Cobalt in PDB 3rkf: Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine

The structure of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine, PDB code: 3rkf was solved by J.Buck, A.Wacker, E.Warkentin, J.Woehnert, J.Wirmer-Bartoschek, H.Schwalbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 2.50
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	52.300, 52.300, 263.400, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 22.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine (pdb code 3rkf). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 26 binding sites of Cobalt where determined in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine, PDB code: 3rkf:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 26 in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:72.7 occ:1.00 CO A:NCO101 0.0 72.7 1.0 N2 A:NCO101 2.0 73.8 1.0 N1 A:NCO101 2.0 69.2 1.0 N3 A:NCO101 2.0 51.9 1.0 N5 A:NCO101 2.0 48.8 1.0 N4 A:NCO101 2.0 67.1 1.0 N6 A:NCO101 2.0 48.2 1.0 O4 A:U47 4.2 45.7 1.0 OP2 A:C50 4.2 59.2 1.0 O6 A:G46 4.4 38.1 1.0 OP2 A:U51 4.7 62.3 1.0

Cobalt binding site 2 out of 26 in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:62.3 occ:1.00 CO A:NCO102 0.0 62.3 1.0 N3 A:NCO102 2.0 52.5 1.0 N2 A:NCO102 2.0 48.0 1.0 N6 A:NCO102 2.0 56.0 1.0 N1 A:NCO102 2.0 54.4 1.0 N4 A:NCO102 2.0 53.0 1.0 N5 A:NCO102 2.0 43.8 1.0 OP2 A:A66 3.9 51.4 1.0 O6 A:G32 4.0 51.2 1.0 O6 A:G31 4.4 49.9 1.0 N7 A:G31 4.7 45.7 1.0

Cobalt binding site 3 out of 26 in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:56.3 occ:1.00 CO A:NCO103 0.0 56.3 1.0 N5 A:NCO103 2.0 48.6 1.0 N1 A:NCO103 2.0 54.3 1.0 N3 A:NCO103 2.0 53.5 1.0 N6 A:NCO103 2.0 64.2 1.0 N2 A:NCO103 2.0 41.8 1.0 N4 A:NCO103 2.0 59.6 1.0 N7 A:G56 4.1 64.7 1.0 O6 A:G56 4.3 62.8 1.0 O4 A:U69 4.5 50.2 1.0 O6 A:G57 4.6 57.8 1.0 C5 A:G56 4.9 65.2 1.0 N7 A:G55 4.9 58.2 1.0 C6 A:G56 4.9 64.6 1.0 O6 A:G68 4.9 45.4 1.0

Cobalt binding site 4 out of 26 in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:85.3 occ:1.00 CO A:NCO104 0.0 85.3 1.0 N3 A:NCO104 2.0 0.0 1.0 N4 A:NCO104 2.0 80.6 1.0 N6 A:NCO104 2.0 87.2 1.0 N5 A:NCO104 2.0 88.6 1.0 N1 A:NCO104 2.0 89.9 1.0 N2 A:NCO104 2.0 82.1 1.0 O6 A:G79 3.7 72.3 1.0 O6 A:G15 3.9 85.2 1.0 O4 A:U80 4.3 77.2 1.0 O6 A:G16 4.3 78.6 1.0 C6 A:G15 4.6 80.2 1.0 N7 A:G15 4.7 82.8 1.0 C6 A:G79 4.8 69.3 1.0 N4 A:C17 4.9 78.9 1.0 C5 A:G15 5.0 81.3 1.0

Cobalt binding site 5 out of 26 in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co82 b:55.8 occ:1.00 CO A:NCO82 0.0 55.8 1.0 N6 A:NCO82 2.0 50.0 1.0 N3 A:NCO82 2.0 44.7 1.0 N1 A:NCO82 2.0 49.2 1.0 N4 A:NCO82 2.0 43.4 1.0 N2 A:NCO82 2.0 45.8 1.0 N5 A:NCO82 2.0 55.5 1.0 O2' A:G62 4.5 46.1 1.0 OP2 A:U63 4.8 63.7 1.0

