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Potassium in PDB 3eoh: Refined Group II Intron Structure

Protein crystallography data

The structure of Refined Group II Intron Structure, PDB code: 3eoh was solved by N.Toor, K.Rajashankar, K.S.Keating, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.70 / 3.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.092, 94.969, 225.972, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.7

Other elements in 3eoh:

The structure of Refined Group II Intron Structure also contains other interesting chemical elements:

Magnesium (Mg) 31 atoms

Potassium Binding Sites:

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

Potassium binding site 1 out of 9 in 3eoh

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Potassium binding site 1 out of 9 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Refined Group II Intron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K443

b:0.6
occ:1.00
 O6 A:G79 3.9 67.1 1.0
O6 A:G80 4.0 75.5 1.0
N7 A:G79 4.0 71.4 1.0
N7 A:G80 4.4 66.2 1.0
C6 A:G79 4.5 63.9 1.0
C5 A:G79 4.6 66.2 1.0
OP2 A:A78 4.6 75.1 1.0
O4 A:U103 4.7 67.9 1.0
C6 A:G80 4.8 68.1 1.0
C5 A:G80 5.0 63.0 1.0

Potassium binding site 2 out of 9 in 3eoh

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Potassium binding site 2 out of 9 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Refined Group II Intron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K444

b:0.5
occ:1.00
 O4 A:U96 3.4 63.5 1.0
O6 A:G97 3.4 61.8 1.0
N4 A:C86 3.5 67.5 1.0
O6 A:G87 3.6 58.5 1.0
N6 A:A95 3.6 54.9 1.0
O4 A:U88 4.0 62.5 1.0
C4 A:U96 4.3 53.9 1.0
C6 A:G97 4.3 54.1 1.0
N3 A:U96 4.3 48.0 1.0
C4 A:C86 4.4 69.7 1.0
N7 A:G87 4.4 64.1 1.0
C6 A:G87 4.5 57.4 1.0
C6 A:A95 4.7 55.5 1.0
N1 A:G97 4.8 47.6 1.0
C4 A:U88 4.9 57.1 1.0
C5 A:G87 4.9 58.5 1.0

Potassium binding site 3 out of 9 in 3eoh

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Potassium binding site 3 out of 9 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Refined Group II Intron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K445

b:0.2
occ:1.00
 O6 A:G97 4.1 61.8 1.0
N7 A:G97 4.2 54.4 1.0
O6 A:G98 4.3 62.8 1.0
N7 A:G98 4.4 49.4 1.0
C6 A:G97 4.7 54.1 1.0
C5 A:G97 4.7 50.0 1.0

Potassium binding site 4 out of 9 in 3eoh

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Potassium binding site 4 out of 9 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Refined Group II Intron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K446

b:0.9
occ:1.00
 O6 A:G266 3.7 86.5 1.0
N7 A:G266 3.7 83.0 1.0
C6 A:G266 4.2 80.6 1.0
C5 A:G266 4.2 80.4 1.0
N7 A:G267 4.3 83.3 1.0
C8 A:G266 4.7 80.8 1.0

Potassium binding site 5 out of 9 in 3eoh

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Potassium binding site 5 out of 9 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Refined Group II Intron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K447

b:0.6
occ:1.00
 O6 A:G275 3.8 99.3 1.0
N7 A:G275 3.9 76.3 1.0
C6 A:G275 4.5 82.9 1.0
C5 A:G275 4.6 70.5 1.0
OP2 A:G274 4.9 70.1 1.0
C8 A:G275 5.0 74.3 1.0

Potassium binding site 6 out of 9 in 3eoh

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Potassium binding site 6 out of 9 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Refined Group II Intron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K448

b:0.7
occ:1.00
 O6 A:G275 3.7 99.3 1.0
O4 A:U273 4.1 71.0 1.0
O6 A:G274 4.6 77.3 1.0
C6 A:G275 4.7 82.9 1.0
C4 A:U273 4.9 65.9 1.0

Potassium binding site 7 out of 9 in 3eoh

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Potassium binding site 7 out of 9 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Refined Group II Intron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K449

b:0.3
occ:1.00
 O4 A:U365 3.6 88.2 1.0
N7 A:A364 4.4 85.6 1.0
C4 A:U365 4.4 83.5 1.0
C5 A:U365 4.5 85.4 1.0
OP2 A:A364 4.5 0.1 1.0
OP2 A:U363 4.6 98.9 1.0

Potassium binding site 8 out of 9 in 3eoh

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Potassium binding site 8 out of 9 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Refined Group II Intron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K450

b:0.1
occ:1.00
 OP2 A:A376 3.3 60.9 1.0
O6 A:G5 3.5 70.7 1.0
O4 A:U4 3.6 78.1 1.0
OP2 A:G3 4.0 0.9 1.0
O4' A:A376 4.0 66.7 1.0
P A:G3 4.2 0.7 1.0
C5' A:A376 4.2 58.4 1.0
C6 A:G5 4.5 66.6 1.0
C4 A:U4 4.5 68.0 1.0
P A:A376 4.6 60.9 1.0
N1 A:G5 4.6 61.4 1.0
C4' A:A376 4.6 58.3 1.0
MG A:MG439 4.7 42.5 1.0
O5' A:A376 4.9 55.5 1.0
O3' A:U375 4.9 59.6 1.0
C5 A:U4 4.9 71.7 1.0

Potassium binding site 9 out of 9 in 3eoh

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Potassium binding site 9 out of 9 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Refined Group II Intron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K451

b:0.2
occ:1.00
 O6 A:G229 4.1 0.9 1.0
N6 A:A228 4.2 0.6 1.0
N7 A:A228 4.4 0.1 1.0
C6 A:A228 4.9 0.5 1.0
C5 A:A228 5.0 0.9 1.0

Reference:

N.Toor, K.Rajashankar, K.S.Keating, A.M.Pyle. Structural Basis For Exon Recognition By A Group II Intron. Nat.Struct.Mol.Biol. V. 15 1221 2008.
ISSN: ISSN 1545-9993
PubMed: 18953333
DOI: 10.1038/NSMB.1509
Page generated: Mon Aug 12 08:06:19 2024

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