Magnesium in PDB 5lkm: Rada Bound to Dtdp

The structure of Rada Bound to Dtdp, PDB code: 5lkm was solved by C.Rapisarda, H.Remaut, R.Fornzes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.21 / 3.50
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	99.400, 169.900, 187.420, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.4

The binding sites of Magnesium atom in the Rada Bound to Dtdp (pdb code 5lkm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Rada Bound to Dtdp, PDB code: 5lkm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Rada Bound to Dtdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rada Bound to Dtdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:0.5 occ:1.00 O1B A:TYD500 1.9 0.0 1.0 OG A:SER102 1.9 0.5 1.0 PB A:TYD500 3.0 0.1 1.0 CB A:SER102 3.1 0.4 1.0 OE1 A:GLU124 3.1 0.8 1.0 O1A A:TYD500 3.1 1.0 1.0 O3B A:TYD500 3.3 0.2 1.0 O3A A:TYD500 3.8 0.4 1.0 PA A:TYD500 3.8 0.4 1.0 CD A:GLU124 3.9 0.5 1.0 NE2 A:HIS213 4.0 0.9 1.0 OE2 A:GLU124 4.0 0.3 1.0 OD2 A:ASP170 4.0 0.6 1.0 OD1 A:ASP170 4.1 0.4 1.0 N A:SER102 4.1 0.4 1.0 O2A A:TYD500 4.1 1.0 1.0 CA A:SER102 4.2 1.0 1.0 CE1 A:HIS213 4.2 0.2 1.0 O2B A:TYD500 4.3 0.2 1.0 CG A:ASP170 4.5 0.6 1.0 OE1 A:GLU125 4.6 0.7 1.0

Magnesium binding site 2 out of 3 in the Rada Bound to Dtdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rada Bound to Dtdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:0.7 occ:1.00 O1B B:TYD500 1.9 0.6 1.0 OG B:SER102 2.2 0.8 1.0 OE2 B:GLU124 2.6 0.1 1.0 PB B:TYD500 3.0 0.9 1.0 O3B B:TYD500 3.2 0.6 1.0 OE1 B:GLU124 3.3 0.1 1.0 CD B:GLU124 3.3 0.4 1.0 CB B:SER102 3.4 0.3 1.0 O1A B:TYD500 3.4 1.0 1.0 NE2 B:HIS213 3.8 0.6 1.0 O3A B:TYD500 3.8 0.8 1.0 PA B:TYD500 4.0 0.4 1.0 CE1 B:HIS213 4.1 0.3 1.0 OD1 B:ASP170 4.2 1.0 1.0 O2B B:TYD500 4.3 0.5 1.0 N B:SER102 4.3 0.2 1.0 OD2 B:ASP170 4.3 0.9 1.0 O2A B:TYD500 4.3 0.8 1.0 CA B:SER102 4.4 0.3 1.0 OE2 B:GLU125 4.6 0.9 1.0 CG B:ASP170 4.7 0.1 1.0 CG B:LYS101 4.8 0.6 1.0 CG B:GLU124 4.8 0.1 1.0 OE1 B:GLU125 4.9 0.9 1.0

Magnesium binding site 3 out of 3 in the Rada Bound to Dtdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rada Bound to Dtdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:98.1 occ:1.00 OG C:SER102 2.2 0.2 1.0 OE1 C:GLU124 2.3 0.6 1.0 O1B C:TYD500 2.4 0.8 1.0 O1A C:TYD500 3.1 0.8 1.0 CB C:SER102 3.4 0.8 1.0 CD C:GLU124 3.4 0.3 1.0 PB C:TYD500 3.5 0.5 1.0 O3B C:TYD500 3.7 0.9 1.0 OD2 C:ASP170 3.9 0.6 1.0 PA C:TYD500 4.0 0.1 1.0 O3A C:TYD500 4.1 0.4 1.0 OD1 C:ASP170 4.1 0.9 1.0 OE2 C:GLU124 4.1 0.8 1.0 NE2 C:HIS213 4.2 0.9 1.0 OE1 C:GLU125 4.4 0.6 1.0 CE1 C:HIS213 4.4 0.6 1.0 CG C:ASP170 4.4 0.3 1.0 O2A C:TYD500 4.4 0.5 1.0 CG C:GLU124 4.5 0.5 1.0 CA C:SER102 4.5 0.7 1.0 N C:SER102 4.6 0.5 1.0 O2B C:TYD500 4.8 0.9 1.0 O C:ASP170 4.9 0.7 1.0 CD C:GLU125 4.9 0.6 1.0 NH1 C:ARG133 5.0 0.1 1.0

L.Marie, C.Rapisarda, V.Morales, M.Berge, T.Perry, A.L.Soulet, C.Gruget, H.Remaut, R.Fronzes, P.Polard. Bacterial Rada Is A Dnab-Type Helicase Interacting with Reca to Promote Bidirectional D-Loop Extension. Nat Commun V. 8 15638 2017.
ISSN: ESSN 2041-1723
PubMed: 28561029
DOI: 10.1038/NCOMMS15638