Sodium in PDB 1q7y: Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit

The structure of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit, PDB code: 1q7y 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)	19.99 / 3.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.902, 300.474, 575.176, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 28

The structure of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium	(Mg)	117 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit (pdb code 1q7y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 86 binding sites of Sodium where determined in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit, PDB code: 1q7y:
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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8301 b:22.7 occ:1.00 O A:HOH4471 2.3 61.3 1.0 OP2 A:C1069 2.4 32.3 1.0 O A:HOH9713 2.6 29.7 1.0 N7 A:G1072 2.6 32.8 1.0 O6 A:G1072 3.0 35.6 1.0 O6 A:G1087 3.0 31.4 1.0 C5 A:G1072 3.3 32.9 1.0 O A:HOH9680 3.4 14.7 1.0 C6 A:G1072 3.5 33.6 1.0 C8 A:G1072 3.7 33.6 1.0 P A:C1069 3.8 32.7 1.0 O A:HOH8590 4.0 42.4 1.0 C6 A:G1087 4.1 32.9 1.0 C5' A:C1068 4.5 37.1 1.0 OP1 A:C1069 4.5 30.9 1.0 O A:HOH3046 4.5 7.0 1.0 O3' A:C1068 4.6 33.3 1.0 C4 A:G1072 4.6 32.9 1.0 O A:HOH4830 4.6 61.1 1.0 C3' A:C1068 4.7 33.7 1.0 N9 A:G1072 4.8 33.6 1.0 N1 A:G1087 4.8 31.5 1.0 O A:HOH3268 4.8 22.8 1.0 OP2 A:C1068 4.8 41.3 1.0 N1 A:G1072 4.8 32.4 1.0 O5' A:C1069 4.9 28.5 1.0

Sodium binding site 2 out of 86 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8302 b:25.6 occ:1.00 O A:HOH5188 2.4 23.5 1.0 OP2 A:U1120 2.5 38.2 1.0 O3' A:G1119 2.6 37.7 1.0 O2' A:G1119 2.8 36.4 1.0 O A:HOH7266 3.0 42.4 1.0 P A:U1120 3.1 38.0 1.0 O A:HOH3676 3.1 28.3 1.0 N7 A:G1121 3.2 36.7 1.0 O6 A:G1121 3.3 36.7 1.0 C3' A:G1119 3.6 38.0 1.0 C2' A:G1119 3.7 37.3 1.0 O A:HOH4044 3.7 63.9 1.0 OP1 A:U1120 3.9 38.4 1.0 C5 A:G1121 4.0 35.4 1.0 C6 A:G1121 4.0 35.4 1.0 O4 A:U1122 4.0 42.6 1.0 MG A:MG8025 4.1 12.4 1.0 C1' A:G1119 4.2 37.1 1.0 C8 A:G1121 4.4 35.2 1.0 O5' A:U1120 4.4 36.2 1.0 O A:HOH6422 4.4 24.4 1.0 C5' A:U1120 4.6 36.1 1.0 OP2 A:G1121 4.6 38.9 1.0 C4 A:U1122 4.7 43.4 1.0 C4' A:G1119 4.8 37.7 1.0 O A:HOH7333 4.9 47.1 1.0 C5 A:U1122 5.0 42.9 1.0

