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Potassium in PDB 8u5t: Structure of Mango II Variant Aptamer Bound to T01-6A-B

Protein crystallography data

The structure of Structure of Mango II Variant Aptamer Bound to T01-6A-B, PDB code: 8u5t was solved by L.F.M.Passalacqua, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.28 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 36.849, 181.111, 105.908, 90, 90, 90
R / Rfree (%) 18.8 / 23.3

Other elements in 8u5t:

The structure of Structure of Mango II Variant Aptamer Bound to T01-6A-B also contains other interesting chemical elements:

Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of Mango II Variant Aptamer Bound to T01-6A-B (pdb code 8u5t). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Structure of Mango II Variant Aptamer Bound to T01-6A-B, PDB code: 8u5t:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 8u5t

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Potassium binding site 1 out of 8 in the Structure of Mango II Variant Aptamer Bound to T01-6A-B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Mango II Variant Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K101

b:37.3
occ:1.00
 O6 A:G23 2.7 45.1 1.0
O6 A:G13 2.7 38.8 1.0
O6 A:G16 2.7 32.7 1.0
O6 A:G29 2.7 43.2 1.0
O6 A:G18 2.8 43.8 1.0
O6 A:G26 2.8 38.6 1.0
O6 A:G21 2.9 37.7 1.0
O6 A:G11 2.9 33.0 1.0
K A:K102 3.6 35.5 1.0
C6 A:G23 3.6 45.2 1.0
C6 A:G13 3.6 41.7 1.0
C6 A:G29 3.6 44.1 1.0
C6 A:G16 3.6 36.8 1.0
C6 A:G26 3.7 39.5 1.0
C6 A:G18 3.7 43.7 1.0
C6 A:G11 3.7 35.9 1.0
C6 A:G21 3.8 39.5 1.0
N1 A:G13 3.8 38.3 1.0
N1 A:G23 3.9 46.0 1.0
N1 A:G29 3.9 45.4 1.0
N1 A:G16 3.9 37.9 1.0
N1 A:G26 4.0 38.1 1.0
N1 A:G18 4.0 43.5 1.0
N1 A:G21 4.1 41.3 1.0
N1 A:G11 4.1 34.3 1.0
C26 A:VLR105 4.5 61.9 1.0
C5 A:G29 4.8 44.7 1.0
C5 A:G23 4.8 48.9 1.0
C5 A:G13 4.8 43.1 1.0
C5 A:G16 4.9 38.3 1.0
C5 A:G11 4.9 38.6 1.0
C5 A:G26 4.9 40.5 1.0
C5 A:G21 4.9 40.3 1.0
C5 A:G18 5.0 43.7 1.0

Potassium binding site 2 out of 8 in 8u5t

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Potassium binding site 2 out of 8 in the Structure of Mango II Variant Aptamer Bound to T01-6A-B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Mango II Variant Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K102

b:35.5
occ:1.00
 O6 A:G11 2.7 33.0 1.0
O6 A:G10 2.7 31.9 1.0
O6 A:G15 2.7 31.3 1.0
O6 A:G16 2.8 32.7 1.0
O6 A:G25 2.8 35.5 1.0
O6 A:G26 2.8 38.6 1.0
O6 A:G21 2.9 37.7 1.0
O6 A:G20 2.9 35.3 1.0
K A:K103 3.4 35.7 0.5
C6 A:G10 3.5 36.3 1.0
K A:K101 3.6 37.3 1.0
C6 A:G16 3.6 36.8 1.0
C6 A:G11 3.6 35.9 1.0
C6 A:G15 3.6 36.7 1.0
C6 A:G25 3.7 37.3 1.0
C6 A:G26 3.7 39.5 1.0
C6 A:G20 3.7 38.4 1.0
N1 A:G10 3.8 34.2 1.0
C6 A:G21 3.8 39.5 1.0
N1 A:G11 3.9 34.3 1.0
N1 A:G16 3.9 37.9 1.0
N1 A:G25 4.0 35.2 1.0
N1 A:G15 4.0 36.1 1.0
N1 A:G26 4.0 38.1 1.0
N1 A:G20 4.1 36.6 1.0
N1 A:G21 4.1 41.3 1.0
C5 A:G10 4.7 38.7 1.0
C5 A:G16 4.7 38.3 1.0
C5 A:G11 4.8 38.6 1.0
C5 A:G26 4.9 40.5 1.0
C5 A:G20 4.9 37.6 1.0
C5 A:G15 4.9 37.8 1.0
C5 A:G25 4.9 38.1 1.0
C2 A:G10 5.0 37.5 1.0

Potassium binding site 3 out of 8 in 8u5t

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Potassium binding site 3 out of 8 in the Structure of Mango II Variant Aptamer Bound to T01-6A-B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Mango II Variant Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:35.7
occ:0.50
 O6 A:G20 2.7 35.3 1.0
O6 A:G10 2.7 31.9 1.0
O6 A:G25 2.8 35.5 1.0
O6 A:G15 2.9 31.3 1.0
K A:K102 3.4 35.5 1.0
C6 A:G25 3.6 37.3 1.0
C6 A:G10 3.6 36.3 1.0
C6 A:G15 3.7 36.7 1.0
C6 A:G20 3.7 38.4 1.0
N1 A:G10 3.9 34.2 1.0
N1 A:G25 3.9 35.2 1.0
N1 A:G15 4.0 36.1 1.0
N1 A:G20 4.0 36.6 1.0
C5 A:G25 4.8 38.1 1.0
C5 A:G15 4.9 37.8 1.0
C5 A:G10 4.9 38.7 1.0
C5 A:G20 4.9 37.6 1.0

