Manganese 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:

Magnesium

(Mg)

25 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the The Escherichia Coli Yybp Riboswitch As A Tandem Riboswitch Regulated By MN2+ and pH, PDB code: 9jgm:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 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 Manganese with other atoms in the Mn 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:Mn210 b:206.9 occ:0.91 OP2 C:C39 2.3 191.8 1.0 C5' C:A38 2.6 201.2 1.0 N7 C:A35 2.7 206.5 1.0 OP1 C:A38 2.9 221.0 1.0 OP2 C:C34 2.9 171.2 1.0 O5' C:A38 3.0 212.0 1.0 C3' C:A38 3.2 191.8 1.0 C8 C:A35 3.2 208.1 1.0 OP1 C:G8 3.2 172.3 1.0 P C:A38 3.3 220.0 1.0 C4' C:A38 3.4 199.9 1.0 P C:C39 3.4 175.5 1.0 O3' C:A38 3.4 187.2 1.0 OP1 C:C34 3.5 198.0 1.0 OP2 C:A38 3.5 208.2 1.0 P C:C34 3.7 191.0 1.0 C5 C:A35 3.9 198.6 1.0 O4' C:A38 4.3 210.8 1.0 O5' C:C39 4.4 169.1 1.0 OP2 C:U33 4.5 174.8 1.0 N9 C:A35 4.5 212.3 1.0 P C:G8 4.5 152.3 1.0 OP1 C:C39 4.6 162.4 1.0 O5' C:C34 4.6 197.0 1.0 C2' C:A38 4.6 195.7 1.0 N6 C:A35 4.6 191.0 1.0 O3' C:G7 4.7 171.5 1.0 C6 C:A35 4.7 189.2 1.0 O3' C:U37 4.8 238.3 1.0 C4 C:A35 4.9 208.4 1.0 C1' C:A38 5.0 203.3 1.0 O3' C:U33 5.0 194.3 1.0

Manganese binding site 2 out of 4 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 Manganese with other atoms in the Mn 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 A:Mn203 b:259.8 occ:1.00 OP2 A:C34 2.2 249.5 1.0 OP1 A:G8 2.2 241.8 1.0 C5' A:A38 2.5 250.8 1.0 OP2 A:C39 2.6 248.8 1.0 P A:C34 2.8 254.9 1.0 N7 A:A35 2.9 244.5 1.0 OP1 A:C34 2.9 256.9 1.0 O3' A:U33 3.3 243.4 1.0 O5' A:A38 3.4 256.4 1.0 C4' A:A38 3.6 245.2 1.0 P A:C39 3.6 238.7 1.0 C8 A:A35 3.6 249.7 1.0 O3' A:A38 3.7 242.2 1.0 OP1 A:U33 3.7 255.1 1.0 P A:G8 3.7 235.9 1.0 C3' A:A38 3.8 244.3 1.0 OP2 A:U33 3.9 246.2 1.0 OP2 A:A38 4.0 253.7 1.0 C5 A:A35 4.0 253.8 1.0 P A:U33 4.1 258.7 1.0 C3' A:U33 4.1 245.8 1.0 N6 A:A35 4.2 241.1 1.0 O5' A:U33 4.2 241.0 1.0 C5' A:U33 4.2 239.4 1.0 O5' A:C34 4.3 252.6 1.0 O3' A:G7 4.3 253.7 1.0 OP1 A:C39 4.4 220.9 1.0 P A:A38 4.4 270.1 1.0 O5' A:G8 4.4 238.2 1.0 C6 A:A35 4.6 250.1 1.0 C4' A:U33 4.7 239.1 1.0 OP2 A:G8 4.7 238.1 1.0 O4' A:A38 4.8 255.2 1.0 C5' A:C34 4.9 246.5 1.0 O5' A:C39 4.9 251.1 1.0 N9 A:A35 4.9 260.3 1.0

Manganese binding site 3 out of 4 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 Manganese with other atoms in the Mn 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 D:Mn208 b:177.2 occ:0.30 OP1 D:G8 2.1 146.0 1.0 OP1 D:A38 2.1 168.9 1.0 OP2 D:C34 2.4 144.8 1.0 OP1 D:C34 2.5 187.3 1.0 P D:C34 2.7 167.6 1.0 P D:G8 2.9 153.5 1.0 O3' D:G7 3.1 146.6 1.0 O5' D:G8 3.2 151.6 1.0 P D:A38 3.4 171.9 1.0 O3' D:U33 3.4 152.9 1.0 O3' D:U37 3.7 177.2 1.0 OP2 D:U33 3.8 139.1 1.0 OP2 D:C39 3.9 134.6 1.0 OP2 D:A38 4.2 174.6 1.0 C5' D:G8 4.2 153.7 1.0 O5' D:C34 4.2 165.6 1.0 C3' D:U33 4.4 151.1 1.0 OP2 D:G8 4.4 137.5 1.0 N7 D:A35 4.4 160.2 1.0 C5' D:U33 4.5 148.8 1.0 O2' D:U37 4.5 189.1 1.0 C3' D:G7 4.5 154.0 1.0 O5' D:A38 4.6 149.3 1.0 C8 D:A35 4.7 165.3 1.0 C5' D:A38 4.7 156.8 1.0 O2' D:G7 4.8 165.7 1.0 P D:U33 4.8 133.7 1.0 C4' D:U33 4.9 148.3 1.0 P D:C39 4.9 142.5 1.0 C3' D:U37 5.0 184.8 1.0

Manganese binding site 4 out of 4 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 Manganese with other atoms in the Mn 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 B:Mn208 b:260.8 occ:1.00 OP2 B:C39 2.2 244.7 1.0 N7 B:A35 2.3 263.2 1.0 C8 B:A35 2.4 268.2 1.0 OP2 B:A38 2.6 257.8 1.0 OP2 B:C34 2.9 246.9 1.0 O5' B:A38 3.1 265.6 1.0 OP1 B:G8 3.3 235.3 1.0 P B:A38 3.4 261.2 1.0 OP2 B:U33 3.4 248.1 1.0 P B:C39 3.6 237.2 1.0 C3' B:A38 3.7 253.4 1.0 C5 B:A35 3.7 264.0 1.0 N9 B:A35 3.8 270.7 1.0 C5' B:A38 3.8 254.6 1.0 O3' B:A38 3.9 246.6 1.0 P B:C34 4.1 261.8 1.0 OP1 B:A38 4.1 251.4 1.0 C4' B:A38 4.3 252.8 1.0 C4 B:A35 4.4 266.7 1.0 OP1 B:C34 4.4 263.0 1.0 O5' B:C39 4.4 242.3 1.0 OP1 B:C39 4.7 225.2 1.0 O5' B:C34 4.7 262.0 1.0 P B:U33 4.7 248.5 1.0 O3' B:U37 4.7 262.3 1.0 C6 B:A35 4.7 248.5 1.0 P B:G8 4.7 219.5 1.0 C1' B:A35 4.8 269.1 1.0 C2' B:A38 4.9 250.2 1.0 N6 B:A35 4.9 235.1 1.0 C2' B:A35 4.9 273.3 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