Sodium binding site 3 out of 86 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8303 b:42.3 occ:1.00 O4 A:U904 2.7 38.0 1.0 OP1 A:G1354 2.8 35.2 1.0 OP1 A:G644 2.9 35.0 1.0 OP2 A:A643 3.0 37.5 1.0 NH2 M:ARG8 3.0 28.4 1.0 O A:HOH9772 3.5 23.6 1.0 C4 A:U904 3.6 36.6 1.0 P A:A643 3.7 39.6 1.0 N3 A:U904 3.8 35.7 1.0 O5' A:A643 3.8 39.4 1.0 P A:G1354 4.0 36.3 1.0 CZ M:ARG8 4.1 28.7 1.0 OP1 A:A643 4.1 39.6 1.0 OP1 A:C1353 4.2 50.1 1.0 P A:G644 4.2 34.4 1.0 OP2 A:G1354 4.4 36.1 1.0 O A:HOH4097 4.5 0.3 1.0 O A:HOH8945 4.5 55.4 1.0 N6 A:A1355 4.5 30.1 1.0 O3' A:C1353 4.6 38.6 1.0 NE M:ARG8 4.6 28.6 1.0 C3' A:A643 4.7 35.9 1.0 C5' A:A643 4.7 38.4 1.0 O3' A:A643 4.7 35.9 1.0 OP2 A:G644 4.8 34.1 1.0 C5 A:U904 4.9 36.7 1.0 NH1 M:ARG8 4.9 29.1 1.0 O A:HOH6073 5.0 39.6 1.0

Sodium binding site 4 out of 86 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8305 b:10.7 occ:1.00 O A:HOH5283 2.2 81.5 1.0 O A:HOH3596 2.2 73.0 1.0 O A:HOH4200 2.5 68.0 1.0 O2' A:A631 2.7 27.7 1.0 N3 A:A630 2.8 28.0 1.0 OP2 A:A2074 3.3 32.2 1.0 O2' A:A630 3.4 28.2 1.0 C2 A:A630 3.5 28.0 1.0 C2' A:A631 3.5 30.2 1.0 N2 A:G2070 3.6 25.4 1.0 C1' A:A630 3.7 27.9 1.0 C4 A:A630 3.8 27.9 1.0 C3' A:A631 4.0 30.7 1.0 O A:HOH9599 4.1 15.3 1.0 N9 A:A630 4.2 28.7 1.0 C2' A:A630 4.2 28.2 1.0 O3' A:A631 4.2 33.0 1.0 N1 A:A629 4.3 28.1 1.0 O3' A:A630 4.3 26.8 1.0 C2 A:G2070 4.4 25.2 1.0 OP1 A:A632 4.4 35.4 1.0 O A:HOH8922 4.5 6.2 1.0 OP2 A:G2072 4.6 39.4 1.0 C2 A:A629 4.6 27.6 1.0 P A:A2074 4.8 31.6 1.0 P A:A632 4.8 34.0 1.0 N1 A:A630 4.8 27.4 1.0 O4' A:A630 4.8 27.0 1.0 C3' A:A630 4.9 27.8 1.0 N3 A:G2070 4.9 25.0 1.0 C1' A:A631 4.9 31.1 1.0

Sodium binding site 5 out of 86 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8306 b:35.2 occ:1.00 N7 A:G2094 2.5 26.7 1.0 O A:HOH8648 2.9 27.0 1.0 N7 A:G2093 3.0 34.5 1.0 N1 A:A2649 3.0 39.4 1.0 O6 A:G2094 3.0 27.2 1.0 O2' A:G2092 3.3 32.4 1.0 C5 A:G2094 3.3 26.6 1.0 C2 A:A2649 3.4 40.0 1.0 C6 A:G2094 3.5 26.4 1.0 C5 A:G2093 3.5 34.1 1.0 N6 A:A2612 3.6 26.4 1.0 C8 A:G2094 3.6 25.6 1.0 N3 A:G2092 3.6 28.8 1.0 C8 A:G2093 3.7 33.9 1.0 C6 A:G2093 3.9 33.6 1.0 O6 A:G2093 3.9 32.1 1.0 N2 A:G2092 3.9 29.3 1.0 C6 A:A2612 4.0 30.2 1.0 C2 A:G2092 4.1 28.2 1.0 C6 A:A2649 4.2 39.0 1.0 C4 A:G2093 4.4 34.6 1.0 C5 A:A2612 4.4 29.3 1.0 C2' A:G2092 4.5 31.2 1.0 N6 A:A2649 4.5 39.7 1.0 C4 A:G2092 4.5 28.6 1.0 N9 A:G2093 4.5 33.7 1.0 C4 A:G2094 4.6 27.3 1.0 N1 A:A2612 4.6 32.2 1.0 C1' A:G2092 4.6 30.9 1.0 N7 A:A2612 4.6 29.5 1.0 N9 A:G2094 4.7 25.7 1.0 N3 A:A2649 4.7 40.1 1.0 N1 A:G2094 4.9 27.4 1.0 N9 A:G2092 4.9 30.2 1.0 N1 A:G2093 5.0 33.5 1.0

