Sodium in PDB 1m90: Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit

The structure of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit, PDB code: 1m90 was solved by J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.661, 299.773, 573.684, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.2

The structure of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium	(Mg)	119 atoms
Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 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 - 80; Page 9, Binding sites: 81 - 86;

Binding sites:

The binding sites of Sodium atom in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit (pdb code 1m90). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 86 binding sites of Sodium where determined in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit, PDB code: 1m90:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 86 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8301 b:46.3 occ:1.00 OP2 A:C1069 2.3 25.5 1.0 O A:HOH4510 2.5 47.9 1.0 N7 A:G1072 2.6 26.6 1.0 O A:HOH9691 2.8 39.2 1.0 O A:HOH9725 2.9 51.6 1.0 O6 A:G1072 3.2 26.8 1.0 O6 A:G1087 3.2 27.7 1.0 C5 A:G1072 3.4 25.9 1.0 C6 A:G1072 3.6 25.1 1.0 C8 A:G1072 3.7 27.2 1.0 P A:C1069 3.7 28.6 1.0 O A:HOH8589 3.8 26.8 1.0 O A:HOH3062 4.2 36.1 1.0 C6 A:G1087 4.2 28.6 1.0 C5' A:C1068 4.3 30.6 1.0 C3' A:C1068 4.3 28.3 1.0 O3' A:C1068 4.4 27.8 1.0 OP1 A:C1069 4.5 24.9 1.0 C4 A:G1072 4.6 26.6 1.0 N9 A:G1072 4.7 26.8 1.0 O5' A:C1069 4.8 28.7 1.0 N1 A:G1087 4.8 28.0 1.0 N1 A:G1072 4.9 24.1 1.0 C4' A:C1068 4.9 29.8 1.0 O A:HOH3805 5.0 60.2 1.0

Sodium binding site 2 out of 86 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8302 b:46.2 occ:1.00 O2' A:G1119 2.9 35.0 1.0 O6 A:G1121 2.9 32.4 1.0 O A:HOH7325 2.9 46.6 1.0 OP2 A:U1120 2.9 37.7 1.0 O A:HOH5228 3.0 53.5 1.0 O3' A:G1119 3.2 36.2 1.0 O A:HOH4084 3.3 35.5 1.0 N7 A:G1121 3.3 34.2 1.0 O4 A:U1122 3.4 36.8 1.0 O A:HOH3701 3.4 33.9 1.0 C6 A:G1121 3.6 30.9 1.0 P A:U1120 3.7 37.3 1.0 C5 A:G1121 3.8 31.6 1.0 C2' A:G1119 3.9 35.0 1.0 MG A:MG8025 3.9 40.5 1.0 C3' A:G1119 4.1 35.6 1.0 O A:HOH6469 4.1 50.1 1.0 C4 A:U1122 4.2 35.5 1.0 C1' A:G1119 4.3 32.8 1.0 C8 A:G1121 4.5 33.4 1.0 C5 A:U1122 4.5 33.7 1.0 OP1 A:U1120 4.6 39.0 1.0 N4 A:C1243 4.9 30.7 1.0 O5' A:U1120 4.9 35.1 1.0 N1 A:G1121 5.0 29.4 1.0 OP1 A:C1238 5.0 41.5 1.0 N6 A:A1242 5.0 34.4 1.0

Sodium binding site 3 out of 86 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8303 b:43.0 occ:1.00 OP1 A:G644 2.8 28.9 1.0 O4 A:U904 2.9 31.1 1.0 OP2 A:A643 3.0 22.2 1.0 OP1 A:G1354 3.2 30.0 1.0 NH2 M:ARG8 3.2 27.4 1.0 O A:HOH9787 3.4 36.6 1.0 O5' A:A643 3.5 22.9 1.0 P A:A643 3.5 24.9 1.0 OP1 A:A643 3.7 27.2 1.0 OP1 A:C1353 3.8 47.6 1.0 C4 A:U904 3.9 29.4 1.0 N3 A:U904 4.1 27.8 1.0 P A:G644 4.1 28.6 1.0 O A:HOH8951 4.2 24.9 1.0 O A:HOH4138 4.2 84.8 1.0 P A:G1354 4.2 27.9 1.0 C5' A:A643 4.3 23.5 1.0 CZ M:ARG8 4.3 27.0 1.0 OP2 A:G1354 4.4 25.6 1.0 C3' A:A643 4.4 25.5 1.0 O3' A:A643 4.6 27.4 1.0 OP2 A:G644 4.7 27.1 1.0 P A:C1353 4.8 50.6 1.0 O3' A:C1353 4.9 30.4 1.0 NE M:ARG8 4.9 24.9 1.0 O5' A:C1353 5.0 44.4 1.0 N6 A:A1355 5.0 22.4 1.0

