Potassium in PDB 3pio: Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit

The structure of Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit, PDB code: 3pio was solved by M.J.Belousoff, T.Shapira, A.Bashan, E.Zimmerman, K.Arakawa, H.Kinashi, H.Rozenberg, A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.25
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	170.590, 410.204, 695.078, 90.00, 90.00, 90.00
R / Rfree (%)	25.2 / 29.4

The structure of Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit also contains other interesting chemical elements:

Magnesium	(Mg)	154 atoms
Sodium	(Na)	42 atoms

Pages:

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

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit (pdb code 3pio). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 15 binding sites of Potassium where determined in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit, PDB code: 3pio:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 15 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


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 Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ X:K3070 b:72.8 occ:1.00 N7 X:G2015 2.9 54.3 1.0 O6 X:G2015 3.6 47.8 1.0 C5 X:G2015 3.8 54.2 1.0 N3 X:C2038 3.9 92.9 1.0 O2 X:C2478 3.9 69.9 1.0 O2 X:C2038 3.9 79.8 1.0 C8 X:G2015 4.0 57.6 1.0 O2 X:U2479 4.0 69.4 1.0 C6 X:G2015 4.0 51.3 1.0 N3 X:C2478 4.2 77.6 1.0 N3 X:A2432 4.2 61.8 1.0 C2 X:A2432 4.3 67.9 1.0 C2 X:C2038 4.4 85.6 1.0 C1' X:G2433 4.5 65.3 1.0 C2 X:C2478 4.5 73.8 1.0 N3 X:G2433 4.5 62.6 1.0 N9 X:G2433 4.9 64.0 1.0 C4 X:C2038 4.9 90.6 1.0 C4 X:G2433 4.9 67.8 1.0 N4 X:C2038 4.9 90.0 1.0 O4' X:G2433 4.9 71.5 1.0 C2 X:U2479 5.0 71.8 1.0

Potassium binding site 2 out of 15 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


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 Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ X:K3071 b:86.1 occ:1.00 O6 X:G1246 4.3 93.1 1.0 O6 X:G1245 4.6 75.4 1.0 O4 X:U1244 4.6 0.6 1.0 N7 X:G1245 4.6 80.6 1.0 C5 X:U1244 4.9 96.3 1.0

Potassium binding site 3 out of 15 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


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 Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ X:K3072 b:0.2 occ:1.00 O6 X:G608 3.6 95.4 1.0 O4 X:U609 3.8 0.1 1.0 O4 X:U670 4.2 0.8 1.0 N7 X:G608 4.3 95.2 1.0 C6 X:G608 4.5 88.9 1.0 N6 X:A671 4.6 91.3 1.0 N4 X:C607 4.7 88.3 1.0 C5 X:G608 4.7 90.6 1.0 C4 X:U609 4.8 0.4 1.0

Potassium binding site 4 out of 15 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


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 Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ X:K3073 b:57.2 occ:1.00 O6 X:G1993 3.8 61.1 1.0 OP2 X:U1280 4.1 58.2 1.0 O4 X:U1994 4.2 41.2 1.0 N7 X:G1993 4.2 55.9 1.0 N7 X:G1992 4.5 42.2 1.0 O6 X:G1992 4.7 40.5 1.0 C6 X:G1993 4.7 53.6 1.0 OP1 X:U1280 4.8 59.6 1.0 C5 X:G1993 4.9 52.6 1.0 C5 X:G1992 5.0 37.4 1.0

Potassium binding site 5 out of 15 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


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 Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ M:K167 b:45.0 occ:1.00 ND2 M:ASN58 3.8 71.7 1.0 OP1 X:G2699 3.9 56.1 1.0 CG M:ASN58 4.1 69.0 1.0 OD1 M:ASN58 4.2 78.7 1.0 OP1 X:U2700 4.4 60.5 1.0 OP2 X:G2665 4.9 44.6 1.0 CB M:ASN58 5.0 57.4 1.0 OH M:TYR105 5.0 45.9 1.0 OP2 X:G2664 5.0 48.6 1.0

Potassium binding site 6 out of 15 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