Potassium binding site 4 out of 8 in 8u5t

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Potassium binding site 4 out of 8 in the Structure of Mango II Variant Aptamer Bound to T01-6A-B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Mango II Variant Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K101

b:34.6
occ:1.00
 O6 B:G11 2.7 41.6 1.0
O6 B:G16 2.7 39.8 1.0
O6 B:G26 2.7 37.5 1.0
O6 B:G21 2.7 38.8 1.0
O6 B:G15 2.8 39.6 1.0
O6 B:G25 2.9 41.1 1.0
O6 B:G20 3.0 35.4 1.0
O6 B:G10 3.0 41.5 1.0
K B:K103 3.4 38.5 1.0
K B:K102 3.4 39.9 1.0
C6 B:G16 3.6 44.4 1.0
C6 B:G26 3.6 42.0 1.0
C6 B:G21 3.6 43.1 1.0
C6 B:G11 3.6 44.3 1.0
C6 B:G20 3.6 41.9 1.0
C6 B:G15 3.7 42.5 1.0
C6 B:G10 3.7 42.4 1.0
C6 B:G25 3.8 42.5 1.0
N1 B:G20 3.9 43.0 1.0
N1 B:G16 3.9 41.4 1.0
N1 B:G21 3.9 42.9 1.0
N1 B:G26 4.0 41.2 1.0
N1 B:G11 4.0 42.1 1.0
N1 B:G10 4.0 44.1 1.0
N1 B:G15 4.0 42.7 1.0
N1 B:G25 4.1 42.9 1.0
C5 B:G26 4.7 42.2 1.0
C5 B:G16 4.8 43.8 1.0
C5 B:G20 4.8 44.4 1.0
C5 B:G21 4.9 45.1 1.0
C5 B:G11 4.9 44.9 1.0
C5 B:G10 4.9 44.7 1.0
C5 B:G15 5.0 45.0 1.0
C5 B:G25 5.0 43.9 1.0

Potassium binding site 5 out of 8 in 8u5t

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Potassium binding site 5 out of 8 in the Structure of Mango II Variant Aptamer Bound to T01-6A-B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of Mango II Variant Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K102

b:39.9
occ:1.00
 O6 B:G18 2.7 45.5 1.0
O6 B:G23 2.7 45.5 1.0
O6 B:G13 2.7 44.7 1.0
O6 B:G26 2.8 37.5 1.0
O6 B:G29 2.8 45.8 1.0
O6 B:G16 2.8 39.8 1.0
O6 B:G21 2.8 38.8 1.0
O6 B:G11 2.9 41.6 1.0
K B:K101 3.4 34.6 1.0
C6 B:G18 3.6 48.7 1.0
C6 B:G23 3.6 49.0 1.0
C6 B:G13 3.6 48.7 1.0
C6 B:G26 3.7 42.0 1.0
C6 B:G21 3.7 43.1 1.0
C6 B:G16 3.7 44.4 1.0
C6 B:G29 3.7 47.5 1.0
C6 B:G11 3.7 44.3 1.0
N1 B:G18 3.9 45.6 1.0
N1 B:G23 3.9 49.5 1.0
N1 B:G16 3.9 41.4 1.0
N1 B:G21 4.0 42.9 1.0
N1 B:G29 4.0 45.0 1.0
N1 B:G26 4.0 41.2 1.0
N1 B:G13 4.0 48.0 1.0
N1 B:G11 4.0 42.1 1.0
C5 B:G21 4.9 45.1 1.0
C5 B:G13 4.9 51.9 1.0
C5 B:G18 4.9 50.0 1.0
C5 B:G26 4.9 42.2 1.0
C5 B:G11 4.9 44.9 1.0
C5 B:G16 4.9 43.8 1.0
C5 B:G29 4.9 48.1 1.0
C5 B:G23 4.9 52.1 1.0

Potassium binding site 6 out of 8 in 8u5t

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Potassium binding site 6 out of 8 in the Structure of Mango II Variant Aptamer Bound to T01-6A-B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of Mango II Variant Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K103

