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Potassium in PDB 5ew4: Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+

Protein crystallography data

The structure of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+, PDB code: 5ew4 was solved by D.R.Tomchick, D.W.Dodd, K.T.Gagnon, D.R.Corey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.92 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.020, 47.615, 58.900, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 23.9

Other elements in 5ew4:

The structure of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ also contains other interesting chemical elements:

Strontium (Sr) 1 atom
Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ (pdb code 5ew4). 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 C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+, PDB code: 5ew4:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 5ew4

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Potassium binding site 1 out of 9 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K101

b:12.9
occ:1.00
 O A:HOH211 2.6 16.9 1.0
O A:HOH276 2.7 24.3 1.0
O A:HOH231 2.7 24.3 1.0
O6 A:G5 2.8 20.1 1.0
O A:HOH225 2.8 17.2 1.0
O A:HOH204 2.8 17.2 1.0
O A:HOH252 2.8 26.2 1.0
N7 A:G5 2.9 20.1 1.0
C6 A:G5 3.4 20.4 1.0
C5 A:G5 3.4 21.5 1.0
H5 A:C4 4.0 25.6 1.0
C8 A:G5 4.1 19.5 1.0
O A:HOH238 4.1 33.6 1.0
O A:HOH261 4.4 32.6 1.0
C5 A:C4 4.4 21.3 1.0
H42 B:C20 4.4 19.0 1.0
O A:HOH270 4.4 26.9 1.0
H41 A:C4 4.4 31.4 1.0
H8 A:G5 4.4 23.4 1.0
O A:HOH215 4.5 22.0 1.0
O6 A:G6 4.5 16.3 1.0
N7 A:G6 4.5 19.0 1.0
OP2 A:C4 4.6 24.9 1.0
O B:HOH279 4.6 30.7 1.0
O A:HOH255 4.6 19.4 1.0
N1 A:G5 4.7 19.7 1.0
C4 A:G5 4.7 21.1 1.0
N4 A:C4 4.7 26.2 1.0
OP2 A:C3 4.8 39.3 1.0
C4 A:C4 4.8 23.3 1.0
O B:HOH229 4.8 20.4 1.0

Potassium binding site 2 out of 9 in 5ew4

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Potassium binding site 2 out of 9 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K102

b:12.8
occ:0.49
 OP1 A:G18 2.7 18.7 1.0
O A:HOH243 2.8 25.8 1.0
O3' A:G17 3.0 13.4 1.0
P A:G18 3.4 16.6 1.0
O A:HOH206 3.9 18.7 1.0
H5'' A:G17 3.9 16.2 1.0
H5' A:G18 4.1 17.5 1.0
H5'' A:G18 4.1 17.5 1.0
H4' A:G17 4.1 16.3 1.0
C3' A:G17 4.2 12.8 1.0
C5' A:G18 4.4 14.6 1.0
O5' A:G18 4.4 14.9 1.0
C4' A:G17 4.5 13.6 1.0
OP2 A:G18 4.5 17.6 1.0
C5' A:G17 4.7 13.5 1.0
H3' A:G17 4.8 15.4 1.0
O2' A:G17 4.9 13.5 1.0

Potassium binding site 3 out of 9 in 5ew4

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Potassium binding site 3 out of 9 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K104

b:15.0
occ:1.00
 O B:HOH249 2.8 32.6 1.0
OP1 B:G17 2.9 18.7 1.0
O B:HOH273 3.1 31.5 1.0
O3' B:C16 3.5 12.2 1.0
P B:G17 3.8 14.9 1.0
HO2' B:C16 4.3 17.9 1.0
H5' B:G17 4.3 14.6 1.0
H5'' B:G17 4.5 14.6 1.0
H4' B:C16 4.6 17.8 1.0
C3' B:C16 4.7 13.6 1.0
C5' B:G17 4.8 12.2 1.0
O B:HOH230 4.8 21.0 1.0
O2' B:C16 4.8 14.9 1.0
O5' B:G17 4.9 11.7 1.0
O B:HOH209 4.9 27.4 1.0
OP2 B:G17 4.9 14.6 1.0

