Magnesium in PDB 5btp: Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp

The structure of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp, PDB code: 5btp was solved by C.P.Jones, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.33 / 2.82
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.661, 92.661, 121.172, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 22.1

The structure of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp also contains other interesting chemical elements:

Potassium

(K)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp (pdb code 5btp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp, PDB code: 5btp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:80.0 occ:1.00 O B:HOH204 2.2 75.3 1.0 N7 B:G20 3.7 73.2 1.0 O6 B:G20 3.8 66.1 1.0 O6 B:G21 4.1 75.2 1.0 MG B:MG107 4.2 0.2 1.0 N4 B:C19 4.3 50.7 1.0 C5 B:G20 4.4 68.1 1.0 C6 B:G20 4.4 66.8 1.0 C5 B:C19 4.5 64.1 1.0 C4 B:C19 4.6 55.7 1.0 N7 B:G21 4.7 62.4 1.0 C8 B:G20 4.7 72.6 1.0 C6 B:G21 4.9 66.3 1.0

Magnesium binding site 2 out of 12 in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:68.5 occ:1.00 N4 B:C65 3.6 62.7 1.0 C5 B:C65 4.2 65.4 1.0 N7 B:A64 4.3 68.0 1.0 O2' B:C24 4.4 66.0 1.0 C4 B:C65 4.4 56.4 1.0 C8 B:A64 4.5 68.7 1.0 O B:HOH204 4.8 75.3 1.0

Magnesium binding site 3 out of 12 in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:69.8 occ:1.00 OP1 B:U16 2.0 75.4 1.0 OP2 B:C35 2.1 50.3 1.0 O B:HOH203 2.2 62.0 1.0 O B:HOH202 2.2 55.7 1.0 O5 B:AMZ108 2.7 59.6 1.0 P B:U16 3.4 69.9 1.0 P B:C35 3.6 69.2 1.0 C6 B:AMZ108 3.7 57.4 1.0 OP2 B:U16 4.0 72.9 1.0 N2 B:AMZ108 4.0 58.3 1.0 C5' B:C35 4.0 65.2 1.0 O5' B:C35 4.1 73.7 1.0 O5' B:U16 4.2 96.0 1.0 OP1 B:C35 4.4 79.4 1.0 O3' B:C15 4.4 71.4 1.0 N3 B:G71 4.5 77.6 1.0 O3' B:A34 4.6 59.3 1.0 O2' B:G71 4.6 89.0 1.0 N2 B:G71 4.6 65.3 1.0 C5' B:U16 4.7 70.9 1.0 O4' B:G17 4.9 59.4 1.0 N3 B:AMZ108 4.9 38.4 1.0 C3A B:AMZ108 4.9 47.7 1.0

Magnesium binding site 4 out of 12 in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:40.7 occ:0.50 O3' B:G21 2.7 62.5 1.0 O2' B:G21 2.7 74.5 1.0 OP2 A:A22 3.1 70.3 1.0 C3' B:G21 3.5 51.0 1.0 OP2 B:A22 3.5 63.0 1.0 P B:A22 3.6 52.6 1.0 C2' B:G21 3.6 49.9 1.0 C4' B:G21 3.8 57.9 1.0 P A:A22 4.1 59.1 1.0 OP1 B:A22 4.2 53.5 1.0 OP1 A:A22 4.4 57.7 1.0 O3' A:G21 4.5 63.1 1.0 C1' B:G21 4.7 52.5 1.0 O4' B:G21 4.7 60.8 1.0 C5' B:G21 4.8 58.4 1.0 C8 A:A22 5.0 64.0 1.0 O5' B:A22 5.0 69.4 1.0

Magnesium binding site 5 out of 12 in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:0.6 occ:1.00 O6 B:G13 2.9 0.8 1.0 O4 B:U12 3.4 0.0 1.0 C6 B:G13 3.8 1.0 1.0 N1 B:G13 4.0 94.3 1.0 C4 B:U12 4.6 0.1 1.0 C5 B:G13 5.0 96.9 1.0