Cobalt binding site 6 out of 26 in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:93.9 occ:1.00 CO A:NCO105 0.0 93.9 1.0 N1 A:NCO105 2.0 51.9 1.0 N3 A:NCO105 2.0 69.2 1.0 N4 A:NCO105 2.0 62.8 1.0 N2 A:NCO105 2.0 68.5 1.0 N6 A:NCO105 2.0 61.2 1.0 N5 A:NCO105 2.0 77.3 1.0 OP2 A:U61 3.9 52.8 1.0 O6 A:G62 4.3 47.9 1.0 N7 A:G62 4.4 40.6 1.0

Cobalt binding site 7 out of 26 in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co106 b:0.8 occ:1.00 CO A:NCO106 0.0 0.8 1.0 N6 A:NCO106 2.0 86.6 1.0 N5 A:NCO106 2.0 96.2 1.0 N4 A:NCO106 2.0 70.4 1.0 N2 A:NCO106 2.0 83.0 1.0 N1 A:NCO106 2.0 86.3 1.0 N3 A:NCO106 2.0 79.9 1.0 OP1 B:G29 4.1 77.5 1.0 OP1 A:A21 4.2 64.8 1.0 OP2 A:A21 4.3 69.4 1.0 O3' B:C28 4.6 69.5 1.0 P A:A21 4.8 66.2 1.0 OP2 A:U22 4.8 57.2 1.0 OP1 A:A23 5.0 52.4 1.0

Cobalt binding site 8 out of 26 in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:70.0 occ:1.00 CO A:NCO108 0.0 70.0 1.0 N1 A:NCO108 2.0 52.8 1.0 N4 A:NCO108 2.0 64.9 1.0 N6 A:NCO108 2.0 44.9 1.0 N3 A:NCO108 2.0 76.0 1.0 N2 A:NCO108 2.0 70.1 1.0 N5 A:NCO108 2.0 60.9 1.0 OP1 A:G27 4.2 48.5 1.0 OP1 A:U67 4.5 55.4 1.0 OP1 A:G68 4.7 66.1 1.0

Cobalt binding site 9 out of 26 in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co110 b:0.6 occ:1.00 CO A:NCO110 0.0 0.6 1.0 N2 A:NCO110 2.0 68.7 1.0 N1 A:NCO110 2.0 60.5 1.0 N6 A:NCO110 2.0 66.6 1.0 N5 A:NCO110 2.0 61.5 1.0 N3 A:NCO110 2.0 81.1 1.0 N4 A:NCO110 2.0 77.0 1.0 OP2 A:A37 4.3 58.1 1.0 OP2 A:G38 4.5 49.4 1.0 N7 A:G38 4.7 41.9 1.0 O3' A:U36 4.8 53.2 1.0

Cobalt binding site 10 out of 26 in the Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of Guanine Riboswitch C61U/G37A Double Mutant Bound to Thio-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:76.6 occ:1.00 CO B:NCO101 0.0 76.6 1.0 N4 B:NCO101 2.0 64.4 1.0 N6 B:NCO101 2.0 67.5 1.0 N5 B:NCO101 2.0 58.3 1.0 N1 B:NCO101 2.0 52.3 1.0 N2 B:NCO101 2.0 68.2 1.0 N3 B:NCO101 2.0 69.4 1.0 O4 B:U47 4.2 41.5 1.0 OP2 B:C50 4.3 57.0 1.0 OP2 B:U51 4.5 56.2 1.0 O6 B:G46 4.8 54.0 1.0 OP1 B:C50 4.8 51.2 1.0 P B:C50 4.9 49.2 1.0

J.Buck, A.Wacker, E.Warkentin, J.Wohnert, J.Wirmer-Bartoschek, H.Schwalbe. Influence of Ground-State Structure and MG2+ Binding on Folding Kinetics of the Guanine-Sensing Riboswitch Aptamer Domain. Nucleic Acids Res. V. 39 9768 2011.
ISSN: ISSN 0305-1048
PubMed: 21890900
DOI: 10.1093/NAR/GKR664