Potassium in PDB 8u5p: Structure of Mango II Aptamer Bound to T01-6A-B

Protein crystallography data

The structure of Structure of Mango II Aptamer Bound to T01-6A-B, PDB code: 8u5p 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) 34.56 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 37.212, 183.72, 108.241, 90, 90, 90
R / Rfree (%) 21.3 / 22.3

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of Mango II Aptamer Bound to T01-6A-B (pdb code 8u5p). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Structure of Mango II Aptamer Bound to T01-6A-B, PDB code: 8u5p:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 8u5p

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Potassium binding site 1 out of 9 in the Structure of Mango II 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 Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K101

b:61.2
occ:1.00
 O6 A:G24 2.8 56.4 1.0
O6 A:G16 2.8 50.6 1.0
O6 A:G27 2.8 55.8 1.0
O6 A:G13 2.8 57.2 1.0
O6 A:G21 2.8 55.9 1.0
O6 A:G18 2.9 62.3 1.0
O6 A:G29 2.9 55.8 1.0
O6 A:G11 2.9 50.3 1.0
K A:K102 3.4 57.6 1.0
C6 A:G16 3.6 53.6 1.0
C6 A:G24 3.6 59.4 1.0
C6 A:G27 3.7 52.6 1.0
C6 A:G29 3.7 58.0 1.0
C6 A:G13 3.7 57.0 1.0
C6 A:G18 3.7 57.6 1.0
C6 A:G11 3.7 51.1 1.0
C6 A:G21 3.8 56.9 1.0
N1 A:G16 3.8 55.7 1.0
N1 A:G18 3.9 55.8 1.0
N1 A:G24 4.0 59.7 1.0
N1 A:G29 4.0 59.4 1.0
N1 A:G27 4.0 51.0 1.0
N1 A:G11 4.0 52.6 1.0
N1 A:G13 4.0 55.5 1.0
N1 A:G21 4.2 57.8 1.0
C5 A:G16 4.8 51.9 1.0
C5 A:G24 4.9 61.5 1.0
C5 A:G27 4.9 52.9 1.0
C5 A:G29 4.9 57.1 1.0
C5 A:G21 4.9 57.1 1.0
C5 A:G11 4.9 49.3 1.0
C26 A:VKI104 4.9 71.8 1.0
C5 A:G13 5.0 54.3 1.0
C5 A:G18 5.0 56.2 1.0

Potassium binding site 2 out of 9 in 8u5p

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Potassium binding site 2 out of 9 in the Structure of Mango II 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 Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K102

b:57.6
occ:1.00
 O6 A:G26 2.7 54.5 1.0
O6 A:G16 2.7 50.6 1.0
O6 A:G15 2.7 49.8 1.0
O6 A:G27 2.8 55.8 1.0
O6 A:G21 2.8 55.9 1.0
O6 A:G11 2.8 50.3 1.0
O6 A:G20 2.9 54.4 1.0
O6 A:G10 3.2 52.0 1.0
K A:K103 3.3 63.6 0.5
K A:K101 3.4 61.2 1.0
C6 A:G16 3.5 53.6 1.0
C6 A:G20 3.6 55.2 1.0
C6 A:G15 3.6 49.3 1.0
C6 A:G26 3.7 53.8 1.0
C6 A:G11 3.7 51.1 1.0
C6 A:G27 3.7 52.6 1.0
C6 A:G21 3.8 56.9 1.0
N1 A:G15 3.8 51.7 1.0
C6 A:G10 3.8 50.5 1.0
N1 A:G16 3.8 55.7 1.0
N1 A:G20 3.8 56.9 1.0
N1 A:G11 3.9 52.6 1.0
N1 A:G10 4.0 50.4 1.0
N1 A:G26 4.0 52.1 1.0
N1 A:G27 4.1 51.0 1.0
N1 A:G21 4.1 57.8 1.0
C5 A:G20 4.7 54.6 1.0
C5 A:G16 4.7 51.9 1.0
C5 A:G15 4.9 47.9 1.0
C5 A:G26 4.9 54.8 1.0
C5 A:G27 4.9 52.9 1.0
C5 A:G10 4.9 48.0 1.0
C5 A:G21 5.0 57.1 1.0
C2 A:G20 5.0 58.3 1.0
C5 A:G11 5.0 49.3 1.0

Potassium binding site 3 out of 9 in 8u5p

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Potassium binding site 3 out of 9 in the Structure of Mango II 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 Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:63.6
occ:0.50
 O6 A:G20 2.6 54.4 1.0
O6 A:G10 2.7 52.0 1.0
O6 A:G26 2.8 54.5 1.0
O6 A:G15 2.9 49.8 1.0
K A:K102 3.3 57.6 1.0
C6 A:G20 3.6 55.2 1.0
C6 A:G15 3.6 49.3 1.0
C6 A:G10 3.6 50.5 1.0
C6 A:G26 3.7 53.8 1.0
N1 A:G10 3.8 50.4 1.0
N1 A:G15 3.8 51.7 1.0
N1 A:G20 3.9 56.9 1.0
N1 A:G26 4.0 52.1 1.0
C5 A:G15 4.8 47.9 1.0
C5 A:G26 4.9 54.8 1.0
C5 A:G20 4.9 54.6 1.0
C5 A:G10 5.0 48.0 1.0

