Fluorine in PDB 4byg: Atpase Crystal Structure

The structure of Atpase Crystal Structure, PDB code: 4byg was solved by D.Mattle, N.D.Drachmann, X.Y.Liu, B.P.Pedersen, J.P.Morth, J.Wang, P.Gourdon, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.984 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.120, 72.910, 329.650, 90.00, 90.00, 90.00
R / Rfree (%)	23.21 / 28.73

The structure of Atpase Crystal Structure also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Aluminium	(Al)	1 atom
Potassium	(K)	1 atom

The binding sites of Fluorine atom in the Atpase Crystal Structure (pdb code 4byg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Atpase Crystal Structure, PDB code: 4byg:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Atpase Crystal Structure


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Atpase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:F995 b:44.5 occ:1.00 F1 A:ALF995 0.0 44.5 1.0 AL A:ALF995 1.8 67.3 1.0 OD1 A:ASP426 2.1 91.0 1.0 F3 A:ALF995 2.5 75.3 1.0 F4 A:ALF995 2.5 35.1 1.0 O A:HOH2014 2.9 63.3 1.0 N A:GLY578 3.0 57.6 1.0 CA A:THR577 3.2 61.7 1.0 CG A:ASP426 3.3 75.0 1.0 OG1 A:THR577 3.5 54.0 1.0 C A:THR577 3.5 61.9 1.0 NZ A:LYS605 3.5 66.1 1.0 F2 A:ALF995 3.6 92.4 1.0 CE A:LYS605 3.7 61.0 1.0 CB A:THR577 3.8 59.6 1.0 O A:LEU576 4.0 70.9 1.0 OD2 A:ASP426 4.0 78.9 1.0 O A:THR277 4.1 95.8 1.0 CA A:GLY578 4.1 60.8 1.0 ND2 A:ASN627 4.2 54.2 1.0 N A:LYS427 4.2 47.7 1.0 N A:THR577 4.3 58.9 1.0 CB A:ASP426 4.4 58.5 1.0 CA A:ASP426 4.5 61.1 1.0 C A:LEU576 4.5 63.1 1.0 O A:HOH2021 4.6 0.4 1.0 OD1 A:ASP628 4.6 78.2 1.0 O A:THR577 4.7 67.6 1.0 MG A:MG996 4.8 68.5 1.0 N A:ASP579 4.9 70.5 1.0 C A:ASP426 4.9 59.8 1.0 N A:THR428 5.0 57.1 1.0

Fluorine binding site 2 out of 4 in the Atpase Crystal Structure


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Atpase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:F995 b:92.4 occ:1.00 F2 A:ALF995 0.0 92.4 1.0 MG A:MG996 1.7 68.5 1.0 AL A:ALF995 1.8 67.3 1.0 OD2 A:ASP426 2.1 78.9 1.0 O A:THR428 2.2 52.6 1.0 F4 A:ALF995 2.5 35.1 1.0 F3 A:ALF995 2.5 75.3 1.0 CG A:ASP426 2.8 75.0 1.0 OD1 A:ASP426 2.8 91.0 1.0 C A:THR428 3.0 49.8 1.0 N A:THR428 3.0 57.1 1.0 O A:HOH2015 3.0 91.1 1.0 O A:HOH2021 3.1 0.4 1.0 O A:HOH2014 3.1 63.3 1.0 CB A:THR428 3.1 55.7 1.0 CA A:THR428 3.2 51.9 1.0 OD1 A:ASP624 3.5 73.5 1.0 F1 A:ALF995 3.6 44.5 1.0 OG1 A:THR428 3.8 57.1 1.0 O A:GLY278 3.9 67.5 1.0 C A:LYS427 4.1 56.0 1.0 N A:LYS427 4.1 47.7 1.0 CB A:ASP426 4.2 58.5 1.0 N A:GLY429 4.3 50.3 1.0 CG2 A:THR428 4.4 52.6 1.0 CG A:ASP624 4.6 68.1 1.0 C A:GLY278 4.7 77.0 1.0 CA A:LYS427 4.7 53.0 1.0 CA A:GLY278 4.8 78.1 1.0 OD2 A:ASP624 4.9 66.2 1.0 OD2 A:ASP628 4.9 51.1 1.0 O A:LYS427 4.9 52.8 1.0 C A:ASP426 4.9 59.8 1.0 OE2 A:GLU279 4.9 92.0 1.0

