Potassium in PDB 4b3m: Crystal Structure of the 30S Ribosome in Complex with Compound 1

The structure of Crystal Structure of the 30S Ribosome in Complex with Compound 1, PDB code: 4b3m was solved by C.L.Ng, K.Lang, D.Shcherbakov, T.Matt, D.Perez-Fernandez, R.Patak, M.Meyer, S.Duscha, R.Akbergenov, H.Boukari, P.Freihofer, I.Kudyba, M.S.K.Reddy, R.S.Nandurikar, V.Ramakrishnan, A.Vasella, E.C.Bottger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.650, 401.650, 175.260, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.1

The structure of Crystal Structure of the 30S Ribosome in Complex with Compound 1 also contains other interesting chemical elements:

Magnesium	(Mg)	240 atoms
Zinc	(Zn)	2 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of the 30S Ribosome in Complex with Compound 1 (pdb code 4b3m). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 17 binding sites of Potassium where determined in the Crystal Structure of the 30S Ribosome in Complex with Compound 1, PDB code: 4b3m:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 17 in the Crystal Structure of the 30S Ribosome in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the 30S Ribosome in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2668 b:99.8 occ:1.00 O6 A:G305 2.9 59.4 1.0 O6 A:G293 3.1 61.4 1.0 O4 A:U304 3.2 61.7 1.0 C6 A:G305 3.8 58.0 1.0 N6 A:A303 4.0 58.4 1.0 C4 A:U304 4.1 58.1 1.0 N3 A:U304 4.1 58.4 1.0 N1 A:G305 4.1 54.9 1.0 C6 A:G293 4.2 59.3 1.0 MG A:MG2748 4.5 80.7 1.0 OP2 A:G292 4.6 56.8 1.0 N7 A:G293 4.7 60.1 1.0 O4 A:U294 4.7 62.2 1.0 C5 A:G293 4.8 60.4 1.0 C5 A:G305 4.9 60.1 1.0

Potassium binding site 2 out of 17 in the Crystal Structure of the 30S Ribosome in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the 30S Ribosome in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2669 b:0.1 occ:1.00 O4 A:U863 3.2 80.7 1.0 OP2 A:C866 3.7 54.6 1.0 N3 A:U863 3.8 76.4 1.0 C4 A:U863 3.8 77.1 1.0 O6 A:G867 4.1 72.4 1.0 C5' A:A865 4.5 57.2 1.0 C6 A:G867 4.8 69.6 1.0 C2 A:U863 5.0 75.0 1.0 O5' A:A865 5.0 57.8 1.0 P A:C866 5.0 57.0 1.0

Potassium binding site 3 out of 17 in the Crystal Structure of the 30S Ribosome in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the 30S Ribosome in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2670 b:0.6 occ:1.00 O6 A:G895 3.2 58.0 1.0 N7 A:G894 3.3 56.9 1.0 O6 A:G894 3.5 57.5 1.0 N7 A:G895 3.9 55.8 1.0 C5 A:G894 3.9 57.0 1.0 C6 A:G894 4.0 57.0 1.0 C6 A:G895 4.0 56.6 1.0 C8 A:G894 4.3 57.3 1.0 C5 A:G895 4.3 54.9 1.0 N4 A:C896 4.7 54.5 1.0 N4 A:C904 4.8 49.0 1.0

Potassium binding site 4 out of 17 in the Crystal Structure of the 30S Ribosome in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the 30S Ribosome in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2671 b:90.8 occ:1.00 OP1 A:G576 2.7 55.5 1.0 P A:G576 3.7 53.5 1.0 O5' A:G576 3.8 46.4 1.0 OP2 A:G577 3.8 51.4 1.0 OP1 A:G575 4.0 56.0 1.0 OP2 A:G576 4.3 52.5 1.0 OP1 A:A815 4.6 49.0 1.0 OP2 A:A815 4.6 51.7 1.0 OP2 A:G575 4.9 60.5 1.0 C5' A:G577 4.9 52.4 1.0 P A:G575 4.9 57.9 1.0

Potassium binding site 5 out of 17 in the Crystal Structure of the 30S Ribosome in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of the 30S Ribosome in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2672 b:97.3 occ:1.00 O6 A:G257 2.8 85.9 1.0 O6 A:G258 3.2 82.2 1.0 OP2 A:G266 3.2 69.2 1.0 OP1 A:G266 3.5 69.2 1.0 P A:G266 3.8 69.6 1.0 C6 A:G257 3.9 84.7 1.0 MG A:MG2771 4.0 89.3 1.0 C6 A:G258 4.1 82.0 1.0 N4 A:C268 4.2 77.5 1.0 N4 A:C269 4.3 88.2 1.0 O4 A:U256 4.3 68.0 1.0 N7 A:G257 4.4 85.0 1.0 C5 A:G257 4.5 84.7 1.0 N7 A:G258 4.6 82.6 1.0 O5' A:G266 4.6 71.7 1.0 C5 A:G258 4.7 81.9 1.0 MG A:MG2628 4.7 68.2 1.0 C4 A:U256 4.9 68.4 1.0

