Magnesium in PDB 6od9: Co-Crystal Structure of the Fusobacterium Ulcerans Ztp Riboswitch Using An X-Ray Free-Electron Laser

The structure of Co-Crystal Structure of the Fusobacterium Ulcerans Ztp Riboswitch Using An X-Ray Free-Electron Laser, PDB code: 6od9 was solved by C.P.Jones, B.Tran, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.19 / 4.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.740, 92.740, 120.480, 90.00, 90.00, 120.00
R / Rfree (%)	25.8 / 30.8

The structure of Co-Crystal Structure of the Fusobacterium Ulcerans Ztp Riboswitch Using An X-Ray Free-Electron Laser also contains other interesting chemical elements:

Caesium	(Cs)	2 atoms
Potassium	(K)	5 atoms

The binding sites of Magnesium atom in the Co-Crystal Structure of the Fusobacterium Ulcerans Ztp Riboswitch Using An X-Ray Free-Electron Laser (pdb code 6od9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Co-Crystal Structure of the Fusobacterium Ulcerans Ztp Riboswitch Using An X-Ray Free-Electron Laser, PDB code: 6od9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Co-Crystal Structure of the Fusobacterium Ulcerans Ztp Riboswitch Using An X-Ray Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Crystal Structure of the Fusobacterium Ulcerans Ztp Riboswitch Using An X-Ray Free-Electron Laser within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:50.9 occ:1.00 OP1 A:U16 2.0 52.9 1.0 OP2 A:C35 2.0 51.4 1.0 O A:HOH203 2.1 75.2 1.0 O A:HOH202 2.1 73.0 1.0 O A:HOH201 2.1 44.4 1.0 O5 A:AMZ102 2.4 54.8 1.0 C6 A:AMZ102 3.3 59.7 1.0 P A:C35 3.4 47.4 1.0 P A:U16 3.5 51.1 1.0 N2 A:AMZ102 3.6 70.0 1.0 C5' A:C35 3.8 40.5 1.0 O5' A:C35 3.9 40.5 1.0 O2' A:G71 4.2 74.6 1.0 OP1 A:C35 4.2 57.8 1.0 O5' A:U16 4.2 59.5 1.0 OP2 A:U16 4.3 57.8 1.0 O3' A:C15 4.4 49.9 1.0 N3 A:G71 4.4 62.9 1.0 O3' A:A34 4.5 53.0 1.0 C1' A:G71 4.7 73.0 1.0 C3A A:AMZ102 4.8 53.9 1.0 C5' A:U16 4.8 55.2 1.0 N2 A:G71 5.0 64.5 1.0 O4' A:G17 5.0 29.3 1.0 C2' A:G71 5.0 81.6 1.0

Magnesium binding site 2 out of 2 in the Co-Crystal Structure of the Fusobacterium Ulcerans Ztp Riboswitch Using An X-Ray Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Crystal Structure of the Fusobacterium Ulcerans Ztp Riboswitch Using An X-Ray Free-Electron Laser within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:25.8 occ:1.00 O5 B:AMZ102 2.0 32.2 1.0 OP1 B:U16 2.0 22.8 1.0 O B:HOH203 2.1 34.7 1.0 O B:HOH201 2.2 34.2 1.0 OP2 B:C35 2.3 38.0 1.0 O B:HOH202 2.3 33.5 1.0 C6 B:AMZ102 2.8 37.9 1.0 N2 B:AMZ102 3.1 40.0 1.0 P B:U16 3.3 23.1 1.0 P B:C35 3.7 30.7 1.0 O5' B:U16 3.8 44.0 1.0 O4' B:G17 4.0 26.4 1.0 OP2 B:U16 4.1 25.6 1.0 C5' B:U16 4.1 32.9 1.0 C3A B:AMZ102 4.1 37.8 1.0 N3 B:AMZ102 4.2 53.7 1.0 O3' B:A34 4.3 24.9 1.0 C1' B:G17 4.3 25.3 1.0 C5' B:C35 4.3 32.4 1.0 O5' B:C35 4.5 31.5 1.0 O3' B:C15 4.5 45.1 1.0 C7A B:AMZ102 4.6 39.4 1.0 N3 B:G71 4.7 48.5 1.0 OP1 B:C35 4.7 31.8 1.0 N9 B:G17 4.9 31.7 1.0 N2 B:G71 4.9 37.2 1.0

C.Jones, B.Tran, C.Conrad, J.Stagno, R.Trachman 3Rd, P.Fischer, A.Meents, A.Ferre-D'amare. Co-Crystal Structure of the Fusobacterium Ulcerans Ztp Riboswitch Using An X-Ray Free-Electron Laser. Acta Crystallogr.,Sect.F V. 75 496 2019.
ISSN: ESSN 2053-230X
PubMed: 31282869
DOI: 10.1107/S2053230X19008549