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Vanadium 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:

Magnesium (Mg) 2 atoms

Vanadium Binding Sites:

The binding sites of Vanadium 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 Vanadium atom.
In total 2 binding sites of Vanadium 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 Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 6s3n

Go back to Vanadium Binding Sites List in 6s3n
Vanadium 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 Vanadium with other atoms in the V 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:V1003

b:83.3
occ:1.00
V A:VO41003 0.0 83.3 1.0
O3 A:VO41003 1.9 84.9 1.0
O4 A:VO41003 1.9 67.4 1.0
O2 A:VO41003 1.9 81.5 1.0
O1 A:VO41003 1.9 79.1 1.0
O3B A:ADP1001 2.8 54.4 1.0
OE1 A:GLN212 3.6 46.1 1.0
NE2 A:GLN212 3.8 45.6 1.0
PB A:ADP1001 3.8 40.5 1.0
MG A:MG1002 3.9 51.1 1.0
NH2 A:ARG462 3.9 43.7 1.0
O A:HOH1109 3.9 40.5 1.0
NH1 A:ARG462 4.0 40.4 1.0
CA A:GLY436 4.1 47.7 1.0
CA A:ALA93 4.1 44.4 1.0
O2B A:ADP1001 4.1 55.3 1.0
O A:HOH1108 4.1 44.3 1.0
CD A:GLN212 4.1 46.0 1.0
NH2 A:ARG256 4.1 56.9 1.0
OE1 A:GLU172 4.1 60.6 1.0
OE2 A:GLU172 4.2 61.7 1.0
CB A:ALA93 4.2 44.1 1.0
N A:GLY94 4.2 44.5 1.0
NZ A:LYS97 4.3 44.1 1.0
N A:GLY436 4.3 54.9 1.0
O1B A:ADP1001 4.4 40.5 1.0
CZ A:ARG462 4.5 42.2 1.0
O A:HOH1102 4.5 49.7 1.0
CD A:GLU172 4.6 59.1 1.0
C A:ALA93 4.7 57.8 1.0
NH1 A:ARG256 4.8 44.6 1.0
CE A:LYS97 4.9 43.9 1.0
C A:GLY436 4.9 47.6 1.0
CZ A:ARG256 5.0 49.6 1.0

Vanadium binding site 2 out of 2 in 6s3n

Go back to Vanadium Binding Sites List in 6s3n
Vanadium 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 Vanadium with other atoms in the V 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:V1003

b:111.9
occ:1.00
V B:VO41003 0.0 111.9 1.0
O1 B:VO41003 1.9 117.0 1.0
O3 B:VO41003 1.9 106.0 1.0
O2 B:VO41003 1.9 108.6 1.0
O4 B:VO41003 1.9 109.4 1.0
O1B B:ADP1001 2.9 69.2 1.0
NE2 B:GLN212 3.7 63.4 1.0
OE1 B:GLU172 3.7 78.6 1.0
PB B:ADP1001 3.8 65.8 1.0
MG B:MG1002 3.9 95.3 1.0
O3B B:ADP1001 3.9 67.9 1.0
O B:HOH1105 3.9 96.8 1.0
NH1 B:ARG462 4.0 62.7 1.0
CA B:GLY436 4.0 65.8 1.0
NH2 B:ARG462 4.0 51.9 1.0
OE1 B:GLN212 4.1 67.0 1.0
O B:HOH1107 4.1 91.6 1.0
N B:GLY436 4.2 60.0 1.0
CD B:GLN212 4.3 67.2 1.0
O B:HOH1101 4.4 64.4 1.0
NH2 B:ARG256 4.4 65.5 1.0
CA B:ALA93 4.4 61.5 1.0
O2B B:ADP1001 4.4 70.0 1.0
CZ B:ARG462 4.5 62.7 1.0
N B:GLY94 4.5 57.3 1.0
NZ B:LYS97 4.5 53.2 1.0
CB B:ALA93 4.5 57.2 1.0
CD B:GLU172 4.5 72.8 1.0
OE2 B:GLU172 4.6 84.2 1.0
NH1 B:ARG256 4.6 61.2 1.0
C B:GLY436 4.8 75.5 1.0
O1A B:ADP1001 4.9 73.9 1.0
O B:GLY436 4.9 99.5 1.0
C B:ALA93 5.0 61.2 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 16:05:46 2021

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