Sodium binding site 4 out of 86 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8305 b:35.8 occ:1.00 O A:HOH4240 2.4 37.2 1.0 O A:HOH5327 2.6 37.6 1.0 O2' A:A630 2.6 28.8 1.0 N3 A:A630 2.6 29.8 1.0 O A:HOH3619 2.7 43.5 1.0 O2' A:A631 2.9 29.7 1.0 C2 A:A630 3.5 29.2 1.0 C1' A:A630 3.5 29.8 1.0 C4 A:A630 3.6 29.5 1.0 C2' A:A631 3.6 27.9 1.0 OP2 A:A2074 3.6 26.4 1.0 C2' A:A630 3.6 29.6 1.0 C3' A:A631 3.9 27.9 1.0 N9 A:A630 3.9 29.6 1.0 O3' A:A630 4.0 27.8 1.0 OP1 A:A632 4.0 29.9 1.0 N2 A:G2070 4.2 26.6 1.0 O3' A:A631 4.2 26.4 1.0 C3' A:A630 4.5 28.4 1.0 N1 A:A629 4.5 26.5 1.0 P A:A632 4.5 29.4 1.0 OP2 A:G2072 4.6 47.5 1.0 O A:HOH8928 4.6 23.8 1.0 C2 A:A629 4.6 27.1 1.0 O A:HOH9605 4.7 50.8 1.0 O4' A:A630 4.7 32.5 1.0 N1 A:A630 4.8 29.7 1.0 C2 A:A628 4.8 30.0 1.0 OP2 A:A632 4.9 29.0 1.0 C2 A:G2070 4.9 27.5 1.0 C5 A:A630 4.9 29.3 1.0

Sodium binding site 5 out of 86 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8306 b:32.1 occ:1.00 N7 A:G2094 2.7 30.1 1.0 N1 A:A2649 2.9 33.6 1.0 O A:HOH8647 3.0 19.3 1.0 N7 A:G2093 3.2 29.7 1.0 O6 A:G2094 3.2 32.4 1.0 O2' A:G2092 3.3 28.5 1.0 C2 A:A2649 3.4 33.6 1.0 N3 A:G2092 3.4 30.9 1.0 C5 A:G2094 3.5 30.1 1.0 C5 A:G2093 3.6 29.9 1.0 O6 A:G2093 3.6 33.8 1.0 N6 A:A2612 3.6 28.3 1.0 C6 A:G2094 3.7 29.9 1.0 C6 A:G2093 3.8 32.1 1.0 C8 A:G2094 3.8 29.2 1.0 N2 A:G2092 3.8 32.3 1.0 C2 A:G2092 3.9 31.1 1.0 C6 A:A2612 3.9 29.5 1.0 C8 A:G2093 4.0 29.3 1.0 C6 A:A2649 4.0 32.1 1.0 N6 A:A2649 4.3 33.1 1.0 C4 A:G2092 4.3 30.4 1.0 C5 A:A2612 4.4 29.0 1.0 N1 A:A2612 4.4 29.9 1.0 C2' A:G2092 4.4 28.4 1.0 C4 A:G2093 4.5 28.8 1.0 C1' A:G2092 4.5 28.6 1.0 N3 A:A2649 4.6 34.8 1.0 N7 A:A2612 4.7 29.5 1.0 N9 A:G2093 4.7 29.2 1.0 N9 A:G2092 4.7 29.6 1.0 C4 A:G2094 4.8 29.5 1.0 N1 A:G2093 4.8 31.9 1.0 N9 A:G2094 4.9 28.5 1.0 N1 A:G2092 5.0 30.2 1.0 O3' A:G2092 5.0 26.5 1.0