Potassium binding site 4 out of 9 in 5ew4

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Potassium binding site 4 out of 9 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K105

b:15.0
occ:1.00
 O A:HOH255 2.7 19.4 1.0
O B:HOH253 2.7 18.4 1.0
O B:HOH279 2.7 30.7 1.0
O A:HOH272 2.8 25.6 1.0
O B:HOH251 2.8 24.5 1.0
O A:HOH270 2.8 26.9 1.0
O B:HOH272 2.8 26.2 1.0
O B:HOH281 2.8 28.7 1.0
H41 A:C7 3.9 16.6 1.0
H5 B:C15 4.2 14.7 1.0
OP2 B:C15 4.4 14.3 1.0
O A:HOH264 4.4 24.8 1.0
H41 B:C15 4.5 17.6 1.0
O A:HOH225 4.5 17.2 1.0
O A:HOH276 4.6 24.3 1.0
O B:HOH255 4.6 22.4 1.0
O A:HOH251 4.6 26.6 1.0
N4 A:C7 4.8 13.8 1.0
K B:K107 4.8 38.7 1.0
C5 B:C15 4.8 12.3 1.0
O A:HOH215 4.8 22.0 1.0
O B:HOH242 5.0 13.6 1.0

Potassium binding site 5 out of 9 in 5ew4

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Potassium binding site 5 out of 9 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K106

b:18.4
occ:1.00
 CL B:CL111 2.4 20.6 1.0
O B:HOH217 2.7 31.9 1.0
O6 B:G5 2.7 26.6 1.0
O B:HOH223 2.8 39.6 1.0
O B:HOH280 2.8 31.5 1.0
O B:HOH236 2.8 33.0 1.0
O B:HOH224 2.8 21.0 1.0
N7 B:G5 2.9 28.2 1.0
C6 B:G5 3.3 27.0 1.0
C5 B:G5 3.4 27.5 1.0
H5 B:C4 3.6 39.4 1.0
C5 B:C4 4.0 32.8 1.0
H41 B:C4 4.0 35.0 1.0
C8 B:G5 4.0 29.3 1.0
O B:HOH202 4.1 30.6 1.0
O B:HOH274 4.2 31.3 1.0
H42 A:C20 4.3 24.2 1.0
OP2 B:C4 4.4 30.1 1.0
H8 B:G5 4.4 35.1 1.0
N4 B:C4 4.4 29.2 1.0
C4 B:C4 4.5 31.5 1.0
O6 B:G6 4.6 23.5 1.0
O B:HOH234 4.6 27.8 1.0
N1 B:G5 4.7 26.2 1.0
C4 B:G5 4.7 28.2 1.0
C6 B:C4 4.7 32.3 1.0
N7 B:G6 4.8 25.8 1.0
H6 B:C4 4.8 38.7 1.0
O B:HOH283 4.9 27.4 1.0
OP2 B:C3 5.0 29.6 1.0
H42 B:C4 5.0 35.0 1.0

Potassium binding site 6 out of 9 in 5ew4

Go back to Potassium Binding Sites List in 5ew4
Potassium binding site 6 out of 9 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K107

b:38.7
occ:1.00
 O B:HOH277 2.7 21.9 1.0
O A:HOH270 2.8 26.9 1.0
O6 B:G17 2.8 10.6 1.0
O B:HOH213 3.0 18.0 1.0
O6 B:G18 3.0 11.1 1.0
O B:HOH229 3.1 20.4 1.0
H42 A:C8 3.5 16.3 1.0
H42 A:C7 3.6 16.6 1.0
O B:HOH226 3.7 11.6 1.0
C6 B:G17 3.7 8.9 1.0
O B:HOH272 3.7 26.2 1.0
O B:HOH242 3.7 13.6 1.0
O B:HOH255 3.9 22.4 1.0
C6 B:G18 3.9 10.7 1.0
N7 B:G17 4.0 10.7 1.0
H41 A:C7 4.1 16.6 1.0
H41 A:C8 4.1 16.3 1.0
N4 A:C8 4.1 13.6 1.0
C5 B:G17 4.2 9.0 1.0
N4 A:C7 4.2 13.8 1.0
O B:HOH253 4.3 18.4 1.0
N7 B:G18 4.3 9.5 1.0
C5 B:G18 4.5 10.5 1.0
O B:HOH228 4.5 20.1 1.0
O A:HOH211 4.6 16.9 1.0
OP2 B:C16 4.6 14.4 1.0
K B:K105 4.8 15.0 1.0
N1 B:G17 4.9 9.3 1.0
O A:HOH276 4.9 24.3 1.0
K B:K108 4.9 9.6 1.0