Magnesium binding site 6 out of 12 in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:97.4 occ:1.00 O4 B:U40 3.0 81.5 1.0 O4 B:U16 3.4 69.5 1.0 OP2 B:A39 3.7 0.6 1.0 C4 B:U40 4.0 68.4 1.0 C5 B:U40 4.3 75.9 1.0 C4 B:U16 4.4 63.0 1.0 N3 B:U16 4.6 76.0 1.0 N7 B:A39 4.8 78.2 1.0

Magnesium binding site 7 out of 12 in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg107 b:0.2 occ:1.00 OP2 B:C24 3.7 97.8 1.0 N1 A:A23 3.7 61.9 1.0 N7 B:G21 4.1 62.4 1.0 C2 A:A23 4.1 56.5 1.0 O5' B:C24 4.2 52.0 1.0 MG B:MG101 4.2 80.0 1.0 OP1 B:G25 4.5 82.2 1.0 O B:HOH204 4.5 75.3 1.0 P B:C24 4.6 68.0 1.0 OP2 B:A23 4.8 75.8 1.0 C8 B:G21 4.8 58.5 1.0 C6 A:A23 4.9 74.4 1.0 O6 B:G21 5.0 75.2 1.0

Magnesium binding site 8 out of 12 in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:84.9 occ:1.00 O6 A:G27 3.8 63.1 1.0 O6 A:G28 3.8 72.5 1.0 O4 A:U26 4.0 57.7 1.0 N7 A:G27 4.2 75.1 1.0 OP1 A:A18 4.4 48.6 1.0 C4 A:U26 4.5 65.0 1.0 C5 A:U26 4.5 65.7 1.0 C6 A:G27 4.6 65.3 1.0 C5 A:G27 4.8 70.3 1.0 C6 A:G28 4.8 68.4 1.0 N7 A:G28 4.9 73.7 1.0

Magnesium binding site 9 out of 12 in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:82.8 occ:1.00 O4 A:U40 2.7 79.7 1.0 O4 A:U16 2.9 95.2 1.0 C4 A:U16 3.8 71.5 1.0 C4 A:U40 3.8 63.8 1.0 N3 A:U16 3.8 68.5 1.0 O6 A:G41 4.3 85.3 1.0 C5 A:U40 4.3 63.6 1.0 OP2 A:A39 4.5 0.6 1.0 N4 A:C15 4.8 83.6 1.0 N3 A:U40 4.9 63.0 1.0

Magnesium binding site 10 out of 12 in the Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Fusobacterium Ulcerans Ztp Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:67.5 occ:1.00 OP1 A:U16 1.9 68.6 1.0 O A:HOH201 2.1 70.9 1.0 OP2 A:C35 2.1 70.7 1.0 O A:HOH202 2.2 73.8 1.0 O5 A:AMZ106 2.4 76.0 1.0 P A:U16 3.3 75.0 1.0 C6 A:AMZ106 3.4 73.8 1.0 P A:C35 3.6 73.5 1.0 N2 A:AMZ106 3.6 70.2 1.0 OP2 A:U16 3.9 66.4 1.0 O5' A:U16 4.0 86.9 1.0 C5' A:C35 4.0 70.5 1.0 O5' A:C35 4.2 83.1 1.0 O3' A:C15 4.4 67.3 1.0 C5' A:U16 4.4 68.3 1.0 N3 A:G71 4.5 83.8 1.0 O3' A:A34 4.5 59.6 1.0 N2 A:G71 4.5 76.7 1.0 O4' A:G17 4.5 60.0 1.0 OP1 A:C35 4.5 80.0 1.0 C3A A:AMZ106 4.7 71.5 1.0 O2' A:G71 4.8 99.8 1.0 N3 A:AMZ106 4.9 60.4 1.0 C1' A:G17 4.9 57.4 1.0 C2 A:G71 4.9 83.7 1.0

C.P.Jones, A.R.Ferre-D'amare. Recognition of the Bacterial Alarmone Zmp Through Long-Distance Association of Two Rna Subdomains. Nat.Struct.Mol.Biol. V. 22 679 2015.
ISSN: ESSN 1545-9985
PubMed: 26280533
DOI: 10.1038/NSMB.3073