Magnesium in PDB 9jgm: The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH

The structure of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH, PDB code: 9jgm was solved by W.W.Xiao, G.F.Liu, T.Chen, Y.L.Zhang, A.L.Ke, R.J.Cai, C.R.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.21 / 3.73
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	144.416, 144.416, 161.788, 90, 90, 120
R / Rfree (%)	23.6 / 28.6

The structure of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Magnesium atom in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH (pdb code 9jgm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 25 binding sites of Magnesium where determined in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH, PDB code: 9jgm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 25 in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:177.8 occ:1.00 N6 C:A4 3.5 212.1 1.0 O6 C:G5 3.6 177.6 1.0 N7 C:G5 3.6 182.1 1.0 C6 C:A4 3.6 215.4 1.0 C5 C:A4 3.7 223.0 1.0 N7 C:A4 3.8 227.8 1.0 C6 C:G5 4.3 187.3 1.0 C5 C:G5 4.3 189.8 1.0 N1 C:A4 4.4 209.1 1.0 C4 C:A4 4.5 217.9 1.0 C8 C:A4 4.6 225.2 1.0 C8 C:G5 4.7 180.0 1.0 OP1 C:G98 4.8 193.3 1.0 O6 C:G6 4.9 190.5 1.0

Magnesium binding site 2 out of 25 in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:145.8 occ:1.00 OP2 C:C31 3.2 150.2 1.0 OP1 C:U30 3.3 189.8 1.0 O5' C:U30 3.4 166.8 1.0 OP1 C:C31 3.6 184.5 1.0 P C:C31 3.6 156.6 1.0 O3' C:U30 3.8 172.6 1.0 P C:U30 3.9 172.8 1.0 C5' C:U30 3.9 177.9 1.0 C3' C:U30 4.2 173.5 1.0 OP2 C:U30 4.5 178.4 1.0 C4' C:U30 4.6 178.7 1.0

Magnesium binding site 3 out of 25 in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:175.0 occ:0.19 OP2 C:G8 2.0 161.9 1.0 OP1 C:U33 2.0 182.7 1.0 OP1 C:A9 2.0 172.9 1.0 C5' C:U33 2.5 167.3 1.0 P C:G8 2.7 152.3 1.0 O5' C:G8 2.9 159.3 1.0 P C:A9 3.0 170.9 1.0 O5' C:U33 3.0 168.8 1.0 P C:U33 3.0 179.7 1.0 OP1 C:G8 3.1 172.3 1.0 O5' C:A9 3.2 181.1 1.0 C3' C:G8 3.3 166.8 1.0 O3' C:G8 3.5 156.7 1.0 OP1 C:G7 3.6 163.6 1.0 C4' C:G8 3.7 164.5 1.0 OP1 C:C39 3.7 162.4 1.0 C4' C:U33 3.8 179.5 1.0 C5' C:G8 3.8 168.1 1.0 O3' C:G32 3.9 161.0 1.0 O3' C:G7 4.2 171.5 1.0 C3' C:G32 4.2 165.9 1.0 C4' C:G32 4.2 163.3 1.0 OP2 C:U33 4.3 174.8 1.0 P C:G7 4.3 173.2 1.0 OP2 C:A9 4.4 144.9 1.0 O5' C:G7 4.4 181.5 1.0 OP2 C:G7 4.4 180.2 1.0 C5' C:G32 4.5 160.8 1.0 C5' C:A9 4.6 176.9 1.0 C2' C:G8 4.7 176.1 1.0 O4' C:U33 4.7 175.8 1.0 OP2 C:C39 4.7 191.8 1.0 P C:C39 4.7 175.5 1.0 C5' C:G7 4.8 182.2 1.0 OP2 C:C34 4.8 171.2 1.0 C3' C:U33 4.8 191.6 1.0 C3' C:G7 4.8 175.9 1.0 O3' C:U33 4.9 194.3 1.0

Magnesium binding site 4 out of 25 in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg204 b:162.1 occ:1.00 OP2 C:G86 2.9 151.4 1.0 N7 C:G86 4.0 139.6 1.0 P C:G86 4.3 139.8 1.0 C8 C:G86 4.4 142.1 1.0 O5' C:G86 4.7 134.1 1.0 OP2 C:A85 4.8 145.5 1.0