Potassium binding site 7 out of 9 in 5ew4

Go back to Potassium Binding Sites List in 5ew4
Potassium binding site 7 out of 9 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K108

b:9.6
occ:1.00
 OP2 B:G17 2.6 14.6 1.0
O B:HOH228 2.7 20.1 1.0
O B:HOH277 2.7 21.9 1.0
O B:HOH231 2.7 21.5 1.0
O B:HOH215 2.8 20.1 1.0
O B:HOH275 2.8 32.9 1.0
O B:HOH213 2.8 18.0 1.0
P B:G17 3.9 14.9 1.0
O5' B:G17 4.1 11.7 1.0
H8 B:G17 4.3 11.2 1.0
O A:HOH261 4.4 32.6 1.0
O B:HOH230 4.4 21.0 1.0
OP2 B:G18 4.5 12.7 1.0
O B:HOH209 4.5 27.4 1.0
N7 B:G17 4.6 10.7 1.0
O B:HOH229 4.6 20.4 1.0
OP1 B:G17 4.6 18.7 1.0
OP2 B:C16 4.6 14.4 1.0
H3' B:C16 4.7 16.3 1.0
C8 B:G17 4.7 9.3 1.0
O B:HOH255 4.7 22.4 1.0
H3' B:G17 4.7 13.7 1.0
O B:HOH233 4.9 29.6 1.0
OP1 B:C16 4.9 20.6 1.0
K B:K107 4.9 38.7 1.0

Potassium binding site 8 out of 9 in 5ew4

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Potassium binding site 8 out of 9 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K109

b:29.2
occ:1.00
 O B:HOH208 2.7 26.3 1.0
O B:HOH212 2.7 31.9 1.0
O B:HOH247 2.8 26.9 1.0
O B:HOH244 4.2 26.5 1.0
MG B:MG103 4.2 41.8 1.0
O A:HOH279 4.5 20.7 1.0
OP2 B:C10 4.6 27.2 1.0
O B:HOH262 4.6 33.1 1.0
O B:HOH278 4.7 35.0 1.0
O6 B:G12 4.7 16.1 1.0
O B:HOH276 4.8 32.6 1.0
N7 B:G11 4.9 12.2 1.0

Potassium binding site 9 out of 9 in 5ew4

Go back to Potassium Binding Sites List in 5ew4
Potassium binding site 9 out of 9 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+


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 C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with SR2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K110

b:26.2
occ:1.00
 O A:HOH257 4.5 35.5 1.0
OP1 A:C4 4.5 31.4 1.0
O B:HOH279 4.6 30.7 1.0
OP2 B:C15 4.6 14.3 1.0
OP1 B:C15 4.6 17.5 1.0
OP1 B:C14 4.7 21.3 1.0
OP2 A:G5 4.8 24.2 1.0
H5'' B:C14 4.8 19.3 1.0

Reference:

D.W.Dodd, D.R.Tomchick, D.R.Corey, K.T.Gagnon. Pathogenic C9ORF72 Antisense Repeat Rna Forms A Double Helix with Tandem C:C Mismatches. Biochemistry V. 55 1283 2016.
ISSN: ISSN 0006-2960
PubMed: 26878348
DOI: 10.1021/ACS.BIOCHEM.6B00136
Page generated: Mon Aug 12 13:29:23 2024

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