Fluorine in PDB 3b9b: Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase

All present enzymatic activity of Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase:
3.6.3.8;

The structure of Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase, PDB code: 3b9b was solved by C.Olesen, M.Picard, A.M.L.Winther, J.P.Morth, J.V.Moller, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.35 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.600, 114.600, 229.300, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 27.1

The structure of Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase (pdb code 3b9b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase, PDB code: 3b9b:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F998 b:30.7 occ:1.00 F1 A:BEF998 0.0 30.7 1.0 BE A:BEF998 1.4 38.0 1.0 F2 A:BEF998 2.2 45.8 1.0 F3 A:BEF998 2.3 35.0 1.0 OD2 A:ASP351 2.5 25.5 1.0 N A:GLY626 2.9 20.4 1.0 NZ A:LYS684 3.0 15.3 1.0 OG1 A:THR625 3.3 23.8 1.0 CA A:THR625 3.4 19.6 1.0 ND2 A:ASN706 3.4 15.2 1.0 CA A:GLY182 3.4 23.4 1.0 C A:THR625 3.6 17.6 1.0 CG A:ASP351 3.7 27.1 1.0 CA A:GLY626 3.9 27.0 1.0 CB A:THR625 3.9 21.7 1.0 MG A:MG996 3.9 13.8 1.0 CE A:LYS684 3.9 25.9 1.0 O A:THR181 4.1 30.8 1.0 N A:GLY182 4.2 10.6 1.0 O A:ILE624 4.2 31.5 1.0 O A:HOH1000 4.3 24.4 1.0 OD1 A:ASP351 4.3 24.3 1.0 N A:ASP627 4.4 21.7 1.0 C A:GLY182 4.4 14.3 1.0 O A:GLY182 4.4 10.2 1.0 CG A:ASN706 4.5 24.4 1.0 C A:THR181 4.5 19.3 1.0 N A:THR625 4.5 32.2 1.0 N A:LYS352 4.6 16.2 1.0 C A:GLY626 4.6 26.7 1.0 OD1 A:ASP707 4.7 32.1 1.0 OD1 A:ASN706 4.7 20.2 1.0 CB A:ASP351 4.7 16.4 1.0 O A:THR625 4.8 40.6 1.0 C A:ILE624 4.8 34.5 1.0 N A:THR353 4.9 14.0 1.0 OG1 A:THR353 4.9 18.6 1.0

Fluorine binding site 2 out of 3 in the Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F998 b:45.8 occ:1.00 F2 A:BEF998 0.0 45.8 1.0 BE A:BEF998 1.4 38.0 1.0 F1 A:BEF998 2.2 30.7 1.0 F3 A:BEF998 2.2 35.0 1.0 MG A:MG996 2.3 13.8 1.0 CA A:GLY182 2.7 23.4 1.0 OD2 A:ASP351 2.8 25.5 1.0 CB A:THR353 3.2 10.8 1.0 O A:THR353 3.4 15.3 1.0 OD1 A:ASP351 3.5 24.3 1.0 CG A:ASP351 3.5 27.1 1.0 OG1 A:THR353 3.5 18.6 1.0 N A:THR353 3.5 14.0 1.0 O A:GLY182 3.5 10.2 1.0 O A:HOH999 3.6 24.5 1.0 C A:GLY182 3.6 14.3 1.0 O A:HOH1000 3.7 24.4 1.0 CA A:THR353 3.7 7.2 1.0 N A:GLY182 3.9 10.6 1.0 C A:THR353 4.0 15.3 1.0 OG1 A:THR625 4.1 23.8 1.0 ND2 A:ASN706 4.4 15.2 1.0 CG2 A:THR353 4.4 15.2 1.0 C A:LYS352 4.5 21.6 1.0 O A:SER178 4.5 32.2 1.0 N A:LYS352 4.5 16.2 1.0 OD1 A:ASP703 4.6 24.6 1.0 NZ A:LYS684 4.6 15.3 1.0 C A:THR181 4.7 19.3 1.0 N A:GLY626 4.8 20.4 1.0 O A:THR181 4.8 30.8 1.0 N A:GLU183 4.9 15.7 1.0 CA A:LYS352 4.9 12.2 1.0 CB A:ASP351 4.9 16.4 1.0 OD1 A:ASN706 4.9 20.2 1.0

Fluorine binding site 3 out of 3 in the Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the E2 Beryllium Fluoride Complex of the Serca CA2+-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F998 b:35.0 occ:1.00 F3 A:BEF998 0.0 35.0 1.0 BE A:BEF998 1.4 38.0 1.0 F2 A:BEF998 2.2 45.8 1.0 F1 A:BEF998 2.3 30.7 1.0 OG1 A:THR625 2.3 23.8 1.0 OD2 A:ASP351 2.8 25.5 1.0 N A:THR353 2.8 14.0 1.0 N A:LYS352 2.9 16.2 1.0 CB A:THR625 3.1 21.7 1.0 CB A:LYS352 3.1 13.5 1.0 CA A:LYS352 3.3 12.2 1.0 CG A:ASP351 3.4 27.1 1.0 C A:LYS352 3.5 21.6 1.0 OG1 A:THR353 3.5 18.6 1.0 CA A:THR625 3.5 19.6 1.0 OD1 A:ASP351 3.6 24.3 1.0 CB A:THR353 3.8 10.8 1.0 CA A:THR353 3.8 7.2 1.0 MG A:MG996 3.9 13.8 1.0 C A:ASP351 4.0 17.7 1.0 N A:GLY626 4.1 20.4 1.0 O A:GLY182 4.1 10.2 1.0 CG A:LYS352 4.3 7.8 1.0 CA A:GLY182 4.3 23.4 1.0 C A:THR625 4.3 17.6 1.0 O A:ILE624 4.3 31.5 1.0 CA A:ASP351 4.4 11.3 1.0 CB A:ASP351 4.5 16.4 1.0 CE A:LYS352 4.5 20.0 1.0 O A:THR353 4.5 15.3 1.0 NZ A:LYS684 4.5 15.3 1.0 CG2 A:THR625 4.5 13.5 1.0 O A:LYS352 4.6 28.3 1.0 C A:THR353 4.6 15.3 1.0 N A:THR625 4.7 32.2 1.0 C A:GLY182 4.7 14.3 1.0 N A:ASP627 4.7 21.7 1.0 NZ A:LYS352 4.7 7.2 1.0 CB A:ASP627 4.8 23.2 1.0 C A:ILE624 4.9 34.5 1.0 CD A:LYS352 4.9 21.9 1.0

C.Olesen, M.Picard, A.M.L.Winther, C.Gyrup, J.P.Morth, C.Oxvig, J.V.Moller, P.Nissen. The Structural Basis of Calcium Transport By the Calcium Pump. Nature V. 450 1036 2007.
ISSN: ISSN 0028-0836
PubMed: 18075584
DOI: 10.1038/NATURE06418