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 Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ X:K3074 b:0.1 occ:1.00 C5 X:U1467 3.3 58.9 1.0 C4' X:A1468 3.5 0.7 1.0 O4 X:U1473 3.7 67.4 1.0 O4 X:U1467 3.9 88.6 1.0 C5' X:A1468 3.9 0.6 1.0 C4 X:U1467 4.0 73.3 1.0 O3' X:A1468 4.2 0.7 1.0 C6 X:U1467 4.2 58.8 1.0 NA X:NA3037 4.3 53.9 1.0 O4' X:A1468 4.3 1.0 1.0 N3 X:U1473 4.3 54.8 1.0 C3' X:A1468 4.4 0.5 1.0 C4 X:U1473 4.5 63.7 1.0 O2' X:A1468 4.5 0.4 1.0

Potassium binding site 7 out of 15 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


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 Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ X:K3075 b:68.8 occ:1.00 O6 X:G1480 4.0 77.5 1.0 O6 X:G1479 4.1 79.2 1.0 N7 X:G1479 4.7 63.3 1.0 C6 X:G1479 4.9 78.6 1.0

Potassium binding site 8 out of 15 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


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 Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ X:K3076 b:0.4 occ:1.00 OP2 X:A2618 3.4 89.2 1.0 N7 X:G2619 3.4 69.9 1.0 OP1 X:A2618 3.9 81.2 1.0 P X:A2618 4.1 86.4 1.0 C8 X:G2619 4.3 72.1 1.0 O6 X:G2619 4.3 81.5 1.0 C5 X:G2619 4.4 70.4 1.0 O6 X:G2620 4.4 78.7 1.0 C6 X:G2619 4.7 72.5 1.0 N7 X:G2620 4.8 68.9 1.0 OP2 X:G2619 4.9 89.4 1.0 O5' X:A2618 4.9 79.5 1.0 OP1 X:A2749 5.0 89.3 1.0

Potassium binding site 9 out of 15 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


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 Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ X:K3077 b:80.7 occ:1.00 OP1 X:U823 3.1 37.0 1.0 N7 X:G1266 3.1 58.9 1.0 O3' X:C574 3.6 37.2 1.0 OP2 X:U823 3.6 58.3 1.0 P X:U823 3.8 51.2 1.0 O6 X:G1266 4.0 58.0 1.0 C8 X:G1266 4.0 60.5 1.0 C5 X:G1266 4.0 55.8 1.0 C4' X:C574 4.2 32.7 1.0 O2' X:C574 4.2 52.4 1.0 OP1 X:U575 4.3 80.3 1.0 C6 X:G1266 4.4 55.8 1.0 C3' X:C574 4.4 38.6 1.0 NE2 O:GLN79 4.5 96.5 1.0 OP1 X:U824 4.5 52.2 1.0 P X:U575 4.7 68.7 1.0 C5' X:C574 4.7 35.3 1.0 O5' X:U823 4.8 54.3 1.0 C2' X:C574 5.0 50.6 1.0

Potassium binding site 10 out of 15 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


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 Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ X:K3078 b:91.7 occ:1.00 OP1 X:C1623 3.5 63.1 1.0 N7 X:G1317 3.5 83.6 1.0 OP2 X:G1316 3.6 40.0 1.0 O6 X:G1317 3.9 60.9 1.0 P X:C1623 4.3 64.7 1.0 O5' X:C1623 4.4 61.3 1.0 C5 X:G1317 4.4 78.4 1.0 C6 X:G1317 4.5 69.8 1.0 C8 X:G1317 4.5 81.6 1.0 OP2 X:G1317 4.6 78.6 1.0 C3' X:C1623 4.6 75.6 1.0 N7 X:G1316 4.7 52.0 1.0 OP2 X:C1623 4.7 59.9 1.0 P X:G1316 4.8 62.6 1.0

M.J.Belousoff, T.Shapira, A.Bashan, E.Zimmerman, H.Rozenberg, K.Arakawa, H.Kinashi, A.Yonath. Crystal Structure of the Synergistic Antibiotic Pair, Lankamycin and Lankacidin, in Complex with the Large Ribosomal Subunit. Proc.Natl.Acad.Sci.Usa V. 108 2717 2011.
ISSN: ISSN 0027-8424
PubMed: 21282615
DOI: 10.1073/PNAS.1019406108