Magnesium binding site 5 out of 25 in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg205 b:148.6 occ:0.95 N7 C:G66 3.4 153.5 1.0 C5 C:C65 3.4 144.1 1.0 C6 C:C65 3.9 155.4 1.0 O6 C:G66 4.0 158.0 1.0 C4 C:C65 4.0 140.6 1.0 C5 C:G66 4.2 147.2 1.0 N4 C:C65 4.2 143.9 1.0 C8 C:G66 4.3 152.5 1.0 C6 C:G66 4.4 147.5 1.0 OP2 C:G66 4.5 164.2 1.0 OP2 C:C65 4.6 152.3 1.0 N1 C:C65 4.7 156.1 1.0 N3 C:C65 4.8 141.7 1.0 O6 C:G67 4.9 143.5 1.0 O5' C:C65 4.9 144.9 1.0

Magnesium binding site 6 out of 25 in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg206 b:141.2 occ:0.78 OP1 C:A92 3.5 161.2 1.0 O5' C:A92 3.8 168.1 1.0 P C:A92 4.3 142.2 1.0 OP1 C:C62 4.7 162.3 1.0 C5' C:A92 4.7 175.4 1.0

Magnesium binding site 7 out of 25 in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg207 b:158.4 occ:0.58 O3' C:A48 3.0 170.3 1.0 O2' C:A48 3.0 162.1 1.0 C5' C:A49 3.1 170.8 1.0 OP1 C:A49 3.5 190.4 1.0 P C:A49 3.7 178.5 1.0 O5' C:A49 3.8 177.7 1.0 C3' C:A48 4.0 165.0 1.0 C2' C:A48 4.0 158.9 1.0 C4' C:A49 4.2 171.8 1.0 C4' C:A48 4.6 176.2 1.0 O4' C:A49 4.7 163.8 1.0

Magnesium binding site 8 out of 25 in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg208 b:164.8 occ:1.00 C5 C:U30 3.1 160.3 1.0 OP2 C:U30 3.2 178.4 1.0 O4 C:U30 3.7 150.8 1.0 C4 C:U30 3.8 153.9 1.0 OP2 C:A29 3.9 191.8 1.0 C6 C:U30 4.1 156.9 1.0 O5' C:A29 4.1 185.3 1.0 C8 C:A29 4.2 157.3 1.0 N7 C:A29 4.2 158.2 1.0 P C:A29 4.5 203.8 1.0 P C:U30 4.6 172.8 1.0 C3' C:A29 4.7 177.9 1.0 N9 C:A29 4.9 160.3 1.0

Magnesium binding site 9 out of 25 in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg209 b:137.4 occ:0.55 OP1 C:C54 3.0 169.7 1.0 P C:C54 4.4 180.0 1.0 OP2 C:C54 4.9 177.9 1.0

Magnesium binding site 10 out of 25 in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:145.1 occ:1.00 O6 A:G90 2.6 184.9 1.0 O4 A:U91 3.3 204.4 1.0 N7 A:G90 3.5 187.0 1.0 C6 A:G90 3.5 178.1 1.0 C5 A:G90 3.8 185.0 1.0 C4 A:U91 4.3 192.7 1.0 O6 A:G68 4.3 165.0 1.0 O4 A:U89 4.3 186.7 1.0 C5 A:U89 4.4 182.6 1.0 C4 A:U89 4.5 182.9 1.0 C8 A:G90 4.7 195.4 1.0 N1 A:G90 4.8 174.0 1.0 C5 A:U91 5.0 192.4 1.0

W.Xiao, G.Liu, T.Chen, Y.Zhang, A.Ke, R.Cai, C.Lu. Escherichia Coli Yybp-Ykoy Riboswitch As A Tandem Riboswitch Regulated By Mn 2+ and pH. Acs Chem.Biol. V. 20 1010 2025.
ISSN: ESSN 1554-8937
PubMed: 40252020
DOI: 10.1021/ACSCHEMBIO.4C00715