Magnesium in PDB 5fhd: Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex

The structure of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex, PDB code: 5fhd was solved by X.Zhou, W.Ren, S.R.Bharath, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.54 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.471, 149.640, 185.140, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.2

The structure of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms

The binding sites of Magnesium atom in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex (pdb code 5fhd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex, PDB code: 5fhd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.0 occ:1.00 F3 A:ALF503 1.9 18.2 1.0 O3B A:ADP501 2.0 15.3 1.0 O A:HOH655 2.1 16.9 1.0 OG1 A:THR35 2.1 19.4 1.0 O A:HOH660 2.1 17.8 1.0 O A:HOH656 2.2 19.7 1.0 CB A:THR35 3.1 23.1 1.0 PB A:ADP501 3.3 19.1 1.0 AL A:ALF503 3.5 20.3 1.0 O1B A:ADP501 3.5 18.2 1.0 F1 A:ALF503 3.7 19.4 1.0 N A:THR35 3.8 16.7 1.0 OE2 A:GLU106 3.8 20.3 1.0 OD2 A:ASP105 3.9 23.4 1.0 CA A:THR35 4.1 18.4 1.0 O1A A:ADP501 4.1 21.1 1.0 OD1 A:ASP105 4.2 21.2 1.0 O A:HOH616 4.2 20.9 1.0 F2 A:ALF503 4.2 17.2 1.0 CG2 A:THR35 4.2 17.9 1.0 O A:HOH682 4.3 23.6 1.0 O3A A:ADP501 4.3 19.1 1.0 O2B A:ADP501 4.3 17.4 1.0 CA A:GLY365 4.4 20.1 1.0 O A:GLY365 4.4 20.6 1.0 O A:HOH626 4.5 17.6 1.0 CG A:ASP105 4.5 23.9 1.0 PA A:ADP501 4.6 18.4 1.0 CD A:GLU106 4.6 25.5 1.0 OD1 A:ASN61 4.6 28.4 1.0 CB A:LYS34 4.7 17.6 1.0 O2A A:ADP501 4.8 20.9 1.0 C A:LYS34 4.9 19.6 1.0 C A:GLY365 4.9 21.7 1.0 O A:HOH627 5.0 30.7 1.0

Magnesium binding site 2 out of 2 in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:21.8 occ:1.00 O1B B:ADP501 2.0 20.3 1.0 F1 B:ALF503 2.0 17.9 1.0 O B:HOH659 2.1 19.3 1.0 OG1 B:THR35 2.1 21.3 1.0 O B:HOH617 2.2 17.9 1.0 O B:HOH674 2.2 19.3 1.0 CB B:THR35 3.1 22.5 1.0 PB B:ADP501 3.3 20.0 1.0 O3B B:ADP501 3.5 19.7 1.0 AL B:ALF503 3.6 21.0 1.0 F4 B:ALF503 3.7 21.2 1.0 N B:THR35 3.8 19.3 1.0 OE2 B:GLU106 3.8 23.3 1.0 OD2 B:ASP105 3.9 22.7 1.0 CA B:THR35 4.0 21.5 1.0 O1A B:ADP501 4.0 21.4 1.0 O B:HOH641 4.1 21.2 1.0 OD1 B:ASP105 4.1 22.9 1.0 CG2 B:THR35 4.2 18.8 1.0 F3 B:ALF503 4.2 21.1 1.0 O B:HOH683 4.3 23.0 1.0 CA B:GLY365 4.3 20.3 1.0 O3A B:ADP501 4.4 19.5 1.0 O2B B:ADP501 4.4 16.1 1.0 O B:GLY365 4.4 20.4 1.0 O B:HOH619 4.4 20.6 1.0 CG B:ASP105 4.5 22.1 1.0 OD1 B:ASN61 4.5 32.5 1.0 CD B:GLU106 4.6 26.4 1.0 PA B:ADP501 4.6 19.2 1.0 CB B:LYS34 4.8 14.9 1.0 O2A B:ADP501 4.9 19.0 1.0 C B:LYS34 4.9 19.6 1.0 C B:GLY365 4.9 24.1 1.0 CE B:LYS34 5.0 17.4 1.0

X.Zhou, W.Ren, S.R.Bharath, X.Tang, Y.He, C.Chen, Z.Liu, D.Li, H.Song. Structural and Functional Insights Into the Unwinding Mechanism of Bacteroides Sp PIF1 Cell Rep V. 14 2030 2016.
ISSN: ESSN 2211-1247
PubMed: 26904952
DOI: 10.1016/J.CELREP.2016.02.008