Potassium binding site 4 out of 9 in 8u5p

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Potassium binding site 4 out of 9 in the Structure of Mango II 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 Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K101

b:78.0
occ:1.00
 O6 B:G15 2.7 75.4 1.0
O6 B:G16 2.7 72.8 1.0
O6 B:G26 2.7 75.1 1.0
O6 B:G11 2.7 72.5 1.0
O6 B:G27 2.8 68.7 1.0
O6 B:G21 3.0 74.0 1.0
O6 B:G20 3.1 76.8 1.0
O6 B:G10 3.1 71.7 1.0
K B:K103 3.4 87.2 1.0
C6 B:G15 3.6 75.1 1.0
K B:K102 3.6 75.0 1.0
C6 B:G16 3.6 74.4 1.0
C6 B:G11 3.7 72.0 1.0
C6 B:G27 3.7 69.9 1.0
C6 B:G20 3.7 77.3 1.0
C6 B:G10 3.7 72.6 1.0
C6 B:G26 3.7 73.7 1.0
C6 B:G21 3.8 74.5 1.0
N1 B:G20 3.9 76.9 1.0
N1 B:G15 3.9 75.5 1.0
N1 B:G10 3.9 74.1 1.0
N1 B:G11 3.9 72.0 1.0
N1 B:G21 4.0 73.8 1.0
N1 B:G16 4.0 74.9 1.0
N1 B:G27 4.0 69.1 1.0
N1 B:G26 4.2 73.1 1.0
C5 B:G16 4.8 72.7 1.0
C5 B:G15 4.8 74.9 1.0
C5 B:G20 4.8 78.3 1.0
C5 B:G10 4.8 71.6 1.0
C5 B:G27 4.9 69.0 1.0
C5 B:G11 4.9 71.8 1.0
C5 B:G26 5.0 73.8 1.0
C2 B:G20 5.0 78.6 1.0

Potassium binding site 5 out of 9 in 8u5p

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Potassium binding site 5 out of 9 in the Structure of Mango II 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 Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K102

b:75.0
occ:1.00
 O6 B:G13 2.7 71.8 1.0
O6 B:G24 2.8 71.7 1.0
O6 B:G18 2.8 70.7 1.0
O6 B:G29 2.9 68.7 1.0
O6 B:G27 2.9 68.7 1.0
O6 B:G21 3.0 74.0 1.0
O6 B:G16 3.0 72.8 1.0
O6 B:G11 3.1 72.5 1.0
K B:K101 3.6 78.0 1.0
C6 B:G13 3.6 71.5 1.0
C6 B:G24 3.6 73.1 1.0
C6 B:G29 3.7 66.6 1.0
C6 B:G18 3.7 73.6 1.0
C6 B:G27 3.7 69.9 1.0
C6 B:G21 3.8 74.5 1.0
C6 B:G16 3.9 74.4 1.0
C6 B:G11 3.9 72.0 1.0
N1 B:G29 3.9 67.0 1.0
N1 B:G13 3.9 68.3 1.0
N1 B:G24 3.9 74.0 1.0
N1 B:G18 4.0 72.8 1.0
N1 B:G21 4.0 73.8 1.0
N1 B:G27 4.0 69.1 1.0
N1 B:G11 4.2 72.0 1.0
N1 B:G16 4.2 74.9 1.0
C5 B:G24 4.8 75.7 1.0
C5 B:G13 4.9 71.5 1.0
C5 B:G29 4.9 64.3 1.0
C5 B:G27 4.9 69.0 1.0
C5 B:G18 5.0 72.7 1.0

Potassium binding site 6 out of 9 in 8u5p

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Potassium binding site 6 out of 9 in the Structure of Mango II 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 Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K103

b:87.2
occ:1.00
 O6 B:G20 2.7 76.8 1.0
O6 B:G10 2.7 71.7 1.0
O6 C:G20 2.7 78.1 1.0
O6 C:G26 2.8 78.2 1.0
O6 B:G15 2.9 75.4 1.0
O6 C:G10 2.9 78.7 1.0
O6 C:G15 2.9 75.7 1.0
O6 B:G26 2.9 75.1 1.0
K B:K101 3.4 78.0 1.0
C6 C:G26 3.5 80.7 1.0
K C:K101 3.6 83.1 1.0
C6 C:G20 3.6 79.5 1.0
C6 B:G15 3.6 75.1 1.0
C6 B:G20 3.6 77.3 1.0
C6 B:G10 3.7 72.6 1.0
C6 C:G15 3.8 75.8 1.0
N1 C:G26 3.8 80.5 1.0
C6 B:G26 3.8 73.7 1.0
N1 C:G20 3.8 80.2 1.0
C6 C:G10 3.8 79.6 1.0
N1 B:G20 3.9 76.9 1.0
N1 B:G10 3.9 74.1 1.0
N1 B:G15 3.9 75.5 1.0
N1 C:G10 4.1 80.1 1.0
N1 C:G15 4.2 75.2 1.0
N1 B:G26 4.2 73.1 1.0
C5 C:G26 4.7 82.2 1.0
C5 B:G15 4.9 74.9 1.0
C5 C:G15 4.9 74.6 1.0
C5 B:G26 4.9 73.8 1.0
C5 C:G20 5.0 78.2 1.0
C5 B:G20 5.0 78.3 1.0
C5 B:G10 5.0 71.6 1.0

