Cobalt in PDB 6p2h: Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches

The structure of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches, PDB code: 6p2h was solved by M.M.Matyjasik, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 2.80
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.805, 91.805, 77.756, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 27.6

The structure of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Cobalt atom in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches (pdb code 6p2h). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches, PDB code: 6p2h:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:75.0 occ:1.00 CO A:NCO102 0.0 75.0 1.0 N1 A:NCO102 2.0 52.8 1.0 N6 A:NCO102 2.0 53.7 1.0 N5 A:NCO102 2.0 74.1 1.0 N3 A:NCO102 2.0 59.4 1.0 N4 A:NCO102 2.0 58.1 1.0 N2 A:NCO102 2.0 73.9 1.0 N7 A:G43 4.4 48.5 1.0 O6 A:G43 4.4 40.6 1.0 O6 A:G42 4.6 62.1 1.0 N7 A:G42 4.6 57.3 1.0 O6 A:G44 4.8 39.3 1.0 OP1 A:C54 4.8 44.4 1.0 C6 A:G42 4.9 51.8 1.0 C5 A:G42 4.9 52.0 1.0 OP2 A:C54 5.0 64.3 1.0

Cobalt binding site 2 out of 5 in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:49.7 occ:1.00 CO A:NCO103 0.0 49.7 1.0 N2 A:NCO103 2.0 25.8 1.0 N4 A:NCO103 2.0 47.3 1.0 N1 A:NCO103 2.0 45.9 1.0 N6 A:NCO103 2.0 43.1 1.0 N5 A:NCO103 2.0 35.7 1.0 N3 A:NCO103 2.0 45.4 1.0 OP1 A:C47 3.7 29.5 1.0 OP2 A:C50 3.9 41.4 1.0 OP2 A:G46 3.9 42.7 1.0 OP1 A:C48 4.0 29.0 1.0 OP2 A:C48 4.4 40.8 1.0 P A:C48 4.6 30.4 1.0 P A:C50 4.8 45.7 1.0 OP1 A:C50 4.9 47.7 1.0

Cobalt binding site 3 out of 5 in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:97.5 occ:1.00 CO A:NCO104 0.0 97.5 1.0 N5 A:NCO104 2.0 47.9 1.0 N1 A:NCO104 2.0 40.8 1.0 N6 A:NCO104 2.0 60.6 1.0 N2 A:NCO104 2.0 74.1 1.0 N3 A:NCO104 2.0 67.5 1.0 N4 A:NCO104 2.0 52.6 1.0 N7 A:G21 4.0 29.0 1.0 OP2 A:A23 4.4 45.1 1.0 O6 A:G21 4.5 38.1 1.0 OP1 A:A23 4.7 32.1 1.0 MG A:MG110 4.8 35.7 1.0 P A:A23 4.9 49.9 1.0 C5 A:G21 4.9 29.3 1.0 C8 A:G21 4.9 25.9 1.0 O3' A:U22 5.0 34.7 1.0

Cobalt binding site 4 out of 5 in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:71.7 occ:1.00 CO A:NCO105 0.0 71.7 1.0 N2 A:NCO105 2.0 46.9 1.0 N5 A:NCO105 2.0 54.0 1.0 N3 A:NCO105 2.0 62.5 1.0 N6 A:NCO105 2.0 34.0 1.0 N1 A:NCO105 2.0 44.0 1.0 N4 A:NCO105 2.0 64.4 1.0 OP2 A:G18 3.3 55.2 1.0 O2A A:GTP17 3.6 63.9 1.0 N7 A:G18 3.9 36.0 1.0 O2 A:C76 4.2 56.0 1.0 C8 A:G18 4.5 38.0 1.0 P A:G18 4.7 48.0 1.0 C5 A:G18 4.9 31.6 1.0 C2 A:C76 4.9 58.8 1.0 C5' A:GTP17 5.0 47.5 1.0

Cobalt binding site 5 out of 5 in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches within 5.0Å range: probe atom residue distance (Å) B Occ A:Co106 b:75.0 occ:0.50 CO A:NCO106 0.0 75.0 0.5 N3 A:NCO106 2.0 57.0 0.5 N4 A:NCO106 2.0 51.4 0.5 N6 A:NCO106 2.0 59.7 0.5 N1 A:NCO106 2.0 48.3 0.5 N5 A:NCO106 2.0 63.8 0.5 N2 A:NCO106 2.0 72.2 0.5 OP2 A:G56 3.0 80.9 1.0 OP2 A:A55 3.8 52.1 1.0 O5' A:A55 4.3 62.9 1.0 P A:A55 4.5 72.5 1.0 P A:G56 4.5 85.2 1.0 OP1 A:U40 4.7 65.0 1.0 OP2 A:U40 4.7 46.4 1.0 OP1 A:A55 4.9 73.1 1.0 C3' A:A55 4.9 68.5 1.0

M.M.Matyjasik, R.T.Batey. Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches. Nucleic Acids Res. V. 47 10931 2019.
ISSN: ESSN 1362-4962
PubMed: 31598729
DOI: 10.1093/NAR/GKZ839