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Magnesium in PDB 6s3n: Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-VO4

Protein crystallography data

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-VO4, PDB code: 6s3n 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) 44.05 / 2.53
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.093, 102.955, 249.697, 90, 90, 90
R / Rfree (%) 19.8 / 25.5

Other elements in 6s3n:

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-VO4 also contains other interesting chemical elements:

Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-VO4 (pdb code 6s3n). 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-VO4, PDB code: 6s3n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6s3n

Go back to Magnesium Binding Sites List in 6s3n
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-VO4


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-VO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:51.1
occ:1.00
O4 A:VO41003 2.0 67.4 1.0
O A:HOH1109 2.0 40.5 1.0
O A:HOH1108 2.0 44.3 1.0
O A:HOH1102 2.1 49.7 1.0
OG1 A:THR98 2.2 51.8 1.0
O2B A:ADP1001 2.4 55.3 1.0
CB A:THR98 3.1 43.2 1.0
PB A:ADP1001 3.5 40.5 1.0
O3B A:ADP1001 3.7 54.4 1.0
O2A A:ADP1001 3.8 49.4 1.0
OD2 A:ASP171 3.8 48.7 1.0
N A:THR98 3.9 49.2 1.0
V A:VO41003 3.9 83.3 1.0
CA A:THR98 4.1 49.2 1.0
O A:GLY436 4.2 50.0 1.0
CG2 A:THR98 4.2 45.2 1.0
OE1 A:GLU172 4.2 60.6 1.0
CA A:GLY436 4.3 47.7 1.0
OD1 A:ASP171 4.4 52.9 1.0
O3A A:ADP1001 4.5 44.0 1.0
PA A:ADP1001 4.5 56.2 1.0
CG A:ASP171 4.5 57.0 1.0
O1B A:ADP1001 4.7 40.5 1.0
O2 A:VO41003 4.7 81.5 1.0
C A:GLY436 4.7 47.6 1.0
O1A A:ADP1001 4.9 60.9 1.0
CG A:GLN124 4.9 42.4 1.0
O1 A:VO41003 5.0 79.1 1.0
O3 A:VO41003 5.0 84.9 1.0

Magnesium binding site 2 out of 2 in 6s3n

Go back to Magnesium Binding Sites List in 6s3n
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-VO4


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-VO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:95.3
occ:1.00
O B:HOH1105 1.3 96.8 1.0
O B:HOH1107 1.7 91.6 1.0
OG1 B:THR98 2.3 69.2 1.0
O4 B:VO41003 2.4 109.4 1.0
O3B B:ADP1001 2.6 67.9 1.0
O B:HOH1101 2.8 64.4 1.0
CB B:THR98 3.4 70.0 1.0
OD2 B:ASP171 3.5 79.6 1.0
OD1 B:ASP171 3.7 84.0 1.0
OE1 B:GLU172 3.8 78.6 1.0
V B:VO41003 3.9 111.9 1.0
PB B:ADP1001 4.0 65.8 1.0
CG B:ASP171 4.0 81.1 1.0
N B:THR98 4.0 62.8 1.0
CD B:GLU172 4.1 72.8 1.0
O3 B:VO41003 4.2 106.0 1.0
CA B:THR98 4.3 65.7 1.0
O1B B:ADP1001 4.3 69.2 1.0
CG B:GLU172 4.3 66.1 1.0
CA B:GLY436 4.4 65.8 1.0
CG2 B:THR98 4.5 70.7 1.0
O1A B:ADP1001 4.5 73.9 1.0
OE2 B:GLU172 4.6 84.2 1.0
O B:GLY436 4.7 99.5 1.0
O1 B:VO41003 4.7 117.0 1.0
O2B B:ADP1001 4.9 70.0 1.0
CB B:LYS97 5.0 66.6 1.0
O3A B:ADP1001 5.0 72.0 1.0

Reference:

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.
Page generated: Mon Jan 25 15:11:59 2021

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