Sodium binding site 6 out of 86 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8307 b:46.9 occ:1.00 O2 A:C40 2.7 48.9 1.0 O2' A:C40 2.7 45.6 1.0 O4' A:G41 2.8 43.6 1.0 O2 A:C443 3.1 52.0 1.0 N1 A:A442 3.1 50.2 1.0 C2' A:C40 3.2 46.4 1.0 C1' A:C40 3.5 47.0 1.0 C2 A:A442 3.6 49.4 1.0 C1' A:G41 3.7 42.1 1.0 C2 A:C40 3.8 48.8 1.0 C4' A:G41 3.9 42.8 1.0 C2 A:C443 4.0 50.1 1.0 N9 A:G41 4.0 42.0 1.0 N1 A:C40 4.1 48.3 1.0 C6 A:A442 4.2 49.3 1.0 C5' A:G41 4.2 42.9 1.0 N6 A:A442 4.4 48.9 1.0 N2 A:G39 4.4 43.1 1.0 C8 A:G41 4.5 41.5 1.0 O5' A:G41 4.6 44.3 1.0 N3 A:C443 4.7 49.6 1.0 C4 A:G41 4.7 41.7 1.0 O4' A:C40 4.7 47.6 1.0 C3' A:C40 4.7 46.1 1.0 C1' A:C443 4.8 49.4 1.0 N1 A:C443 4.8 50.1 1.0 O A:HOH5408 4.8 49.0 1.0 N3 A:A442 4.9 49.4 1.0 N3 A:C40 4.9 49.5 1.0 O A:HOH6511 5.0 62.2 1.0 C2 A:G39 5.0 45.3 1.0

Sodium binding site 7 out of 86 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8308 b:43.3 occ:1.00 O2 A:U1724 2.2 37.6 1.0 O2 A:C1394 2.3 34.2 1.0 O A:HOH9938 2.4 30.9 1.0 O4 A:U1432 2.6 36.3 1.0 C2 A:U1724 3.4 37.5 1.0 C2 A:C1394 3.5 32.4 1.0 O6 A:G1433 3.7 47.7 1.0 C4 A:U1432 3.8 35.5 1.0 O2' A:C1394 4.0 31.7 1.0 C2' A:C1394 4.1 34.5 1.0 O A:HOH8817 4.1 32.1 1.0 O2' A:U1724 4.2 34.4 1.0 C1' A:U1724 4.2 35.3 1.0 N3 A:U1724 4.3 37.1 1.0 C6 A:G1433 4.3 44.5 1.0 N3 A:U1432 4.3 35.5 1.0 C1' A:C1394 4.3 33.8 1.0 N1 A:U1724 4.3 36.9 1.0 N3 A:C1394 4.3 30.9 1.0 C2' A:U1724 4.4 35.3 1.0 O A:HOH6677 4.4 66.2 1.0 N1 A:C1394 4.4 32.9 1.0 O A:HOH5005 4.5 56.9 1.0 O A:HOH4372 4.5 48.7 1.0 N1 A:G1433 4.7 45.6 1.0 O2' A:C1725 4.8 31.2 1.0 OP2 A:U1722 4.9 42.1 1.0 C5 A:U1432 5.0 35.1 1.0

Sodium binding site 8 out of 86 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8309 b:32.1 occ:1.00 O J:PRO155 2.7 47.8 1.0 O3' A:A1133 2.8 38.3 1.0 O J:VAL153 2.8 43.6 1.0 O J:LYS150 2.8 52.0 1.0 OP1 A:G1134 3.0 37.5 1.0 O2' A:A1133 3.1 35.9 1.0 O J:THR154 3.5 43.5 1.0 P A:G1134 3.6 38.9 1.0 C J:PRO155 3.6 47.9 1.0 C3' A:A1133 3.8 37.0 1.0 C J:THR154 3.9 43.5 1.0 C2' A:A1133 4.0 35.7 1.0 C J:VAL153 4.0 42.6 1.0 C J:LYS150 4.0 51.6 1.0 C5' A:G1134 4.3 39.2 1.0 N J:PRO155 4.3 44.5 1.0 C4' A:A1133 4.3 36.2 1.0 N J:THR156 4.4 50.9 1.0 O2' A:G2520 4.4 40.9 1.0 O5' A:G1134 4.4 37.4 1.0 CA J:PRO155 4.4 45.7 1.0 CA J:THR156 4.5 52.8 1.0 CA J:THR154 4.6 42.6 1.0 N J:THR154 4.8 42.7 1.0 OP2 A:G1134 4.8 36.1 1.0 N J:VAL153 4.9 43.5 1.0 CA J:MET151 4.9 50.6 1.0 N J:MET151 4.9 51.6 1.0 CG2 J:VAL153 4.9 38.5 1.0 C J:MET151 5.0 49.3 1.0 O J:MET151 5.0 48.7 1.0 CA J:LYS150 5.0 51.9 1.0

