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Potassium in PDB 8u5z: Structure of Mango II Variant Aptamer Bound to T01-7M-B

Protein crystallography data

The structure of Structure of Mango II Variant Aptamer Bound to T01-7M-B, PDB code: 8u5z 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) 45.27 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 36.98, 181.08, 107.446, 90, 90, 90
R / Rfree (%) 18 / 22.2

Other elements in 8u5z:

The structure of Structure of Mango II Variant Aptamer Bound to T01-7M-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 T01-7M-B (pdb code 8u5z). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the Structure of Mango II Variant Aptamer Bound to T01-7M-B, PDB code: 8u5z:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 8u5z

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Potassium binding site 1 out of 10 in the Structure of Mango II Variant Aptamer Bound to T01-7M-B


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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 T01-7M-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K101

b:31.3
occ:1.00
 O6 A:G23 2.7 24.9 1.0
O6 A:G26 2.8 26.8 1.0
O6 A:G18 2.8 25.9 1.0
O6 A:G13 2.8 24.9 1.0
O6 A:G16 2.9 29.0 1.0
O6 A:G29 2.9 24.0 1.0
O6 A:G21 2.9 28.4 1.0
O6 A:G11 3.1 25.2 1.0
K A:K102 3.5 30.7 1.0
C6 A:G23 3.6 26.2 1.0
C6 A:G29 3.6 23.7 1.0
C6 A:G26 3.7 24.2 1.0
C6 A:G13 3.7 25.8 1.0
C6 A:G18 3.7 26.4 1.0
C6 A:G16 3.7 26.3 1.0
C6 A:G21 3.7 28.4 1.0
N1 A:G29 3.8 24.0 1.0
N1 A:G23 3.8 26.0 1.0
C6 A:G11 3.9 28.0 1.0
N1 A:G13 3.9 24.1 1.0
N1 A:G16 4.0 27.4 1.0
N1 A:G26 4.0 24.5 1.0
N1 A:G21 4.0 29.1 1.0
N1 A:G18 4.0 26.2 1.0
N1 A:G11 4.1 25.1 1.0
C5 A:G29 4.8 23.6 1.0
C5 A:G23 4.8 30.1 1.0
C5 A:G21 4.9 28.4 1.0
C5 A:G18 4.9 27.1 1.0
C5 A:G26 4.9 26.6 1.0
C5 A:G13 4.9 31.2 1.0
C5 A:G16 5.0 26.6 1.0

Potassium binding site 2 out of 10 in 8u5z

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Potassium binding site 2 out of 10 in the Structure of Mango II Variant Aptamer Bound to T01-7M-B


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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 T01-7M-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K102

b:30.7
occ:1.00
 O6 A:G11 2.8 25.2 1.0
O6 A:G25 2.8 30.1 1.0
O6 A:G15 2.8 25.8 1.0
O6 A:G16 2.8 29.0 1.0
O6 A:G26 2.9 26.8 1.0
O6 A:G10 2.9 28.6 1.0
O6 A:G21 2.9 28.4 1.0
O6 A:G20 3.0 30.9 1.0
K A:K103 3.4 28.1 0.5
K A:K101 3.5 31.3 1.0
C6 A:G10 3.5 28.3 1.0
C6 A:G26 3.6 24.2 1.0
C6 A:G11 3.7 28.0 1.0
C6 A:G16 3.7 26.3 1.0
C6 A:G25 3.7 31.9 1.0
C6 A:G20 3.7 28.3 1.0
N1 A:G10 3.8 24.8 1.0
C6 A:G21 3.8 28.4 1.0
C6 A:G15 3.8 27.9 1.0
N1 A:G11 3.9 25.1 1.0
N1 A:G26 3.9 24.5 1.0
N1 A:G20 4.0 29.2 1.0
N1 A:G25 4.0 30.5 1.0
N1 A:G21 4.0 29.1 1.0
N1 A:G16 4.0 27.4 1.0
N1 A:G15 4.2 26.9 1.0
C5 A:G10 4.7 30.3 1.0
C5 A:G26 4.8 26.6 1.0
C5 A:G16 4.9 26.6 1.0
C5 A:G20 4.9 28.0 1.0
C2 A:G10 4.9 28.8 1.0
C5 A:G25 5.0 28.1 1.0
C5 A:G11 5.0 28.7 1.0

