Magnesium in PDB 6l3g: Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases

The structure of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases, PDB code: 6l3g was solved by N.Su, S.R.Bharath, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.57 / 3.30
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	131.265, 131.265, 117.183, 90.00, 90.00, 120.00
R / Rfree (%)	24.4 / 30.3

The structure of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases (pdb code 6l3g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases, PDB code: 6l3g:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.3 occ:1.00 F3 A:ALF503 2.0 77.2 1.0 OG1 A:THR35 2.0 76.1 1.0 O A:HOH602 2.2 61.1 1.0 O1B A:ADP501 2.4 52.8 1.0 F1 A:ALF503 3.0 70.6 1.0 CB A:THR35 3.0 69.4 1.0 AL A:ALF503 3.3 58.8 1.0 O2A A:ADP501 3.5 79.1 1.0 PB A:ADP501 3.6 60.6 1.0 O3A A:ADP501 3.8 72.0 1.0 N A:THR35 3.8 65.2 1.0 OE2 A:GLU106 3.9 59.6 1.0 PA A:ADP501 3.9 63.4 1.0 CA A:THR35 4.0 56.5 1.0 O1A A:ADP501 4.0 56.2 1.0 OD2 A:ASP105 4.0 47.4 1.0 CG2 A:THR35 4.2 61.5 1.0 O3B A:ADP501 4.2 68.8 1.0 CA A:GLY365 4.3 57.2 1.0 O A:GLY365 4.3 73.8 1.0 OD1 A:ASP105 4.3 70.7 1.0 OD1 A:ASN61 4.4 69.4 1.0 F2 A:ALF503 4.4 55.3 1.0 CG A:ASP105 4.6 65.5 1.0 CD A:GLU106 4.7 64.2 1.0 CB A:LYS34 4.8 62.8 1.0 O2B A:ADP501 4.8 64.6 1.0 C A:GLY365 4.8 62.8 1.0 C A:LYS34 4.8 61.7 1.0 F4 A:ALF503 5.0 54.0 1.0

Magnesium binding site 2 out of 2 in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:55.7 occ:1.00 F3 B:ALF503 1.9 67.3 1.0 OG1 B:THR35 2.0 56.5 1.0 O B:HOH602 2.0 50.9 1.0 O3B B:ADP501 2.2 65.7 1.0 CB B:THR35 3.1 71.9 1.0 PB B:ADP501 3.4 65.0 1.0 AL B:ALF503 3.5 54.4 1.0 N B:THR35 3.6 77.1 1.0 F2 B:ALF503 3.7 64.8 1.0 O3A B:ADP501 3.8 80.9 1.0 O2B B:ADP501 3.8 58.1 1.0 CA B:THR35 3.9 79.5 1.0 OD2 B:ASP105 4.1 49.4 1.0 OD1 B:ASP105 4.1 59.8 1.0 OE2 B:GLU106 4.1 72.5 1.0 F1 B:ALF503 4.2 67.2 1.0 CG2 B:THR35 4.3 69.3 1.0 O2A B:ADP501 4.3 86.3 1.0 CB B:LYS34 4.4 63.5 1.0 PA B:ADP501 4.5 82.4 1.0 CG B:ASP105 4.6 57.2 1.0 C B:LYS34 4.6 72.5 1.0 O1A B:ADP501 4.6 58.1 1.0 O1B B:ADP501 4.7 73.8 1.0 CE B:LYS34 4.7 65.8 1.0 CA B:GLY365 4.7 77.8 1.0 CD B:GLU106 4.8 74.5 1.0 NZ B:LYS34 4.9 60.5 1.0 O B:GLY365 4.9 82.5 1.0 CA B:LYS34 5.0 66.6 1.0

N.Su, A.K.Byrd, S.R.Bharath, O.Yang, Y.Jia, X.Tang, T.Ha, K.D.Raney, H.Song. Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases. Nat Commun V. 10 5375 2019.
ISSN: ESSN 2041-1723
PubMed: 31772234
DOI: 10.1038/S41467-019-13414-9