Cobalt in PDB 3npq: Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A

The structure of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A, PDB code: 3npq was solved by F.E.Reyes, A.E.Edwards, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.01 / 2.18
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.793, 103.241, 69.583, 90.00, 97.90, 90.00
R / Rfree (%)	23.5 / 24.5

Pages:

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

Binding sites:

The binding sites of Cobalt atom in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A (pdb code 3npq). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 15 binding sites of Cobalt where determined in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A, PDB code: 3npq:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 15 in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Co56 b:67.6 occ:1.00 CO A:NCO56 0.0 67.6 1.0 N6 A:NCO56 2.0 51.4 1.0 N4 A:NCO56 2.0 64.1 1.0 N3 A:NCO56 2.0 56.3 1.0 N1 A:NCO56 2.0 46.5 1.0 N2 A:NCO56 2.0 48.0 1.0 N5 A:NCO56 2.0 61.6 1.0 O6 A:G15 3.8 44.4 1.0 OP2 A:C28 4.1 49.5 1.0 O A:HOH112 4.6 35.6 1.0 O A:HOH311 4.7 42.9 1.0 OP2 A:C13 4.8 59.9 1.0 O A:HOH326 4.8 33.0 1.0 O A:HOH228 4.9 39.4 1.0 C6 A:G15 5.0 40.5 1.0

Cobalt binding site 2 out of 15 in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Co57 b:73.4 occ:1.00 CO A:NCO57 0.0 73.4 1.0 N4 A:NCO57 2.0 69.7 1.0 N1 A:NCO57 2.0 55.2 1.0 N5 A:NCO57 2.0 70.0 1.0 N6 A:NCO57 2.0 84.2 1.0 N2 A:NCO57 2.0 53.4 1.0 N3 A:NCO57 2.0 85.4 1.0 O A:HOH320 3.5 50.1 1.0 O A:HOH84 4.0 57.1 1.0 O A:HOH254 4.3 43.4 1.0 OP1 A:A24 4.6 42.1 1.0 O A:HOH141 4.9 42.8 1.0 N7 A:G25 4.9 35.9 1.0 O A:HOH551 5.0 50.2 1.0

Cobalt binding site 3 out of 15 in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Co58 b:72.0 occ:1.00 CO A:NCO58 0.0 72.0 1.0 N6 A:NCO58 2.0 52.6 1.0 N4 A:NCO58 2.0 44.5 1.0 N2 A:NCO58 2.0 49.7 1.0 N1 A:NCO58 2.0 53.8 1.0 N5 A:NCO58 2.0 42.0 1.0 N3 A:NCO58 2.0 43.3 1.0 OP2 A:C16 4.0 53.3 1.0 N6 A:A18 4.1 38.0 1.0 N7 A:A17 4.1 51.6 1.0 O2' A:G15 4.1 47.2 1.0 OP2 A:A17 4.3 51.8 1.0 O2 A:C28 4.3 43.1 1.0 O A:HOH141 4.3 42.8 1.0 O A:HOH84 4.3 57.1 1.0 O6 A:G19 4.4 38.1 1.0 O A:HOH254 4.4 43.4 1.0 N7 A:A18 4.5 42.1 1.0 O A:HOH471 4.6 50.6 1.0 N3 A:C27 4.6 39.5 1.0 C8 A:A17 4.7 50.9 1.0 N4 A:C26 4.8 37.1 1.0 C5 A:C16 4.9 43.8 1.0 N4 A:C27 4.9 36.0 1.0

Cobalt binding site 4 out of 15 in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Co59 b:89.3 occ:1.00 CO A:NCO59 0.0 89.3 1.0 N4 A:NCO59 2.0 64.5 1.0 N6 A:NCO59 2.0 68.4 1.0 N1 A:NCO59 2.0 63.9 1.0 N3 A:NCO59 2.0 79.9 1.0 N5 A:NCO59 2.0 55.2 1.0 N2 A:NCO59 2.0 79.5 1.0 O A:HOH491 3.7 51.4 1.0 OP1 A:G23 3.8 54.6 1.0 OP2 A:G23 4.7 37.6 1.0 N7 A:G21 4.7 41.8 1.0 P A:G23 4.7 41.2 1.0

Cobalt binding site 5 out of 15 in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Co60 b:21.2 occ:1.00 CO A:NCO60 0.0 21.2 1.0 N4 A:NCO60 2.0 21.2 1.0 N1 A:NCO60 2.0 21.2 1.0 N6 A:NCO60 2.0 21.2 1.0 N2 A:NCO60 2.0 21.2 1.0 N3 A:NCO60 2.0 21.2 1.0 N5 A:NCO60 2.0 21.2 1.0 O A:HOH348 3.6 47.4 1.0 O A:HOH296 3.8 33.4 1.0 O A:HOH398 3.9 38.5 1.0 O A:HOH531 4.0 50.2 1.0 OP1 A:A9 4.1 52.7 1.0 O A:HOH191 4.2 32.3 1.0 N7 A:G7 4.5 20.4 1.0 OP2 A:G7 4.6 38.6 1.0 O A:HOH527 4.8 50.2 1.0