Potassium binding site 3 out of 10 in 8u5z

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Potassium binding site 3 out of 10 in the Structure of Mango II Variant Aptamer Bound to T01-7M-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 T01-7M-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:28.1
occ:0.50
 O6 A:G10 2.7 28.6 1.0
O6 A:G20 2.8 30.9 1.0
O6 A:G15 2.9 25.8 1.0
O6 A:G25 2.9 30.1 1.0
K A:K102 3.4 30.7 1.0
C6 A:G10 3.6 28.3 1.0
C6 A:G20 3.7 28.3 1.0
C6 A:G15 3.7 27.9 1.0
N1 A:G10 3.8 24.8 1.0
C6 A:G25 3.8 31.9 1.0
N1 A:G20 4.0 29.2 1.0
N1 A:G15 4.1 26.9 1.0
N1 A:G25 4.1 30.5 1.0
C5 A:G15 4.9 29.4 1.0
C5 A:G10 4.9 30.3 1.0
C5 A:G25 5.0 28.1 1.0

Potassium binding site 4 out of 10 in 8u5z

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Potassium binding site 4 out of 10 in the Structure of Mango II Variant Aptamer Bound to T01-7M-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 T01-7M-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K104

b:50.7
occ:1.00
 O3' A:A5 2.9 34.1 1.0
O A:HOH240 2.9 40.9 1.0
OP1 A:C6 3.0 32.1 1.0
O A:HOH217 3.1 39.5 1.0
P A:C6 3.6 36.7 1.0
O A:HOH235 3.9 40.7 1.0
C4' A:A5 4.0 35.3 1.0
C3' A:A5 4.0 31.3 1.0
C5' A:A5 4.1 31.7 1.0
OP2 A:C6 4.5 35.8 1.0
O2' A:A5 4.8 33.1 1.0
O5' A:C6 4.8 33.7 1.0
C5' A:C6 4.9 34.9 1.0

Potassium binding site 5 out of 10 in 8u5z

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Potassium binding site 5 out of 10 in the Structure of Mango II Variant Aptamer Bound to T01-7M-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 T01-7M-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K105

b:52.1
occ:1.00
 O2 A:U4 2.8 36.6 1.0
O2 A:C34 2.9 34.0 1.0
O A:HOH238 3.3 40.3 1.0
O2' A:U4 3.8 48.8 1.0
C2 A:C34 3.9 35.5 1.0
C2 A:U4 4.0 36.8 1.0
N2 A:G3 4.0 31.4 1.0
C1' A:U4 4.2 38.5 1.0
C1' A:C34 4.2 34.0 1.0
C2' A:U4 4.3 41.0 1.0
C2 A:A33 4.4 31.4 1.0
N1 A:C34 4.5 32.6 1.0
O4' A:A5 4.5 37.4 1.0
N1 A:U4 4.6 33.9 1.0
N3 A:C34 4.7 35.1 1.0
O2' A:C34 4.8 41.4 1.0
N3 A:A33 4.9 32.5 1.0
C2 A:G3 4.9 32.0 1.0
C2' A:C34 5.0 35.9 1.0

Potassium binding site 6 out of 10 in 8u5z

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Potassium binding site 6 out of 10 in the Structure of Mango II Variant Aptamer Bound to T01-7M-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 T01-7M-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K101

b:30.5
occ:1.00
 O6 B:G16 2.8 31.1 1.0
O6 B:G11 2.8 31.5 1.0
O6 B:G25 2.8 32.2 1.0
O6 B:G15 2.8 34.6 1.0
O6 B:G26 2.8 27.8 1.0
O6 B:G21 2.9 31.0 1.0
O6 B:G10 3.0 32.8 1.0
O6 B:G20 3.1 32.8 1.0
K B:K103 3.3 33.7 1.0
K B:K102 3.5 34.6 1.0
C6 B:G16 3.6 29.5 1.0
C6 B:G10 3.7 32.4 1.0
C6 B:G26 3.7 27.9 1.0
C6 B:G20 3.7 34.1 1.0
C6 B:G11 3.7 30.1 1.0
C6 B:G15 3.8 30.8 1.0
C6 B:G25 3.8 31.8 1.0
C6 B:G21 3.8 33.6 1.0
N1 B:G10 3.9 30.4 1.0
N1 B:G20 3.9 30.5 1.0
N1 B:G26 4.0 26.6 1.0
N1 B:G16 4.0 29.7 1.0
N1 B:G21 4.0 29.4 1.0
N1 B:G11 4.1 28.6 1.0
N1 B:G15 4.1 30.5 1.0
N1 B:G25 4.2 28.0 1.0
C5 B:G16 4.8 30.1 1.0
C5 B:G10 4.8 31.9 1.0
C5 B:G26 4.8 26.3 1.0
C5 B:G20 4.8 34.3 1.0
C5 B:G25 5.0 31.4 1.0
C5 B:G11 5.0 31.2 1.0
C5 B:G15 5.0 30.3 1.0

