Magnesium in PDB 3pip: 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: 3pip was solved by M.J.Belousoff, T.Shapira, A.Bashan, E.Zimmerman, 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 / 3.45
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.723, 408.562, 693.334, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 30.1

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:

Potassium	(K)	4 atoms
Sodium	(Na)	5 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 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 73;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit (pdb code 3pip). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 73 binding sites of Magnesium where determined in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit, PDB code: 3pip:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 73 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 Magnesium with other atoms in the Mg 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:Mg2883 b:23.4 occ:1.00 N6 X:A1667 3.1 59.0 1.0 OP2 X:G1987 3.8 82.0 1.0 O6 X:G1668 3.9 78.1 1.0 C6 X:A1667 4.3 65.3 1.0 N7 X:A1667 4.3 80.3 1.0 C5 X:A1667 4.7 72.4 1.0 OP1 X:G1987 4.8 96.5 1.0 C6 X:G1668 4.8 68.5 1.0 P X:G1987 4.8 89.2 1.0

Magnesium binding site 2 out of 73 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 Magnesium with other atoms in the Mg 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:Mg2884 b:72.6 occ:1.00 OP1 X:G1284 2.7 81.3 1.0 OP2 X:G1284 3.5 81.2 1.0 P X:G1284 3.5 84.3 1.0 OP2 X:U1286 4.1 49.2 1.0 C5' X:G1284 4.5 57.5 1.0 OP2 X:G1666 4.6 80.3 1.0 O5' X:G1284 4.6 65.5 1.0 OP1 X:G1987 4.7 96.5 1.0 OP1 X:U1286 4.7 52.2 1.0 OP1 X:A1285 4.7 59.5 1.0 O3' X:C1283 4.9 77.1 1.0 P X:U1286 4.9 51.1 1.0

Magnesium binding site 3 out of 73 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 Magnesium with other atoms in the Mg 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:Mg2885 b:68.5 occ:1.00 OP1 X:G2555 1.5 86.3 1.0 OP1 X:A2556 2.3 68.4 1.0 P X:G2555 3.0 88.9 1.0 O3' X:C2554 3.5 45.5 1.0 N2 X:G2555 3.6 0.9 1.0 P X:A2556 3.7 73.0 1.0 OP2 X:G2555 3.9 87.9 1.0 OP2 X:G2036 3.9 75.6 1.0 O5' X:G2555 4.0 44.2 1.0 OP1 X:G2036 4.1 73.1 1.0 OP2 X:A2556 4.3 74.8 1.0 C5' X:G2555 4.3 45.6 1.0 P X:G2036 4.5 74.3 1.0 O3' X:G2555 4.5 57.5 1.0 C3' X:G2555 4.6 55.9 1.0 OP2 X:G2035 4.6 64.0 1.0 C2 X:G2555 4.7 0.8 1.0 O5' X:A2556 4.7 52.6 1.0 N3 X:G2555 4.8 93.9 1.0 C3' X:C2554 4.8 52.0 1.0

Magnesium binding site 4 out of 73 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 Magnesium with other atoms in the Mg 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:Mg2886 b:54.2 occ:1.00 OP2 X:G2557 3.7 65.2 1.0 OP1 X:G2557 3.9 62.6 1.0 N7 X:A2034 4.1 75.2 1.0 OP2 X:A2034 4.2 33.4 1.0 NH1 B:ARG137 4.2 88.1 1.0 OP1 X:U2592 4.2 61.1 1.0 C8 X:A2034 4.3 76.0 1.0 P X:G2557 4.3 71.7 1.0 NH2 B:ARG137 4.6 85.2 1.0 N7 X:A2593 4.6 83.1 1.0 OP2 X:A2593 4.8 74.3 1.0 CZ B:ARG137 4.9 84.6 1.0 OP2 X:C2033 4.9 81.2 1.0

Magnesium binding site 5 out of 73 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 Magnesium with other atoms in the Mg 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:Mg2887 b:35.2 occ:1.00 OP1 X:C1989 2.5 84.5 1.0 OP1 X:A2031 2.6 50.9 1.0 OP1 X:A1281 2.7 60.7 1.0 O3' X:U1280 3.7 81.6 1.0 P X:A2031 3.8 45.9 1.0 P X:A1281 3.8 57.8 1.0 OP2 X:G2032 3.8 35.9 1.0 P X:C1989 4.0 84.1 1.0 O5' X:A2031 4.1 40.4 1.0 OP2 X:A2031 4.4 47.6 1.0 O3' X:A1988 4.5 65.8 1.0 C5' X:A2031 4.5 49.7 1.0 OP2 X:A1281 4.6 42.4 1.0 C5' X:C1989 4.7 27.5 1.0 O5' X:C1989 4.8 25.0 1.0 C3' X:U1280 5.0 78.5 1.0 OP2 X:C1989 5.0 85.8 1.0