Sodium binding site 6 out of 86 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8307 b:34.4 occ:1.00 O2' A:C40 2.7 51.2 1.0 O4' A:G41 3.0 53.0 1.0 O2 A:C443 3.1 52.1 1.0 O2 A:C40 3.5 53.6 1.0 N1 A:A442 3.5 66.0 1.0 C2' A:C40 3.6 51.8 1.0 C2 A:A442 3.8 65.2 1.0 C4' A:G41 3.9 52.4 1.0 C1' A:C40 4.0 52.7 1.0 C2 A:C443 4.0 54.3 1.0 C1' A:G41 4.1 51.8 1.0 C5' A:G41 4.1 51.5 1.0 O A:HOH5368 4.2 65.8 1.0 C1' A:C443 4.2 57.7 1.0 C2 A:C40 4.5 54.0 1.0 N1 A:C443 4.5 55.5 1.0 O A:HOH6465 4.6 52.9 1.0 O5' A:G41 4.6 52.8 1.0 C6 A:A442 4.6 65.1 1.0 N9 A:G41 4.6 51.5 1.0 N1 A:C40 4.8 53.3 1.0 O2' A:C443 4.8 58.9 1.0 N2 A:G39 4.8 41.0 1.0 N3 A:C443 4.9 54.4 1.0 N6 A:A442 4.9 66.1 1.0 C2' A:C443 5.0 58.6 1.0

Sodium binding site 7 out of 86 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8308 b:40.3 occ:1.00 O A:HOH9918 2.1 52.2 1.0 O2 A:U1724 2.1 46.0 1.0 O2 A:C1394 2.3 46.4 1.0 O4 A:U1432 2.5 38.4 1.0 C2 A:U1724 3.3 46.0 1.0 C2 A:C1394 3.5 45.7 1.0 O A:HOH8816 3.6 2.9 1.0 C4 A:U1432 3.7 39.0 1.0 O2' A:U1724 3.9 41.5 1.0 O6 A:G1433 3.9 47.0 1.0 C1' A:U1724 4.0 42.5 1.0 C2' A:U1724 4.1 41.7 1.0 N1 A:U1724 4.1 43.8 1.0 N3 A:U1724 4.2 47.1 1.0 C2' A:C1394 4.3 49.2 1.0 O2' A:C1394 4.3 50.0 1.0 N3 A:C1394 4.3 44.1 1.0 N3 A:U1432 4.3 39.9 1.0 O A:HOH4963 4.3 74.9 1.0 O A:HOH6639 4.4 71.4 1.0 C1' A:C1394 4.4 48.8 1.0 N1 A:C1394 4.4 47.2 1.0 C6 A:G1433 4.4 47.0 1.0 O2' A:C1725 4.6 35.6 1.0 O A:HOH4336 4.7 50.7 1.0 C5 A:U1432 4.8 39.1 1.0 N1 A:G1433 4.8 47.6 1.0 O3' A:C1725 4.9 39.8 1.0

