Magnesium in PDB 8jy0: Crystal Structure of Rhobast Complexed with Tmr-Dn

The structure of Crystal Structure of Rhobast Complexed with Tmr-Dn, PDB code: 8jy0 was solved by Y.Zhang, Y.Xiao, Z.Xu, X.Fang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.95 / 2.75
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	108.531, 158.936, 182.424, 90, 90, 90
R / Rfree (%)	20.2 / 23.1

The binding sites of Magnesium atom in the Crystal Structure of Rhobast Complexed with Tmr-Dn (pdb code 8jy0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Rhobast Complexed with Tmr-Dn, PDB code: 8jy0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Rhobast Complexed with Tmr-Dn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Rhobast Complexed with Tmr-Dn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:68.4 occ:1.00 OP2 B:C8 2.9 42.7 1.0 OP1 B:G37 3.1 44.4 1.0 O2' B:A36 3.5 52.8 1.0 C2' B:A36 3.9 51.3 1.0 C3' B:A36 3.9 50.3 1.0 O3' B:A36 4.2 51.4 1.0 MG B:MG202 4.3 46.0 0.8 P B:G37 4.3 56.8 1.0 P B:C8 4.3 47.4 1.0 OP2 B:A36 4.4 46.3 1.0 OP2 B:C53 4.8 49.6 1.0 O5' B:C8 5.0 53.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Rhobast Complexed with Tmr-Dn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Rhobast Complexed with Tmr-Dn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:46.0 occ:0.81 OP2 B:A36 2.2 46.3 1.0 O3' B:G35 2.7 43.8 1.0 O2' B:G35 2.8 45.4 1.0 OP2 B:C53 2.9 49.6 1.0 P B:A36 3.0 47.8 1.0 C2' B:G35 3.6 44.1 1.0 C2' B:A36 3.6 51.3 1.0 C8 B:A36 3.6 49.8 1.0 C3' B:G35 3.7 46.1 1.0 O3' B:C52 3.8 47.7 1.0 P B:C53 3.9 47.7 1.0 O5' B:A36 4.1 49.1 1.0 OP1 B:A36 4.1 45.4 1.0 O2' B:A36 4.3 52.8 1.0 MG B:MG201 4.3 68.4 1.0 C3' B:A36 4.3 50.3 1.0 C5 B:C53 4.4 42.5 1.0 N9 B:A36 4.4 46.0 1.0 C1' B:A36 4.4 47.2 1.0 O5' B:C53 4.6 47.1 1.0 O4' B:A36 4.6 47.5 1.0 N7 B:A36 4.6 49.1 1.0 C5' B:A36 4.7 46.7 1.0 C4' B:A36 4.8 46.7 1.0 C4' B:G35 4.8 49.7 1.0 C6 B:C53 4.8 41.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Rhobast Complexed with Tmr-Dn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Rhobast Complexed with Tmr-Dn within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:59.0 occ:1.00 OP2 D:C8 2.4 57.8 1.0 O D:HOH309 2.4 53.4 1.0 OP1 D:G37 2.5 49.2 1.0 P D:C8 3.7 61.4 1.0 P D:G37 3.8 63.8 1.0 O2' D:A36 3.9 45.9 1.0 C3' D:U7 4.1 47.3 1.0 O3' D:A36 4.2 57.6 1.0 O3' D:U7 4.2 58.3 1.0 C2' D:U7 4.4 51.0 1.0 C3' D:A36 4.4 50.8 1.0 OP2 D:G37 4.5 59.4 1.0 OP1 D:C8 4.5 49.1 1.0 C2' D:A36 4.6 51.2 1.0 O5' D:C8 4.8 57.1 1.0 N7 D:G37 4.9 63.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Rhobast Complexed with Tmr-Dn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Rhobast Complexed with Tmr-Dn within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:51.4 occ:0.66 OP2 D:C53 2.5 57.0 1.0 O2' D:G35 2.7 51.4 1.0 OP2 D:A36 2.8 49.0 1.0 O3' D:C52 3.2 53.8 1.0 O3' D:G35 3.3 54.6 1.0 P D:C53 3.4 47.4 1.0 P D:A36 3.5 55.7 1.0 C2' D:G35 3.6 52.2 1.0 C8 D:A36 3.6 48.7 1.0 C2' D:A36 3.7 51.2 1.0 O5' D:A36 3.9 56.0 1.0 O5' D:C53 4.0 52.3 1.0 C3' D:G35 4.0 52.8 1.0 C5 D:C53 4.2 49.1 1.0 O2' D:A36 4.2 45.9 1.0 C6 D:C53 4.4 48.7 1.0 N9 D:A36 4.4 46.4 1.0 N7 D:A36 4.5 49.6 1.0 C3' D:C52 4.5 57.0 1.0 C3' D:A36 4.5 50.8 1.0 C1' D:A36 4.6 52.8 1.0 C4' D:C52 4.7 55.5 1.0 OP1 D:C53 4.8 42.9 1.0 O4' D:A36 4.9 53.0 1.0 OP1 D:A36 4.9 53.4 1.0 C5' D:A36 5.0 52.1 1.0

Y.Zhang, Z.Xu, Y.Xiao, H.Jiang, X.Zuo, X.Li, X.Fang. Structural Mechanisms For Binding and Activation of A Contact-Quenched Fluorophore By Rhobast. Nat Commun V. 15 4206 2024.
ISSN: ESSN 2041-1723
PubMed: 38760339
DOI: 10.1038/S41467-024-48478-9