Magnesium binding site 6 out of 73 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 Magnesium with other atoms in the Mg 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:Mg2888 b:51.8 occ:1.00 OP2 X:A1282 2.0 63.4 1.0 OP1 X:A1988 2.4 78.0 1.0 P X:A1282 3.5 65.5 1.0 P X:A1988 3.7 72.4 1.0 O5' X:A1282 4.2 38.7 1.0 C8 X:A1282 4.2 49.4 1.0 OP2 X:A1988 4.3 58.6 1.0 O3' X:A1281 4.3 0.9 1.0 O5' X:A1988 4.3 90.2 1.0 N7 X:A1282 4.4 50.2 1.0 OP1 X:A1282 4.4 52.0 1.0 OP2 X:A1281 4.4 42.4 1.0 C5' X:A1282 4.4 36.6 1.0 O5' X:A1281 4.5 70.2 1.0 C3' X:A1281 4.5 92.4 1.0 C5' X:A1988 4.6 83.8 1.0 OP2 X:C1989 4.6 85.8 1.0 P X:A1281 4.9 57.8 1.0 O3' X:G1987 4.9 83.1 1.0

Magnesium binding site 7 out of 73 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 Magnesium with other atoms in the Mg 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:Mg2889 b:61.1 occ:1.00 OP1 X:U1365 2.8 0.3 1.0 O3' X:C1364 3.7 0.6 1.0 P X:U1365 3.9 0.5 1.0 O2' X:A1587 4.2 0.9 1.0 C5' X:A1588 4.3 0.4 1.0 OP2 X:C1388 4.4 0.6 1.0 O3' X:A1587 4.7 0.8 1.0 OP1 X:C1388 4.7 0.5 1.0 OP2 X:U1365 4.8 0.7 1.0 C3' X:C1364 5.0 0.8 1.0

Magnesium binding site 8 out of 73 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 Magnesium with other atoms in the Mg 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:Mg2890 b:59.2 occ:1.00 OP2 X:A984 2.6 82.6 1.0 P X:A984 3.3 94.9 1.0 OP1 X:A984 3.4 0.0 1.0 OP1 X:G579 3.5 89.9 1.0 O3' X:G983 3.6 84.4 1.0 N1 X:A834 3.9 0.9 1.0 N6 X:A834 4.2 0.3 1.0 N6 X:A833 4.3 0.8 1.0 C5 X:U577 4.4 80.8 1.0 OP2 X:G579 4.4 58.5 1.0 P X:G579 4.4 76.3 1.0 C6 X:A834 4.5 0.2 1.0 N1 X:A833 4.6 0.3 1.0 O5' X:A984 4.8 0.3 1.0 O2' X:G983 4.8 0.4 1.0 C2 X:A834 4.8 0.0 1.0 C4 X:U577 4.8 79.2 1.0 OP2 X:U578 4.8 79.5 1.0 C5' X:U578 4.9 69.6 1.0 C6 X:U577 4.9 79.0 1.0 C6 X:A833 4.9 0.8 1.0 C3' X:G983 4.9 92.3 1.0 O3' X:U578 5.0 56.2 1.0 O4 X:U577 5.0 73.3 1.0

Magnesium binding site 9 out of 73 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 Magnesium with other atoms in the Mg 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:Mg2891 b:50.2 occ:1.00 OP1 X:A2692 2.2 65.1 1.0 OP1 X:A2690 2.6 51.7 1.0 OP1 X:C1310 3.1 81.8 1.0 P X:A2692 3.2 70.4 1.0 O3' X:C2689 3.5 51.2 1.0 OP2 X:A2692 3.5 74.2 1.0 P X:A2690 3.6 52.7 1.0 O5' X:A2692 4.1 43.4 1.0 C5' X:C1310 4.2 44.3 1.0 OP2 X:A2690 4.3 43.0 1.0 P X:C1310 4.4 77.1 1.0 O3' X:C2691 4.5 72.7 1.0 O3' X:G1309 4.7 44.1 1.0 C3' X:C2689 4.8 46.6 1.0 O5' X:C1310 4.8 45.4 1.0 O5' X:A2690 5.0 42.9 1.0 C5' X:C2689 5.0 17.4 1.0

Magnesium binding site 10 out of 73 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 Magnesium with other atoms in the Mg 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:Mg2892 b:71.9 occ:1.00 OP2 X:G2694 2.1 98.7 1.0 OP2 X:A2692 2.2 74.2 1.0 OP2 X:U2693 3.2 32.1 1.0 OP2 X:A2690 3.2 43.0 1.0 P X:G2694 3.5 96.9 1.0 P X:A2692 3.6 70.4 1.0 C5' X:A2692 3.7 36.8 1.0 OP1 X:G2694 3.9 94.7 1.0 O5' X:A2692 4.0 43.4 1.0 CB K:SER15 4.2 48.4 1.0 OG K:SER15 4.2 53.4 1.0 O2' X:C2691 4.3 66.9 1.0 O3' X:U2693 4.3 43.0 1.0 O3' X:C2691 4.4 72.7 1.0 P X:A2690 4.4 52.7 1.0 C3' X:C2691 4.5 71.6 1.0 OP1 X:A2690 4.6 51.7 1.0 P X:U2693 4.6 42.9 1.0 OP1 X:C2689 4.6 70.0 1.0 O5' X:G2694 4.7 36.3 1.0 OP1 X:A2692 4.7 65.1 1.0 C2' X:C2691 4.8 71.0 1.0 C4' X:U2693 4.8 45.5 1.0 C5' X:G2694 4.8 43.8 1.0 C3' X:U2693 4.9 43.9 1.0 ND2 K:ASN13 5.0 70.0 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