Magnesium in PDB 9bz1: Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica

The structure of Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica, PDB code: 9bz1 was solved by C.J.Jones, A.R.Ferre D'amare, B.Tran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.06 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.069, 47.642, 113.791, 90, 120.42, 90
R / Rfree (%)	21 / 24.8

The structure of Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica also contains other interesting chemical elements:

Potassium

(K)

8 atoms

The binding sites of Magnesium atom in the Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica (pdb code 9bz1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica, PDB code: 9bz1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:77.0 occ:1.00 O A:HOH206 2.2 60.1 1.0 O A:HOH207 2.2 63.9 1.0 O A:HOH214 2.2 66.5 1.0 O A:HOH213 2.2 70.4 1.0 O A:HOH221 2.2 65.0 1.0 O A:HOH222 2.2 82.5 1.0 O2 A:U83 3.6 65.8 1.0 O2 A:C16 3.7 70.6 1.0 N2 A:G82 4.2 64.7 1.0 O2' A:U83 4.4 65.0 1.0 O2' A:C16 4.4 71.4 1.0 C1' A:U83 4.6 64.7 1.0 C2 A:U83 4.6 63.0 1.0 C1' A:C16 4.8 67.5 1.0 C2 A:C16 4.8 64.8 1.0 C2' A:U83 4.9 68.2 1.0

Magnesium binding site 2 out of 6 in the Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:83.9 occ:1.00 O A:HOH208 2.2 77.6 1.0 O A:HOH203 2.2 76.5 1.0 O A:HOH219 2.2 82.7 1.0 O A:HOH205 2.2 89.1 1.0 O A:HOH220 2.2 90.3 1.0 O A:HOH218 2.2 84.2 1.0 O6 A:G23 3.3 82.9 1.0 O6 A:G24 3.7 76.0 1.0 C6 A:G23 4.1 81.9 1.0 N7 A:G23 4.1 81.8 1.0 OP1 A:A15 4.2 68.8 1.0 C5 A:G23 4.5 82.2 1.0 O4 A:U22 4.5 75.8 1.0 C6 A:G24 4.7 77.8 1.0 N4 A:C30 4.8 74.1 1.0 N4 A:C31 4.9 70.9 1.0 N7 A:G24 4.9 81.7 1.0

Magnesium binding site 3 out of 6 in the Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:61.5 occ:1.00 OP2 A:C30 2.1 60.6 1.0 OP1 A:U13 2.1 57.4 1.0 O A:HOH204 2.1 64.2 1.0 OAC A:5AC105 2.1 57.6 1.0 O A:HOH201 2.2 58.3 1.0 CAG A:5AC105 3.3 53.8 1.0 P A:U13 3.3 56.0 1.0 P A:C30 3.5 60.6 1.0 C5' A:C30 3.7 68.5 1.0 O5' A:U13 3.7 52.6 1.0 NAA A:5AC105 3.8 54.6 1.0 O4' A:G14 3.9 61.9 1.0 OP2 A:U13 4.0 58.2 1.0 O5' A:C30 4.1 67.2 1.0 O3' A:A29 4.2 60.6 1.0 C1' A:G14 4.3 58.7 1.0 C5' A:U13 4.3 51.4 1.0 CAI A:5AC105 4.5 51.1 1.0 O3' A:C12 4.6 59.9 1.0 NAB A:5AC105 4.7 54.8 1.0 OP1 A:C30 4.7 61.5 1.0 N2 A:G86 4.7 58.1 1.0 N3 A:G86 4.7 58.6 1.0 OP2 A:C31 4.8 67.4 1.0 O2' A:G86 4.8 63.6 1.0 C4' A:G14 5.0 58.9 1.0

Magnesium binding site 4 out of 6 in the Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:80.2 occ:1.00 OP2 A:C58 2.1 103.9 1.0 OP1 A:U57 2.5 88.4 1.0 P A:C58 3.5 104.3 1.0 O4 A:U59 3.8 74.2 1.0 P A:U57 3.9 78.2 1.0 OP1 A:C58 4.1 105.0 1.0 O5' A:U57 4.2 95.3 1.0 O5' A:C58 4.4 103.9 1.0 C5' A:A56 4.5 79.4 1.0 C5' A:U57 4.5 95.5 1.0 O3' A:U57 4.5 106.0 1.0 C4 A:U59 4.6 73.9 1.0 C5 A:U59 4.7 74.3 1.0 OP2 A:U57 4.8 77.7 1.0 O3' A:A56 4.9 81.5 1.0 OP2 A:A56 4.9 79.8 1.0 C3' A:U57 5.0 105.1 1.0

Magnesium binding site 5 out of 6 in the Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:51.5 occ:1.00 OP2 B:C58 2.3 67.7 1.0 OP1 B:U57 2.4 60.1 1.0 O4 B:U59 3.5 42.5 1.0 P B:C58 3.6 66.1 1.0 P B:U57 3.8 56.2 1.0 OP1 B:C58 4.1 60.3 1.0 O5' B:U57 4.3 59.5 1.0 C4 B:U59 4.4 44.1 1.0 O5' B:C58 4.5 65.2 1.0 C5' B:A56 4.5 53.3 1.0 C5' B:U57 4.5 62.7 1.0 C5 B:U59 4.5 48.9 1.0 OP2 B:U57 4.6 53.0 1.0 O3' B:U57 4.7 69.1 1.0 OP2 B:A56 4.8 50.6 1.0 O3' B:A56 4.9 51.9 1.0

Magnesium binding site 6 out of 6 in the Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:41.2 occ:1.00 OP1 B:U13 1.9 41.6 1.0 OP2 B:C30 2.0 36.3 1.0 O B:HOH205 2.1 41.3 1.0 O B:HOH203 2.1 38.9 1.0 O B:HOH206 2.2 40.8 1.0 OAC B:5AC103 2.2 39.2 1.0 CAG B:5AC103 3.3 40.3 1.0 P B:U13 3.3 50.9 1.0 P B:C30 3.5 41.1 1.0 NAA B:5AC103 3.7 35.5 1.0 C5' B:C30 3.9 45.0 1.0 O5' B:U13 3.9 43.9 1.0 OP2 B:U13 4.0 43.2 1.0 O5' B:C30 4.0 41.3 1.0 N3 B:G86 4.2 34.7 1.0 O3' B:A29 4.3 42.1 1.0 O3' B:C12 4.4 37.7 1.0 OP1 B:C30 4.4 46.7 1.0 N2 B:G86 4.4 42.4 1.0 CAI B:5AC103 4.6 37.0 1.0 O4' B:G14 4.6 43.2 1.0 O2' B:G86 4.6 41.9 1.0 C5' B:U13 4.6 36.2 1.0 C2 B:G86 4.7 38.9 1.0 C1' B:G14 4.8 37.7 1.0 OP2 B:C31 4.8 42.9 1.0 C1' B:G86 4.9 38.7 1.0 NAB B:5AC103 5.0 40.5 1.0

C.P.Jones, B.Tran, A.R.Ferre-D'amare. Cocrystal Structure of Clostridium Beijerinckii Ztp Riboswitch with Aica To Be Published.