Potassium binding site 7 out of 10 in 8u5z

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Potassium binding site 7 out of 10 in the Structure of Mango II Variant Aptamer Bound to T01-7M-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 T01-7M-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K102

b:34.6
occ:1.00
 O6 B:G26 2.7 27.8 1.0
O6 B:G13 2.8 39.7 1.0
O6 B:G16 2.8 31.1 1.0
O6 B:G18 2.8 31.7 1.0
O6 B:G23 2.8 40.9 1.0
O6 B:G11 2.9 31.5 1.0
O6 B:G21 3.0 31.0 1.0
O6 B:G29 3.0 33.2 1.0
K B:K101 3.5 30.5 1.0
C6 B:G26 3.6 27.9 1.0
C6 B:G13 3.6 37.7 1.0
C6 B:G16 3.7 29.5 1.0
C6 B:G18 3.7 33.4 1.0
C6 B:G23 3.7 38.6 1.0
C6 B:G21 3.8 33.6 1.0
C6 B:G29 3.8 30.8 1.0
C6 B:G11 3.8 30.1 1.0
N1 B:G18 3.9 29.3 1.0
N1 B:G13 3.9 31.9 1.0
N1 B:G23 3.9 38.9 1.0
N1 B:G26 3.9 26.6 1.0
N1 B:G29 4.0 28.3 1.0
N1 B:G16 4.0 29.7 1.0
N1 B:G21 4.0 29.4 1.0
N1 B:G11 4.1 28.6 1.0
C07 B:W6F104 4.7 59.9 1.0
C5 B:G26 4.9 26.3 1.0
C5 B:G16 4.9 30.1 1.0
C5 B:G13 4.9 38.2 1.0
C5 B:G11 4.9 31.2 1.0
C5 B:G23 4.9 39.0 1.0
C48 B:W6F104 4.9 61.4 1.0
C5 B:G18 4.9 35.7 1.0
C5 B:G21 4.9 32.9 1.0
C5 B:G29 5.0 31.9 1.0

Potassium binding site 8 out of 10 in 8u5z

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Potassium binding site 8 out of 10 in the Structure of Mango II Variant Aptamer Bound to T01-7M-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 T01-7M-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K103

b:33.7
occ:1.00
 O6 C:G20 2.7 32.1 1.0
O6 B:G20 2.7 32.8 1.0
O6 C:G10 2.7 32.9 1.0
O6 B:G10 2.7 32.8 1.0
O6 B:G15 2.8 34.6 1.0
O6 C:G25 2.8 30.6 1.0
O6 B:G25 2.8 32.2 1.0
O6 C:G15 2.9 32.5 1.0
K B:K101 3.3 30.5 1.0
K C:K101 3.3 31.5 1.0
C6 C:G25 3.6 31.1 1.0
C6 B:G15 3.7 30.8 1.0
C6 B:G10 3.7 32.4 1.0
C6 B:G20 3.7 34.1 1.0
C6 C:G20 3.7 32.1 1.0
C6 C:G10 3.7 31.8 1.0
C6 B:G25 3.7 31.8 1.0
C6 C:G15 3.8 29.9 1.0
N1 B:G10 3.9 30.4 1.0
N1 B:G20 3.9 30.5 1.0
N1 C:G10 3.9 33.9 1.0
N1 C:G25 4.0 33.9 1.0
N1 C:G20 4.0 32.2 1.0
N1 B:G15 4.0 30.5 1.0
N1 B:G25 4.1 28.0 1.0
N1 C:G15 4.2 30.9 1.0
C5 C:G25 4.8 35.6 1.0
C5 B:G15 4.8 30.3 1.0
C5 B:G25 4.9 31.4 1.0
C5 C:G20 4.9 32.4 1.0
C5 C:G15 5.0 32.1 1.0
C5 B:G10 5.0 31.9 1.0
C5 B:G20 5.0 34.3 1.0
C5 C:G10 5.0 31.5 1.0