Potassium binding site 6 out of 17 in the Crystal Structure of the 30S Ribosome in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of the 30S Ribosome in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2673 b:1.0 occ:1.00 OP1 A:A535 2.7 85.4 1.0 O3' A:U534 2.9 77.1 1.0 O4 A:U512 3.3 97.6 1.0 P A:A535 3.4 83.3 1.0 O6 A:G538 3.9 77.1 1.0 O2' A:U534 3.9 77.7 1.0 N4 A:C513 3.9 87.9 1.0 C3' A:U534 4.1 78.2 1.0 C4 A:U512 4.3 95.7 1.0 O6 A:G537 4.4 87.9 1.0 O5' A:A535 4.5 71.1 1.0 OP2 A:A535 4.5 81.9 1.0 C5' A:A535 4.5 67.6 1.0 C4' A:U534 4.5 79.2 1.0 C2' A:U534 4.6 78.0 1.0 N6 A:A539 4.8 98.4 1.0 C5 A:U512 4.9 94.2 1.0 OP2 A:C536 5.0 69.7 1.0

Potassium binding site 7 out of 17 in the Crystal Structure of the 30S Ribosome in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of the 30S Ribosome in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2674 b:0.4 occ:1.00 O6 A:G595 3.3 78.1 1.0 O6 A:G594 3.6 71.3 1.0 N7 A:G594 3.7 72.2 1.0 C6 A:G595 3.8 77.6 1.0 N7 A:G593 3.9 69.1 1.0 N1 A:G595 4.0 78.8 1.0 MG A:MG2549 4.1 57.4 1.0 O2' A:U641 4.2 63.7 1.0 C6 A:G594 4.4 70.9 1.0 C5 A:G594 4.4 71.8 1.0 C8 A:G593 4.6 70.4 1.0 OP2 A:G593 4.6 82.1 1.0 C5 A:G593 4.8 69.0 1.0 C8 A:G594 4.8 72.6 1.0 O6 A:G593 4.9 67.8 1.0 C5 A:G595 4.9 77.4 1.0

Potassium binding site 8 out of 17 in the Crystal Structure of the 30S Ribosome in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of the 30S Ribosome in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2675 b:0.4 occ:1.00 O6 A:G473 3.0 0.4 1.0 O6 A:G474 3.4 0.1 1.0 C6 A:G473 3.6 0.7 1.0 N7 A:G473 3.7 0.7 1.0 C5 A:G473 3.9 0.7 1.0 N7 A:G474 4.0 0.6 1.0 C6 A:G474 4.3 0.3 1.0 OP2 A:A472 4.4 88.1 1.0 OP2 A:G471 4.5 89.2 1.0 C5 A:G474 4.5 0.3 1.0 N1 A:G473 4.7 0.7 1.0 N4 A:C458 4.8 0.0 1.0 C8 A:G473 4.8 0.6 1.0 N2 A:G460 4.9 0.5 1.0

Potassium binding site 9 out of 17 in the Crystal Structure of the 30S Ribosome in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of the 30S Ribosome in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2676 b:0.1 occ:1.00 O6 A:G558 3.0 59.7 1.0 N7 A:G557 3.3 57.2 1.0 OP2 A:G557 3.9 57.1 1.0 C8 A:G557 4.0 56.3 1.0 C6 A:G558 4.0 59.1 1.0 C5 A:G557 4.3 57.6 1.0 NZ L:LYS16 4.3 0.6 1.0 N7 A:G558 4.3 58.8 1.0 C5 A:G558 4.5 58.3 1.0 O6 A:G557 4.6 61.8 1.0 C6 A:G557 4.8 58.2 1.0 C5 A:C556 4.9 61.3 1.0 OP2 A:C556 5.0 59.0 1.0

Potassium binding site 10 out of 17 in the Crystal Structure of the 30S Ribosome in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of the 30S Ribosome in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2677 b:0.1 occ:1.00 O6 A:G1185 2.6 87.2 1.0 O6 A:G1186 3.5 85.2 1.0 C6 A:G1185 3.5 85.8 1.0 N7 A:G1185 4.0 86.1 1.0 C5 A:G1185 4.1 85.5 1.0 C6 A:G1186 4.4 86.0 1.0 N7 A:G1186 4.5 85.1 1.0 N4 A:C1115 4.6 82.2 1.0 N1 A:G1185 4.6 84.0 1.0 N7 A:G1184 4.8 91.5 1.0 C5 A:G1186 4.8 85.7 1.0 O6 A:G1184 4.8 90.5 1.0

D.Perez-Fernandez, D.Shcherbakov, T.Matt, N.C.Leong, I.Kudyba, S.Duscha, H.Boukari, R.Patak, S.R.Dubakka, K.Lang, M.Meyer, R.Akbergenov, P.Freihofer, S.Vaddi, P.Thommes, V.Ramakrishnan, A.Vasella, E.C.Bottger. 4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics Nat.Commun. V. 5 3112 2014.
ISSN: ESSN 2041-1723
PubMed: 24473108
DOI: 10.1038/NCOMMS4112