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Potassium in PDB 4aqy: Structure of Ribosome-Apramycin Complexes

Protein crystallography data

The structure of Structure of Ribosome-Apramycin Complexes, PDB code: 4aqy was solved by T.Matt, C.L.Ng, K.Lang, S.H.Sha, R.Akbergenov, D.Shcherbakov, M.Meyer, S.Duscha, J.Xie, S.R.Dubbaka, D.Perez-Fernandez, A.Vasella, V.Ramakrishnan, J.Schacht, E.C.Bottger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.180, 402.180, 175.000, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.5

Other elements in 4aqy:

The structure of Structure of Ribosome-Apramycin Complexes also contains other interesting chemical elements:

Magnesium (Mg) 203 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Potassium atom in the Structure of Ribosome-Apramycin Complexes (pdb code 4aqy). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 15 binding sites of Potassium where determined in the Structure of Ribosome-Apramycin Complexes, PDB code: 4aqy:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 15 in 4aqy

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Potassium binding site 1 out of 15 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2670

b:0.9
occ:1.00
N7 A:G577 3.1 78.3 1.0
OP2 A:U813 3.3 92.8 1.0
OP1 A:G577 3.5 93.5 1.0
C8 A:G577 3.6 78.8 1.0
C5 A:G577 4.3 79.2 1.0
P A:U813 4.3 93.3 1.0
OP1 A:U813 4.3 90.8 1.0
N6 A:A816 4.5 74.8 1.0
N2 A:G765 4.7 84.0 1.0
O6 A:G577 4.7 82.3 1.0
P A:G577 4.9 94.6 1.0
C6 A:G577 4.9 80.6 1.0
N9 A:G577 5.0 80.4 1.0

Potassium binding site 2 out of 15 in 4aqy

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Potassium binding site 2 out of 15 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2671

b:0.7
occ:1.00
N7 A:G894 3.5 88.2 1.0
O6 A:G895 3.7 95.7 1.0
O6 A:G894 4.1 85.0 1.0
N7 A:G895 4.2 97.4 1.0
C5 A:G894 4.3 86.9 1.0
C8 A:G894 4.4 89.2 1.0
C6 A:G894 4.5 86.0 1.0
C6 A:G895 4.5 95.2 1.0
C5 A:G895 4.8 96.2 1.0
OP2 A:G894 4.8 0.2 1.0
C5 A:C893 4.8 95.6 1.0
N4 A:C896 4.9 90.7 1.0

Potassium binding site 3 out of 15 in 4aqy

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Potassium binding site 3 out of 15 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2672

b:0.4
occ:1.00
N7 A:G305 3.5 0.4 1.0
OP2 A:C291 3.7 88.8 1.0
O6 A:G305 3.9 99.6 1.0
OP1 A:C291 4.0 87.5 1.0
C5 A:G305 4.3 0.9 1.0
P A:C291 4.3 88.7 1.0
O4 A:U304 4.4 0.1 1.0
C4 A:U304 4.4 0.3 1.0
C6 A:G305 4.4 0.0 1.0
C8 A:G305 4.5 0.2 1.0
C5 A:U304 4.5 0.5 1.0
OP1 A:C290 5.0 91.1 1.0
O3' A:C290 5.0 88.8 1.0
N3 A:U304 5.0 0.9 1.0

Potassium binding site 4 out of 15 in 4aqy

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Potassium binding site 4 out of 15 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2673

b:0.5
occ:1.00
OP1 A:G576 2.7 0.8 1.0
OP1 A:G575 3.7 1.0 1.0
O5' A:G576 3.7 87.5 1.0
P A:G576 3.8 0.4 1.0
OP2 A:G575 4.2 0.4 1.0
P A:G575 4.3 0.3 1.0
O5' A:G575 4.7 95.5 1.0
OP2 A:G576 4.7 0.4 1.0
OP2 A:G577 4.9 96.3 1.0
C5' A:G576 5.0 85.0 1.0

Potassium binding site 5 out of 15 in 4aqy

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Potassium binding site 5 out of 15 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2674

b:0.9
occ:1.00
O6 A:G257 2.9 0.6 1.0
MG A:MG2708 3.2 0.4 1.0
O6 A:G258 3.3 0.2 1.0
OP2 A:G266 3.4 0.6 1.0
OP1 A:G266 3.6 0.5 1.0
C6 A:G257 3.9 0.9 1.0
P A:G266 4.0 0.1 1.0
N7 A:G257 4.0 0.3 1.0
O4 A:U256 4.2 0.3 1.0
C6 A:G258 4.2 0.7 1.0
C5 A:G257 4.3 0.4 1.0
N7 A:G258 4.5 0.9 1.0
C5 A:U256 4.6 0.6 1.0
C4 A:U256 4.6 0.8 1.0
N4 A:C268 4.7 0.3 1.0
C5 A:G258 4.7 0.5 1.0
N4 A:C269 4.7 0.4 1.0
O5' A:G266 4.8 99.4 1.0
MG A:MG2634 4.9 86.7 1.0