Sodium binding site 9 out of 86 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8310 b:39.6 occ:1.00 O6 A:G2579 2.7 35.0 1.0 N7 A:G2579 3.0 34.8 1.0 O A:HOH4043 3.0 39.8 1.0 N3 A:A2577 3.1 35.2 1.0 N7 A:G2578 3.1 36.1 1.0 O4' A:A2577 3.2 38.0 1.0 C6 A:G2579 3.4 33.4 1.0 O6 A:G2578 3.5 39.2 1.0 C5 A:G2579 3.5 34.3 1.0 C5 A:G2578 3.6 37.4 1.0 C6 A:G2578 3.7 38.4 1.0 C1' A:A2577 3.8 37.0 1.0 C2 A:A2577 3.8 33.8 1.0 O A:HOH7269 3.9 51.3 1.0 C4 A:A2577 3.9 33.5 1.0 C8 A:G2578 4.0 35.9 1.0 C4' A:A2577 4.1 39.5 1.0 O A:HOH5826 4.2 49.7 1.0 C8 A:G2579 4.2 35.8 1.0 N9 A:A2577 4.2 34.0 1.0 C4 A:G2578 4.6 36.8 1.0 N4 A:C2556 4.6 37.4 1.0 N1 A:G2579 4.7 32.6 1.0 O6 A:G2580 4.8 35.4 1.0 N9 A:G2578 4.8 36.9 1.0 N3 A:U2554 4.8 29.2 1.0 N1 A:G2578 4.8 38.3 1.0 C4 A:G2579 4.8 34.1 1.0 O A:HOH5509 5.0 63.3 1.0 O3' A:A2577 5.0 39.9 1.0

Sodium binding site 10 out of 86 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8311 b:55.7 occ:1.00 O A:HOH3102 2.4 27.2 1.0 O6 A:G2525 2.5 37.4 1.0 O A:HOH4193 2.6 51.4 1.0 N7 A:G2524 2.8 32.3 1.0 O A:HOH8704 3.0 31.9 1.0 O A:HOH5904 3.3 53.9 1.0 C6 A:G2525 3.5 35.3 1.0 C8 A:G2524 3.7 33.0 1.0 C5 A:G2524 3.9 31.1 1.0 O A:HOH3148 4.0 29.8 1.0 C5 A:U2523 4.0 35.8 1.0 O6 A:G2524 4.1 28.5 1.0 C4 A:U2523 4.2 35.0 1.0 OP2 A:G2524 4.3 36.8 1.0 C5 A:G2525 4.3 34.7 1.0 C6 A:G2524 4.4 30.8 1.0 N7 A:G2525 4.4 33.5 1.0 O4 A:U2523 4.5 36.6 1.0 N1 A:G2525 4.5 33.1 1.0 C6 A:U2523 4.5 35.3 1.0 O2' A:C2493 4.5 33.0 1.0 N3 A:U2523 4.7 33.9 1.0 OP2 A:U2523 4.8 39.0 1.0 N9 A:G2524 4.9 33.0 1.0 C2' A:C2493 4.9 33.2 1.0

J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz. Structural Insights Into Peptide Bond Formation. Proc.Natl.Acad.Sci.Usa V. 99 11670 2002.
ISSN: ISSN 0027-8424
PubMed: 12185246
DOI: 10.1073/PNAS.172404099