Fluorine binding site 3 out of 4 in the Atpase Crystal Structure


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Atpase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:F995 b:75.3 occ:1.00 F3 A:ALF995 0.0 75.3 1.0 AL A:ALF995 1.8 67.3 1.0 O A:HOH2021 2.2 0.4 1.0 OD1 A:ASP426 2.4 91.0 1.0 F1 A:ALF995 2.5 44.5 1.0 F2 A:ALF995 2.5 92.4 1.0 O A:HOH2014 2.8 63.3 1.0 MG A:MG996 2.9 68.5 1.0 OD2 A:ASP426 2.9 78.9 1.0 CG A:ASP426 2.9 75.0 1.0 ND2 A:ASN627 3.1 54.2 1.0 OD1 A:ASP628 3.6 78.2 1.0 F4 A:ALF995 3.6 35.1 1.0 OD2 A:ASP628 3.7 51.1 1.0 OD1 A:ASN627 3.7 52.8 1.0 CG A:ASN627 3.8 59.1 1.0 CG A:ASP628 4.0 64.5 1.0 O A:HOH2015 4.0 91.1 1.0 O A:THR277 4.0 95.8 1.0 CA A:GLY278 4.0 78.1 1.0 CB A:ASP426 4.3 58.5 1.0 CE A:LYS605 4.5 61.0 1.0 O A:THR428 4.5 52.6 1.0 O A:GLY278 4.6 67.5 1.0 OD1 A:ASP624 4.6 73.5 1.0 C A:GLY278 4.7 77.0 1.0 C A:THR277 4.7 91.3 1.0 N A:GLY278 4.8 88.9 1.0 CA A:GLY625 4.9 61.2 1.0 N A:GLY625 5.0 52.4 1.0

Fluorine binding site 4 out of 4 in the Atpase Crystal Structure


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Atpase Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:F995 b:35.1 occ:1.00 F4 A:ALF995 0.0 35.1 1.0 AL A:ALF995 1.8 67.3 1.0 F2 A:ALF995 2.5 92.4 1.0 F1 A:ALF995 2.5 44.5 1.0 N A:THR428 2.5 57.1 1.0 OD1 A:ASP426 2.6 91.0 1.0 N A:LYS427 2.8 47.7 1.0 O A:HOH2014 3.1 63.3 1.0 CB A:LYS427 3.2 52.2 1.0 CA A:LYS427 3.2 53.0 1.0 CG A:ASP426 3.2 75.0 1.0 OG1 A:THR577 3.2 54.0 1.0 C A:LYS427 3.3 56.0 1.0 OG1 A:THR428 3.3 57.1 1.0 OD2 A:ASP426 3.5 78.9 1.0 CA A:THR428 3.6 51.9 1.0 F3 A:ALF995 3.6 75.3 1.0 CB A:THR428 3.6 55.7 1.0 CB A:THR577 3.9 59.6 1.0 C A:ASP426 4.0 59.8 1.0 O A:THR428 4.1 52.6 1.0 OE2 A:GLU279 4.2 92.0 1.0 MG A:MG996 4.2 68.5 1.0 CA A:THR577 4.3 61.7 1.0 C A:THR428 4.3 49.8 1.0 CB A:ASP426 4.4 58.5 1.0 CA A:ASP426 4.4 61.1 1.0 N A:GLY578 4.5 57.6 1.0 CG A:LYS427 4.5 53.8 1.0 O A:LYS427 4.5 52.8 1.0 CE A:LYS427 4.5 59.3 1.0 O A:LEU576 4.9 70.9 1.0 CD A:LYS427 4.9 53.4 1.0 C A:THR577 4.9 61.9 1.0

D.Mattle, N.D.Drachmann, X.Y.Liu, B.P.Pedersen, J.P.Morth, J.Wang, P.Gourdon, P.Nissen. Dephosphorylation of Pib-Type Cu(I)-Atpases As Studied By Metallofluoride Complexes To Be Published.