Sodium binding site 8 out of 86 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8310 b:22.2 occ:1.00 O4' A:A2577 2.6 36.0 1.0 O A:HOH4003 2.9 62.7 1.0 N7 A:G2579 3.0 36.3 1.0 N3 A:A2577 3.1 36.0 1.0 N7 A:G2578 3.1 38.5 1.0 O6 A:G2579 3.1 35.9 1.0 C1' A:A2577 3.3 35.5 1.0 C4' A:A2577 3.5 37.5 1.0 C5 A:G2578 3.7 39.6 1.0 C5 A:G2579 3.7 35.7 1.0 C6 A:G2579 3.8 36.4 1.0 C4 A:A2577 3.8 34.8 1.0 O6 A:G2578 3.8 41.3 1.0 C8 A:G2578 3.9 37.9 1.0 N9 A:A2577 3.9 35.2 1.0 C2 A:A2577 4.0 36.5 1.0 C6 A:G2578 4.0 40.0 1.0 O A:HOH7212 4.1 90.0 1.0 C8 A:G2579 4.1 36.5 1.0 O A:HOH4198 4.3 42.0 1.0 O A:HOH5779 4.3 40.8 1.0 C3' A:A2577 4.5 38.0 1.0 O3' A:A2577 4.5 39.1 1.0 C5' A:A2577 4.6 37.3 1.0 C2' A:A2577 4.6 36.1 1.0 C4 A:G2578 4.7 39.6 1.0 N9 A:G2578 4.8 38.1 1.0 OP2 A:G2579 5.0 36.2 1.0 O A:HOH5467 5.0 15.3 1.0

Sodium binding site 9 out of 86 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8311 b:43.4 occ:1.00 O A:HOH3085 1.9 8.5 1.0 O6 A:G2525 2.3 31.8 1.0 O A:HOH4153 2.4 0.0 1.0 N7 A:G2524 2.9 33.4 1.0 C6 A:G2525 3.3 33.2 1.0 O A:HOH5856 3.4 74.8 1.0 O A:HOH8700 3.6 1.1 1.0 C8 A:G2524 3.8 34.0 1.0 O A:HOH3130 3.8 10.3 1.0 C5 A:G2524 3.8 33.5 1.0 O6 A:G2524 3.9 32.8 1.0 C5 A:U2523 4.0 37.1 1.0 O2' A:C2493 4.1 37.1 1.0 C5 A:G2525 4.1 33.3 1.0 O4 A:U2523 4.1 37.7 1.0 C4 A:U2523 4.1 37.3 1.0 C6 A:G2524 4.2 33.5 1.0 N1 A:G2525 4.3 33.2 1.0 N7 A:G2525 4.3 33.4 1.0 C2' A:C2493 4.4 37.4 1.0 C6 A:U2523 4.6 35.7 1.0 OP2 A:G2524 4.6 38.7 1.0 OP2 A:U2523 4.7 38.9 1.0 N3 A:U2523 4.9 36.5 1.0 N9 A:G2524 5.0 34.0 1.0

Sodium binding site 10 out of 86 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8313 b:47.9 occ:1.00 O A:HOH4622 2.1 8.1 1.0 O A:HOH3343 2.4 15.3 1.0 O A:HOH9468 2.4 63.9 1.0 O6 A:G2399 2.4 36.6 1.0 O A:HOH5999 3.1 5.5 1.0 O A:HOH5555 3.2 53.0 1.0 O A:HOH4570 3.3 46.5 1.0 C6 A:G2399 3.3 37.0 1.0 O4 A:U2389 3.4 35.4 1.0 N7 A:G2399 3.5 36.6 1.0 O6 A:G2400 3.6 43.9 1.0 C5 A:G2399 3.7 37.1 1.0 O A:HOH9899 3.9 3.1 1.0 OP2 A:A2398 4.0 45.7 1.0 O A:HOH5771 4.1 47.2 1.0 C4 A:U2389 4.2 36.2 1.0 N3 A:U2389 4.3 36.3 1.0 C6 A:G2400 4.4 44.2 1.0 N7 A:G2400 4.5 43.0 1.0 N1 A:G2399 4.6 35.0 1.0 C8 A:G2399 4.7 36.9 1.0 C5 A:G2400 4.8 43.8 1.0 O A:HOH9832 4.8 28.9 1.0 O2 A:U2390 4.8 41.5 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