Sodium 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
Potassium	(K)	15 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 42 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 42 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 Sodium with other atoms in the Na 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:Na3033 b:38.3 occ:1.00 O4 X:U2222 3.9 83.7 1.0 O4 X:U2057 4.1 82.0 1.0 O6 X:G2221 4.1 92.6 1.0 N7 X:G2217 4.5 94.6 1.0 C8 X:G2217 4.5 91.9 1.0 N7 X:G2221 4.5 83.7 1.0 N6 X:A2060 4.6 67.7 1.0 N7 X:A2220 4.7 81.6 1.0 N6 X:A2220 4.7 86.7 1.0 O4 X:U2058 4.8 0.6 1.0 C4 X:U2222 4.8 77.0 1.0 C4 X:U2057 4.9 83.5 1.0 C5 X:U2057 4.9 87.7 1.0 C5 X:A2220 5.0 85.6 1.0 C6 X:G2221 5.0 90.8 1.0 C6 X:A2220 5.0 87.5 1.0

Sodium binding site 2 out of 42 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 Sodium with other atoms in the Na 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:Na3034 b:50.5 occ:1.00 N7 X:G1985 3.9 47.3 1.0 O6 X:G1985 4.1 53.0 1.0 O6 X:G1986 4.2 45.6 1.0 N2 X:G1670 4.4 45.4 1.0 O6 X:G1987 4.6 39.0 1.0 C5 X:G1985 4.7 51.1 1.0 C6 X:G1985 4.7 51.8 1.0 C8 X:G1985 4.9 48.4 1.0

Sodium binding site 3 out of 42 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 Sodium with other atoms in the Na 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:Na3035 b:50.8 occ:1.00 OP1 X:A813 2.8 87.6 1.0 O2' X:A815 3.4 68.5 1.0 N3 X:C169 4.0 70.8 1.0 P X:A813 4.1 85.4 1.0 C4' X:A815 4.4 70.2 1.0 O2 X:C169 4.4 81.3 1.0 C2' X:A815 4.5 66.0 1.0 O3' X:A815 4.6 77.3 1.0 O4' X:A815 4.6 69.3 1.0 C2 X:C169 4.7 74.5 1.0 OP2 X:A813 4.7 80.3 1.0 C8 X:A813 4.7 82.8 1.0 N7 X:A813 4.7 83.7 1.0 C3' X:A815 4.8 70.8 1.0 N4 X:C169 4.8 83.3 1.0 C1' X:A815 4.9 66.1 1.0 C4 X:C169 4.9 76.9 1.0 N1 X:A168 5.0 72.9 1.0 O5' X:A813 5.0 58.4 1.0

Sodium binding site 4 out of 42 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 Sodium with other atoms in the Na 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:Na3036 b:79.5 occ:1.00 O4 X:U187 3.5 98.5 1.0 O6 X:G188 3.9 99.9 1.0 C4 X:U187 4.0 95.9 1.0 N6 X:A189 4.2 0.6 1.0 C5 X:U187 4.3 92.7 1.0 N7 X:G188 4.8 0.6 1.0 C6 X:G188 4.9 0.5 1.0

Sodium binding site 5 out of 42 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 Sodium with other atoms in the Na 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 X:Na3037 b:53.9 occ:1.00 K X:K3074 4.3 0.1 1.0 O4 X:U1473 4.4 67.4 1.0

Sodium binding site 6 out of 42 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 Sodium with other atoms in the Na 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:Na3038 b:59.3 occ:1.00 N1 X:G540 2.8 0.1 1.0 OP1 X:U2005 2.8 55.0 1.0 N2 X:G540 3.3 0.8 1.0 C2 X:G540 3.5 0.4 1.0 O6 X:G540 3.6 0.8 1.0 C6 X:G540 3.7 0.3 1.0 P X:U2005 4.2 62.9 1.0 OP1 X:C2027 4.3 77.6 1.0 OP2 X:U2005 4.6 68.0 1.0 O3' X:U2004 4.8 59.8 1.0 N3 X:G540 4.8 0.0 1.0 C5 X:G540 5.0 0.6 1.0

Sodium binding site 7 out of 42 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 Sodium with other atoms in the Na 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:Na3039 b:51.3 occ:1.00 OP1 X:A991 3.1 55.7 1.0 N3 X:C993 3.6 68.8 1.0 N6 X:A992 3.8 84.6 1.0 N4 X:C993 3.9 67.7 1.0 N7 X:A992 4.0 83.6 1.0 C4 X:C993 4.2 63.3 1.0 C2 X:C993 4.5 64.3 1.0 O2 X:C993 4.6 66.3 1.0 P X:A991 4.6 66.7 1.0 C6 X:A992 4.7 78.5 1.0 C5 X:A992 4.7 80.4 1.0 N7 X:A991 4.7 74.5 1.0 O2' X:A990 4.9 72.2 1.0 C2' X:A990 4.9 65.8 1.0

Sodium binding site 8 out of 42 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 Sodium with other atoms in the Na 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 Y:Na125 b:62.9 occ:1.00 O6 Y:G85 3.5 83.2 1.0 N7 Y:G84 4.0 87.6 1.0 OP2 Y:C83 4.2 93.4 1.0 N7 Y:G85 4.2 93.1 1.0 C6 Y:G85 4.5 86.5 1.0 N6 Y:A86 4.6 93.1 1.0 C8 Y:G84 4.7 80.3 1.0 C5 Y:G85 4.8 90.5 1.0 C5 Y:G84 4.9 90.2 1.0 O6 Y:G84 4.9 99.6 1.0

Sodium binding site 9 out of 42 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 Sodium with other atoms in the Na 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 Z:Na61 b:48.8 occ:1.00 OP2 X:C2591 2.9 59.2 1.0 NE2 Z:HIS4 3.1 89.4 1.0 CD2 Z:HIS4 3.4 91.2 1.0 CE1 Z:HIS4 3.6 87.2 1.0 C6 X:U2590 3.8 75.4 1.0 C5 X:U2590 3.9 77.7 1.0 CG Z:HIS4 4.0 91.2 1.0 ND1 Z:HIS4 4.1 89.0 1.0 O2' X:A2556 4.2 43.7 1.0 P X:C2591 4.3 64.0 1.0 OP2 X:U2590 4.4 80.1 1.0 C4' X:A2556 4.5 49.0 1.0 C3' X:U2590 4.6 58.9 1.0 O3' X:A2556 4.8 45.9 1.0 OP1 X:C2558 4.9 65.3 1.0 O3' X:U2590 4.9 52.6 1.0

Sodium binding site 10 out of 42 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 Sodium with other atoms in the Na 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:Na3040 b:70.7 occ:1.00 O6 X:G2393 3.6 0.3 1.0 N7 X:G2392 3.9 1.0 1.0 OP2 X:A2391 4.3 0.7 1.0 N7 X:G2393 4.4 0.9 1.0 O6 X:G2392 4.5 0.8 1.0 C6 X:G2393 4.6 0.5 1.0 C5 X:G2392 4.7 0.9 1.0 C8 X:G2392 4.7 0.1 1.0 C5 X:G2393 4.9 0.6 1.0 C2 X:A2381 4.9 0.4 1.0 C6 X:G2392 5.0 0.7 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