Magnesium in PDB 6s3i: Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4, PDB code: 6s3i was solved by Y.X.Dai, W.F.Chen, F.Y.Teng, N.N.Liu, X.M.Hou, S.X.Dou, S.Rety, X.G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.57 / 2.46
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.195, 61.195, 260.358, 90, 90, 90
R / Rfree (%)	24.4 / 30.2

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4 also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4 (pdb code 6s3i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4, PDB code: 6s3i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4


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 Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:62.8 occ:1.00 OG1 A:THR98 1.8 45.0 1.0 F1 A:MF41003 1.9 61.3 1.0 O A:HOH1111 2.0 45.3 1.0 O A:HOH1105 2.1 45.7 1.0 O A:HOH1106 2.3 48.8 1.0 O3B A:ADP1001 2.6 45.0 1.0 CB A:THR98 2.9 45.1 1.0 HB A:THR98 3.0 54.4 1.0 HA2 A:GLY436 3.3 60.8 1.0 HG21 A:THR98 3.4 54.3 1.0 H A:THR98 3.5 54.1 1.0 MG A:MF41003 3.7 72.6 1.0 OE2 A:GLU172 3.7 44.6 1.0 OD2 A:ASP171 3.7 44.9 1.0 CG2 A:THR98 3.7 45.0 1.0 O A:GLY436 3.8 52.0 1.0 PB A:ADP1001 3.8 44.9 1.0 HA3 A:GLY436 4.0 60.8 1.0 CA A:GLY436 4.0 50.4 1.0 O1B A:ADP1001 4.1 56.0 1.0 CA A:THR98 4.1 45.6 1.0 HG2 A:GLN124 4.1 68.8 1.0 N A:THR98 4.1 44.9 1.0 O1A A:ADP1001 4.2 44.8 1.0 HG23 A:THR98 4.2 54.3 1.0 OD1 A:ASP171 4.3 45.0 1.0 C A:GLY436 4.4 44.9 1.0 HA A:THR98 4.4 55.0 1.0 CG A:ASP171 4.4 45.0 1.0 HG2 A:GLU172 4.4 54.2 1.0 HG3 A:GLN124 4.5 68.8 1.0 HG22 A:THR98 4.5 54.3 1.0 F2 A:MF41003 4.6 45.0 1.0 CD A:GLU172 4.6 44.6 1.0 F3 A:MF41003 4.7 44.6 1.0 HB2 A:LYS97 4.7 54.2 1.0 HE21 A:GLN124 4.7 72.9 1.0 CG A:GLN124 4.8 57.1 1.0 O2B A:ADP1001 4.8 50.2 1.0 F4 A:MF41003 4.8 54.3 1.0 HH22 A:ARG256 4.8 85.0 1.0 PA A:ADP1001 4.9 44.3 1.0 O3A A:ADP1001 4.9 49.7 1.0 O2A A:ADP1001 5.0 53.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4


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 Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:72.6 occ:1.00 MG A:MF41003 0.0 72.6 1.0 F2 A:MF41003 1.8 45.0 1.0 F3 A:MF41003 1.8 44.6 1.0 F4 A:MF41003 1.8 54.3 1.0 F1 A:MF41003 1.8 61.3 1.0 O1B A:ADP1001 2.8 56.0 1.0 HA2 A:GLY436 2.9 60.8 1.0 HH22 A:ARG462 3.0 72.7 1.0 HE22 A:GLN212 3.0 62.0 1.0 HH12 A:ARG462 3.4 66.1 1.0 OE2 A:GLU172 3.5 44.6 1.0 HH12 A:ARG256 3.6 55.2 1.0 MG A:MG1002 3.7 62.8 1.0 PB A:ADP1001 3.7 44.9 1.0 HZ1 A:LYS97 3.7 55.8 1.0 H A:GLY94 3.8 54.2 1.0 NH2 A:ARG462 3.8 60.4 1.0 HZ2 A:LYS97 3.8 55.8 1.0 H A:GLY436 3.8 54.2 1.0 NE2 A:GLN212 3.8 51.4 1.0 CA A:GLY436 3.8 50.4 1.0 HA A:ALA93 3.9 54.5 1.0 O3B A:ADP1001 3.9 45.0 1.0 OE1 A:GLN212 4.0 54.0 1.0 HH22 A:ARG256 4.0 85.0 1.0 NH1 A:ARG462 4.1 54.8 1.0 O A:HOH1105 4.1 45.7 1.0 HB1 A:ALA93 4.1 54.8 1.0 N A:GLY436 4.2 44.9 1.0 NZ A:LYS97 4.2 46.3 1.0 O2B A:ADP1001 4.2 50.2 1.0 HH21 A:ARG462 4.3 72.7 1.0 CD A:GLN212 4.4 54.6 1.0 CZ A:ARG462 4.4 66.4 1.0 NH1 A:ARG256 4.4 45.7 1.0 HA3 A:GLY436 4.5 60.8 1.0 O A:HOH1106 4.5 48.8 1.0 HE21 A:GLN212 4.5 62.0 1.0 O A:HOH1111 4.5 45.3 1.0 HG3 A:GLN435 4.5 54.2 1.0 N A:GLY94 4.6 44.9 1.0 C A:GLY436 4.6 44.9 1.0 CD A:GLU172 4.6 44.6 1.0 CA A:ALA93 4.6 45.2 1.0 HB2 A:ALA93 4.6 54.8 1.0 O A:GLY436 4.7 52.0 1.0 CB A:ALA93 4.7 45.4 1.0 NH2 A:ARG256 4.8 70.6 1.0 HZ3 A:LYS97 4.8 55.8 1.0 HH11 A:ARG462 4.8 66.1 1.0 HE2 A:LYS97 4.9 53.7 1.0 OE1 A:GLU172 4.9 44.5 1.0 HH11 A:ARG256 5.0 55.2 1.0

Y.X.Dai, W.F.Chen, F.Y.Teng, N.N.Liu, X.M.Hou, S.X.Dou, S.Rety, X.G.Xi. Unraveling the Structural and Mechanistic Basis of SF1B Helicase Dimerization: Inhibitory Regulation of Thermus Oshimau PIF1 Activity To Be Published.