Potassium binding site 6 out of 15 in 4aqy

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Potassium binding site 6 out of 15 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2675

b:0.3
occ:1.00
OP2 A:C536 3.3 0.4 1.0
OP1 A:A535 3.4 0.9 1.0
N7 A:G537 3.9 0.4 1.0
O6 A:G537 3.9 0.3 1.0
O6 A:G538 4.0 1.0 1.0
C5 A:C536 4.5 0.7 1.0
C6 A:G537 4.5 0.7 1.0
C5 A:G537 4.5 1.0 1.0
C5' A:A535 4.6 0.4 1.0
P A:A535 4.6 0.1 1.0
N4 A:C536 4.7 0.3 1.0
C4 A:C536 4.8 0.8 1.0
P A:C536 4.8 0.9 1.0
C8 A:G537 4.9 0.4 1.0
O3' A:U534 5.0 0.9 1.0
C6 A:G538 5.0 0.6 1.0

Potassium binding site 7 out of 15 in 4aqy

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Potassium binding site 7 out of 15 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2676

b:0.2
occ:1.00
O6 A:G558 2.8 0.5 1.0
N7 A:G557 3.5 0.4 1.0
C6 A:G558 3.8 0.9 1.0
NZ L:LYS20 4.0 0.2 1.0
C8 A:G557 4.3 0.4 1.0
O6 A:G557 4.5 0.3 1.0
C5 A:G557 4.5 0.2 1.0
N7 A:G558 4.5 0.7 1.0
C5 A:G558 4.5 0.9 1.0
OP2 A:G557 4.8 95.9 1.0
C6 A:G557 4.8 0.8 1.0
N1 A:G558 4.9 0.3 1.0

Potassium binding site 8 out of 15 in 4aqy

Go back to Potassium Binding Sites List in 4aqy
Potassium binding site 8 out of 15 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2677

b:0.1
occ:1.00
N7 A:G247 2.5 0.9 1.0
C8 A:G247 3.5 0.0 1.0
C5 A:G247 3.5 0.4 1.0
O6 A:G247 3.6 0.1 1.0
C6 A:G247 3.9 0.0 1.0
N1 A:G278 4.0 0.9 1.0
N2 A:G278 4.4 0.1 1.0
C2 A:G278 4.6 0.4 1.0
N9 A:G247 4.7 0.2 1.0
O6 A:G278 4.7 0.3 1.0
C4 A:G247 4.7 0.1 1.0
C6 A:G278 4.8 0.8 1.0

Potassium binding site 9 out of 15 in 4aqy

Go back to Potassium Binding Sites List in 4aqy
Potassium binding site 9 out of 15 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2678

b:0.8
occ:1.00
O4 A:U129 3.0 0.7 1.0
O6 A:G231 3.2 0.0 1.0
O6 A:G232 3.3 80.8 1.0
N4 A:C233 3.7 92.9 1.0
O6 A:G128 3.9 95.8 1.0
C6 A:G231 3.9 99.4 1.0
C4 A:U129 4.1 0.9 1.0
N3 A:U129 4.3 0.3 1.0
C6 A:G232 4.3 80.6 1.0
N7 A:G232 4.3 79.9 1.0
C5 A:G231 4.5 100.0 1.0
N4 A:C131 4.6 87.1 1.0
N7 A:G231 4.6 0.1 1.0
C5 A:G232 4.7 80.2 1.0
C4 A:C233 4.7 94.1 1.0
N1 A:G231 4.8 98.1 1.0

Potassium binding site 10 out of 15 in 4aqy

Go back to Potassium Binding Sites List in 4aqy
Potassium binding site 10 out of 15 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Structure of Ribosome-Apramycin Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2679

b:0.6
occ:1.00
O6 A:G226 3.4 97.1 1.0
O6 A:G227 3.5 0.9 1.0
N7 A:G226 3.5 99.0 1.0
C6 A:G226 4.0 96.5 1.0
C5 A:G226 4.1 97.5 1.0
N7 A:G227 4.2 0.9 1.0
N4 A:C225 4.2 0.2 1.0
C6 A:G227 4.3 0.2 1.0
C8 A:G226 4.5 0.7 1.0
C5 A:G227 4.6 0.9 1.0
C4 A:C225 4.7 0.7 1.0
C5 A:C225 4.7 0.1 1.0

Reference:

T.Matt, C.L.Ng, K.Lang, S.H.Sha, R.Akbergenov, D.Shcherbakov, M.Meyer, S.Duscha, J.Xie, S.R.Dubbaka, D.Perez-Fernandez, A.Vasella, V.Ramakrishnan, J.Schacht, E.C.Bottger. Dissociation of Antibacterial Activity and Aminoglycoside Ototoxicity in the 4-Monosubstituted 2-Deoxystreptamine Apramycin. Proc.Natl.Acad.Sci.Usa V. 109 10984 2012.
ISSN: ISSN 0027-8424
PubMed: 22699498
DOI: 10.1073/PNAS.1204073109
Page generated: Sun Dec 13 23:26:26 2020

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