Cobalt binding site 6 out of 15 in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Co56 b:94.9 occ:1.00 CO B:NCO56 0.0 94.9 1.0 N4 B:NCO56 2.0 86.1 1.0 N1 B:NCO56 2.0 80.4 1.0 N3 B:NCO56 2.0 85.3 1.0 N5 B:NCO56 2.0 0.0 1.0 N2 B:NCO56 2.0 67.5 1.0 N6 B:NCO56 2.0 70.2 1.0 OP1 B:A24 4.0 50.7 1.0 O B:HOH168 4.2 42.9 1.0 N7 B:G25 4.4 52.1 1.0 OP2 B:A24 4.6 41.1 1.0 P B:A24 4.9 46.5 1.0 O6 B:G25 5.0 46.4 1.0

Cobalt binding site 7 out of 15 in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Co57 b:76.0 occ:1.00 CO B:NCO57 0.0 76.0 1.0 N4 B:NCO57 2.0 47.6 1.0 N1 B:NCO57 2.0 52.6 1.0 N5 B:NCO57 2.0 51.0 1.0 N3 B:NCO57 2.0 49.7 1.0 N2 B:NCO57 2.0 63.9 1.0 N6 B:NCO57 2.0 48.3 1.0 OP2 B:C16 4.0 45.9 1.0 N6 B:A18 4.0 42.1 1.0 O2' B:G15 4.1 36.6 1.0 N7 B:A17 4.2 40.0 1.0 O B:HOH533 4.2 50.2 1.0 O B:HOH359 4.2 53.2 1.0 O2 B:C28 4.2 34.3 1.0 O B:HOH168 4.3 42.9 1.0 O6 B:G19 4.3 43.3 1.0 OP2 B:A17 4.4 43.3 1.0 N3 B:C27 4.5 37.6 1.0 N7 B:A18 4.6 44.8 1.0 N4 B:C26 4.7 37.0 1.0 N4 B:C27 4.7 34.5 1.0 C8 B:A17 4.8 42.5 1.0 C5 B:C16 4.9 38.0 1.0 C2 B:C28 4.9 32.7 1.0

Cobalt binding site 8 out of 15 in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Co58 b:84.5 occ:1.00 CO B:NCO58 0.0 84.5 1.0 N2 B:NCO58 2.0 60.0 1.0 N6 B:NCO58 2.0 69.9 1.0 N1 B:NCO58 2.0 68.9 1.0 N4 B:NCO58 2.0 85.6 1.0 N3 B:NCO58 2.0 68.0 1.0 N5 B:NCO58 2.0 71.3 1.0 O6 B:G15 3.8 42.0 1.0 O B:HOH349 4.0 48.3 1.0 OP2 B:C28 4.2 49.9 1.0 OP2 B:A29 4.9 49.7 1.0 C6 B:G15 5.0 35.9 1.0 OP2 B:C13 5.0 75.4 1.0

Cobalt binding site 9 out of 15 in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Co59 b:0.5 occ:1.00 CO B:NCO59 0.0 0.5 1.0 N2 B:NCO59 2.0 89.9 1.0 N5 B:NCO59 2.0 99.3 1.0 N1 B:NCO59 2.0 79.5 1.0 N4 B:NCO59 2.0 66.4 1.0 N3 B:NCO59 2.0 83.5 1.0 N6 B:NCO59 2.0 65.7 1.0 O B:HOH291 3.8 53.6 1.0 O B:HOH75 3.9 47.6 1.0 OP1 B:G23 4.1 57.4 1.0 N7 B:G21 4.2 52.0 1.0 OP2 B:G23 4.5 38.9 1.0 C8 B:G21 4.8 52.4 1.0 P B:G23 4.9 39.5 1.0 C5 B:G21 5.0 53.7 1.0

Cobalt binding site 10 out of 15 in the Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Structure of the S-Adenosylhomocysteine Riboswitch at 2.18 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Co60 b:21.2 occ:1.00 CO B:NCO60 0.0 21.2 1.0 N3 B:NCO60 2.0 21.2 1.0 N4 B:NCO60 2.0 21.2 1.0 N1 B:NCO60 2.0 21.2 1.0 N5 B:NCO60 2.0 21.2 1.0 N2 B:NCO60 2.0 21.2 1.0 N6 B:NCO60 2.0 21.2 1.0 O B:HOH530 3.6 50.2 1.0 O B:HOH517 3.8 50.2 1.0 O B:HOH452 3.8 50.6 1.0 O B:HOH444 3.8 50.6 1.0 OP1 B:A9 4.0 57.4 1.0 N7 B:G7 4.4 41.9 1.0 OP2 B:G7 4.4 39.8 1.0 O B:HOH77 4.4 38.9 1.0 O B:HOH488 4.8 51.4 1.0 C8 B:G7 4.9 40.1 1.0 OP2 B:A9 4.9 48.8 1.0 P B:A9 5.0 50.9 1.0

A.L.Edwards, F.E.Reyes, A.Heroux, R.T.Batey. Structural Basis For Recognition of S-Adenosylhomocysteine By Riboswitches. Rna V. 16 2144 2010.
ISSN: ISSN 1355-8382
PubMed: 20864509
DOI: 10.1261/RNA.2341610