Potassium binding site 9 out of 10 in 8u5z

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Potassium binding site 9 out of 10 in the Structure of Mango II Variant Aptamer Bound to T01-7M-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 Variant Aptamer Bound to T01-7M-B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K101

b:31.5
occ:1.00
 O6 C:G26 2.7 34.6 1.0
O6 C:G25 2.8 30.6 1.0
O6 C:G15 2.8 32.5 1.0
O6 C:G21 2.8 31.9 1.0
O6 C:G16 2.9 35.2 1.0
O6 C:G11 2.9 34.0 1.0
O6 C:G20 2.9 32.1 1.0
O6 C:G10 3.0 32.9 1.0
K B:K103 3.3 33.7 1.0
K C:K102 3.5 36.1 1.0
C6 C:G26 3.6 32.6 1.0
C6 C:G20 3.7 32.1 1.0
C6 C:G10 3.7 31.8 1.0
C6 C:G25 3.7 31.1 1.0
C6 C:G21 3.7 31.2 1.0
C6 C:G15 3.7 29.9 1.0
C6 C:G16 3.7 34.1 1.0
C6 C:G11 3.8 35.5 1.0
N1 C:G10 3.9 33.9 1.0
N1 C:G26 4.0 32.7 1.0
N1 C:G25 4.0 33.9 1.0
N1 C:G21 4.0 32.5 1.0
N1 C:G20 4.0 32.2 1.0
N1 C:G15 4.1 30.9 1.0
N1 C:G11 4.1 36.2 1.0
N1 C:G16 4.1 30.1 1.0
C5 C:G20 4.8 32.4 1.0
C5 C:G26 4.8 33.3 1.0
C5 C:G10 4.8 31.5 1.0
C5 C:G16 4.9 31.7 1.0
C5 C:G21 4.9 31.1 1.0
C5 C:G15 4.9 32.1 1.0
C5 C:G25 4.9 35.6 1.0

Potassium binding site 10 out of 10 in 8u5z

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Potassium binding site 10 out of 10 in the Structure of Mango II Variant Aptamer Bound to T01-7M-B


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Structure of Mango II Variant Aptamer Bound to T01-7M-B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K102

b:36.1
occ:1.00
 O6 C:G29 2.7 33.5 1.0
O6 C:G16 2.7 35.2 1.0
O6 C:G21 2.8 31.9 1.0
O6 C:G13 2.8 36.7 1.0
O6 C:G18 2.9 39.1 1.0
O6 C:G26 2.9 34.6 1.0
O6 C:G23 2.9 33.5 1.0
O6 C:G11 3.0 34.0 1.0
K C:K101 3.5 31.5 1.0
C6 C:G29 3.6 34.2 1.0
C6 C:G16 3.6 34.1 1.0
C6 C:G13 3.6 42.2 1.0
C6 C:G21 3.7 31.2 1.0
C6 C:G18 3.7 36.2 1.0
C6 C:G26 3.7 32.6 1.0
C6 C:G23 3.8 35.4 1.0
C6 C:G11 3.8 35.5 1.0
N1 C:G13 3.9 41.9 1.0
N1 C:G16 3.9 30.1 1.0
N1 C:G18 3.9 35.1 1.0
N1 C:G29 4.0 40.1 1.0
N1 C:G26 4.0 32.7 1.0
N1 C:G21 4.0 32.5 1.0
N1 C:G23 4.0 37.3 1.0
N1 C:G11 4.0 36.2 1.0
C5 C:G29 4.8 34.7 1.0
C5 C:G16 4.8 31.7 1.0
C5 C:G21 4.8 31.1 1.0
C5 C:G13 4.8 42.4 1.0
C5 C:G18 4.9 36.5 1.0
C5 C:G26 4.9 33.3 1.0

Reference:

L.F.M.Passalacqua, A.R.Ferre-D'amare. Structure of Mango II Variant Aptamer Bound to T01-7M-B To Be Published.
Page generated: Tue Aug 13 01:05:13 2024

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