Potassium binding site 7 out of 9 in 8u5p

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Potassium binding site 7 out of 9 in the Structure of Mango II 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 Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K101

b:83.1
occ:1.00
 O6 C:G27 2.7 80.8 1.0
O6 C:G16 2.7 79.2 1.0
O6 C:G15 2.7 75.7 1.0
O6 C:G21 2.8 81.4 1.0
O6 C:G26 2.8 78.2 1.0
O6 C:G11 3.0 82.7 1.0
O6 C:G20 3.1 78.1 1.0
O6 C:G10 3.3 78.7 1.0
K C:K102 3.4 89.8 1.0
C6 C:G27 3.5 81.8 1.0
C6 C:G16 3.5 79.0 1.0
K B:K103 3.6 87.2 1.0
C6 C:G15 3.7 75.8 1.0
C6 C:G26 3.7 80.7 1.0
C6 C:G21 3.7 83.0 1.0
N1 C:G16 3.7 79.2 1.0
N1 C:G27 3.8 82.3 1.0
C6 C:G20 3.8 79.5 1.0
C6 C:G11 3.9 83.0 1.0
C6 C:G10 3.9 79.6 1.0
N1 C:G26 3.9 80.5 1.0
N1 C:G21 4.0 84.4 1.0
N1 C:G11 4.0 81.6 1.0
N1 C:G10 4.1 80.1 1.0
N1 C:G20 4.1 80.2 1.0
N1 C:G15 4.1 75.2 1.0
C5 C:G27 4.7 81.5 1.0
C5 C:G16 4.7 76.9 1.0
C5 C:G15 4.9 74.6 1.0
C5 C:G20 4.9 78.2 1.0
C5 C:G21 5.0 83.2 1.0
C5 C:G26 5.0 82.2 1.0
C2 C:G16 5.0 79.6 1.0

Potassium binding site 8 out of 9 in 8u5p

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Potassium binding site 8 out of 9 in the Structure of Mango II 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 Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K102

b:89.8
occ:1.00
 O6 C:G24 2.7 84.6 1.0
O6 C:G18 2.8 83.0 1.0
O6 C:G13 2.8 82.9 1.0
O6 C:G16 2.8 79.2 1.0
O6 C:G27 2.9 80.8 1.0
O6 C:G29 2.9 84.0 1.0
O6 C:G11 3.0 82.7 1.0
O6 C:G21 3.1 81.4 1.0
K C:K101 3.4 83.1 1.0
C6 C:G16 3.6 79.0 1.0
C6 C:G13 3.6 83.9 1.0
C6 C:G18 3.7 80.7 1.0
C6 C:G24 3.7 83.6 1.0
C6 C:G27 3.7 81.8 1.0
C6 C:G29 3.7 86.2 1.0
N1 C:G16 3.8 79.2 1.0
C6 C:G11 3.9 83.0 1.0
N1 C:G27 3.9 82.3 1.0
N1 C:G13 3.9 84.5 1.0
N1 C:G18 3.9 77.6 1.0
C6 C:G21 3.9 83.0 1.0
N1 C:G24 4.0 82.0 1.0
N1 C:G29 4.1 85.2 1.0
N1 C:G11 4.1 81.6 1.0
N1 C:G21 4.2 84.4 1.0
C5 C:G16 4.8 76.9 1.0
C5 C:G13 4.9 85.2 1.0
C5 C:G18 4.9 80.5 1.0
C5 C:G29 4.9 85.7 1.0
C5 C:G27 4.9 81.5 1.0
C5 C:G24 4.9 86.8 1.0

Potassium binding site 9 out of 9 in 8u5p

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Potassium binding site 9 out of 9 in the Structure of Mango II 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 9 of Structure of Mango II Aptamer Bound to T01-6A-B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K103

b:135.1
occ:1.00
 OP1 C:G29 3.6 111.8 1.0
C2' C:A28 3.9 111.8 1.0
C1' C:A28 4.3 115.5 1.0
C3' C:A28 4.4 107.2 1.0
P C:G29 4.9 113.2 1.0

Reference:

L.F.M.Passalacqua, A.R.Ferre-D'amare. Structure of Mango II Aptamer Bound to T01-6A-B To Be Published.
Page generated: Tue Aug 13 01:01:57 2024

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