5 1.0
K A:K101 3.3 54.0 0.5
K B:K101 3.6 56.4 0.5
C6 A:G7 3.8 66.3 1.0
C6 B:G7 3.8 60.8 1.0
C6 B:G1 3.8 59.4 1.0
C6 A:G1 3.9 55.3 1.0
N1 A:G7 4.1 64.6 1.0
N1 B:G7 4.1 59.5 1.0
N1 B:G1 4.2 55.1 1.0
N1 A:G1 4.3 59.7 1.0
C5 B:G1 5.0 60.9 1.0
C5 A:G7 5.0 61.2 1.0

Potassium binding site 5 out of 9 in 8x0s

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Potassium binding site 5 out of 9 in the Crystal Structure of R(G4C2)2


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of R(G4C2)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K105

b:85.8
occ:0.50
 N3 A:C11 3.0 56.6 1.0
O6 A:G4 3.1 60.9 1.0
O6 A:G10 3.2 62.2 1.0
O2 A:C11 3.6 62.3 1.0
C2 A:C11 3.8 64.5 1.0
C6 A:G4 3.9 62.7 1.0
C6 A:G10 4.0 62.0 1.0
K A:K103 4.0 57.0 0.5
C4 A:C11 4.0 60.4 1.0
N4 A:C11 4.0 62.5 1.0
N1 A:G4 4.3 62.4 1.0
N1 A:G10 4.3 65.4 1.0

Potassium binding site 6 out of 9 in 8x0s

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Potassium binding site 6 out of 9 in the Crystal Structure of R(G4C2)2


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of R(G4C2)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K101

b:56.4
occ:0.50
 O6 B:G2 2.7 51.3 1.0
O6 B:G8 2.8 52.9 1.0
O6 B:G7 2.8 58.4 1.0
O6 B:G1 2.9 53.6 1.0
K B:K102 3.3 59.0 0.5
K A:K104 3.6 67.1 0.5
C6 B:G2 3.6 58.6 1.0
C6 B:G8 3.7 59.5 1.0
C6 B:G7 3.8 60.8 1.0
C6 B:G1 3.9 59.4 1.0
N1 B:G2 4.0 57.1 1.0
N1 B:G8 4.1 61.9 1.0
N1 B:G7 4.2 59.5 1.0
N1 B:G1 4.2 55.1 1.0
C5 B:G2 4.7 59.3 1.0
C5 B:G8 4.9 64.0 1.0
C5 B:G7 5.0 54.6 1.0

Potassium binding site 7 out of 9 in 8x0s

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Potassium binding site 7 out of 9 in the Crystal Structure of R(G4C2)2


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of R(G4C2)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K102

b:59.0
occ:0.50
 O6 B:G9 2.8 46.3 1.0
O6 B:G2 2.8 51.3 1.0
O6 B:G3 2.8 64.5 1.0
O6 B:G8 2.9 52.9 1.0
K B:K103 3.2 65.2 0.5
K B:K101 3.3 56.4 0.5
C6 B:G2 3.7 58.6 1.0
C6 B:G9 3.8 56.7 1.0
C6 B:G3 3.8 68.2 1.0
C6 B:G8 3.8 59.5 1.0
N1 B:G2 4.1 57.1 1.0
N1 B:G8 4.2 61.9 1.0
N1 B:G9 4.2 56.6 1.0
N1 B:G3 4.2 68.5 1.0
C5 B:G2 5.0 59.3 1.0

Potassium binding site 8 out of 9 in 8x0s

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Potassium binding site 8 out of 9 in the Crystal Structure of R(G4C2)2


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of R(G4C2)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K103

b:65.2
occ:0.50
 O6 B:G10 2.8 54.3 1.0
O6 B:G9 2.8 46.3 1.0
O6 B:G3 2.9 64.5 1.0
O6 B:G4 2.9 65.5 1.0
K B:K102 3.2 59.0 0.5
C6 B:G10 3.7 57.5 1.0
C6 B:G9 3.7 56.7 1.0
C6 B:G3 3.8 68.2 1.0
C6 B:G4 3.8 58.0 1.0
K B:K104 4.1 89.2 0.5
N1 B:G10 4.1 58.5 1.0
N1 B:G3 4.1 68.5 1.0
N1 B:G9 4.1 56.6 1.0
N1 B:G4 4.2 56.5 1.0
C5 B:G10 4.9 56.3 1.0
C5 B:G9 4.9 59.1 1.0
C5 B:G3 5.0 66.8 1.0

Potassium binding site 9 out of 9 in 8x0s

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Potassium binding site 9 out of 9 in the Crystal Structure of R(G4C2)2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of R(G4C2)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K104

b:89.2
occ:0.50
 N3 B:C11 3.1 72.5 1.0
O6 B:G10 3.3 54.3 1.0
O6 B:G4 3.3 65.5 1.0
O2 B:C11 3.6 66.2 1.0
C2 B:C11 3.8 77.7 1.0
C4 B:C11 4.0 78.1 1.0
N4 B:C11 4.0 78.1 1.0
C6 B:G10 4.0 57.5 1.0
C6 B:G4 4.1 58.0 1.0
K B:K103 4.1 65.2 0.5
N1 B:G10 4.3 58.5 1.0
N1 B:G4 4.4 56.5 1.0

Reference:

Y.Geng, C.Liu, N.Xu, M.C.Suen, H.Miao, Y.Xie, B.Zhang, X.Chen, Y.Song, Z.Wang, Q.Cai, G.Zhu. Crystal Structure of A Tetrameric Rna G-Quadruplex Formed By Hexanucleotide Repeat Expansions of C9ORF72 in Als/Ftd. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38860430
DOI: 10.1093/NAR/GKAE473
Page generated: Tue Aug 13 01:14:54 2024

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