b:38.5
occ:1.00
 O6 C:G20 2.7 40.8 1.0
O6 B:G10 2.8 41.5 1.0
O6 B:G15 2.8 39.6 1.0
O6 C:G10 2.8 38.2 1.0
O6 B:G20 2.8 35.4 1.0
O6 C:G25 2.8 43.2 1.0
O6 C:G15 2.9 43.4 1.0
O6 B:G25 2.9 41.1 1.0
K C:K101 3.4 38.8 1.0
K B:K101 3.4 34.6 1.0
C6 B:G15 3.6 42.5 1.0
C6 C:G20 3.6 44.1 1.0
C6 C:G25 3.6 43.4 1.0
C6 B:G10 3.7 42.4 1.0
C6 B:G20 3.7 41.9 1.0
C6 C:G10 3.7 45.3 1.0
C6 C:G15 3.7 44.4 1.0
C6 B:G25 3.8 42.5 1.0
N1 B:G15 3.9 42.7 1.0
N1 C:G20 3.9 44.3 1.0
N1 B:G10 3.9 44.1 1.0
N1 B:G20 3.9 43.0 1.0
N1 C:G25 4.0 45.0 1.0
N1 C:G10 4.1 47.2 1.0
N1 C:G15 4.1 45.7 1.0
N1 B:G25 4.2 42.9 1.0
C5 B:G15 4.8 45.0 1.0
C5 C:G25 4.8 44.9 1.0
C5 C:G15 4.9 44.9 1.0
C5 C:G20 4.9 44.6 1.0
C5 B:G10 4.9 44.7 1.0
C5 B:G25 5.0 43.9 1.0

Potassium binding site 7 out of 8 in 8u5t

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Potassium binding site 7 out of 8 in the Structure of Mango II Variant Aptamer Bound to T01-6A-B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of Mango II Variant Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K101

b:38.8
occ:1.00
 O6 C:G26 2.7 43.6 1.0
O6 C:G16 2.7 42.7 1.0
O6 C:G21 2.7 44.5 1.0
O6 C:G25 2.8 43.2 1.0
O6 C:G20 2.8 40.8 1.0
O6 C:G15 2.8 43.4 1.0
O6 C:G11 2.8 46.6 1.0
O6 C:G10 2.9 38.2 1.0
K B:K103 3.4 38.5 1.0
K C:K102 3.5 49.2 1.0
C6 C:G20 3.5 44.1 1.0
C6 C:G26 3.5 45.3 1.0
C6 C:G21 3.6 44.1 1.0
C6 C:G16 3.6 45.5 1.0
C6 C:G25 3.6 43.4 1.0
C6 C:G10 3.7 45.3 1.0
C6 C:G15 3.7 44.4 1.0
C6 C:G11 3.8 49.0 1.0
N1 C:G20 3.8 44.3 1.0
N1 C:G21 3.9 45.6 1.0
N1 C:G25 3.9 45.0 1.0
N1 C:G16 4.0 43.9 1.0
N1 C:G10 4.0 47.2 1.0
N1 C:G26 4.0 44.8 1.0
N1 C:G15 4.1 45.7 1.0
N1 C:G11 4.1 49.6 1.0
C5 C:G26 4.7 47.9 1.0
C5 C:G20 4.7 44.6 1.0
C5 C:G16 4.8 48.0 1.0
C5 C:G21 4.8 45.1 1.0
C5 C:G10 4.8 46.5 1.0
C5 C:G25 4.9 44.9 1.0
C5 C:G15 5.0 44.9 1.0

Potassium binding site 8 out of 8 in 8u5t

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Potassium binding site 8 out of 8 in the Structure of Mango II Variant Aptamer Bound to T01-6A-B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Structure of Mango II Variant Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K102

b:49.2
occ:1.00
 O6 C:G18 2.7 50.3 1.0
O6 C:G16 2.7 42.7 1.0
O6 C:G23 2.7 47.8 1.0
O6 C:G13 2.8 54.8 1.0
O6 C:G21 2.8 44.5 1.0
O6 C:G26 2.8 43.6 1.0
O6 C:G29 2.8 58.6 1.0
O6 C:G11 3.0 46.6 1.0
C6 C:G16 3.5 45.5 1.0
K C:K101 3.5 38.8 1.0
C6 C:G18 3.6 51.9 1.0
C6 C:G23 3.6 53.7 1.0
C6 C:G13 3.6 59.9 1.0
C6 C:G21 3.7 44.1 1.0
C6 C:G29 3.7 58.4 1.0
C6 C:G26 3.7 45.3 1.0
C6 C:G11 3.8 49.0 1.0
N1 C:G23 3.9 52.1 1.0
N1 C:G16 3.9 43.9 1.0
N1 C:G13 3.9 60.6 1.0
N1 C:G29 3.9 56.1 1.0
N1 C:G18 3.9 53.5 1.0
N1 C:G21 4.0 45.6 1.0
N1 C:G11 4.0 49.6 1.0
N1 C:G26 4.0 44.8 1.0
C5 C:G16 4.7 48.0 1.0
C26 C:VLR103 4.8 73.2 1.0
C5 C:G18 4.8 50.3 1.0
C5 C:G21 4.8 45.1 1.0
C5 C:G26 4.9 47.9 1.0
C5 C:G13 4.9 62.3 1.0
C5 C:G29 4.9 55.6 1.0
C5 C:G23 4.9 55.9 1.0
C5 C:G11 5.0 49.1 1.0

Reference:

L.F.M.Passalacqua, A.R.Ferre-D'amare. Structure of Mango II Variant Aptamer Bound to T01-6A-B To Be Published.
Page generated: Tue Aug 13 01:05:19 2024

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