Fluorine in PDB 2zbf: Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium

All present enzymatic activity of Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium:
3.6.3.8;

The structure of Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium, PDB code: 2zbf was solved by C.Toyoshima, H.Ogawa, Y.Norimatsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	11.98 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.522, 136.473, 106.619, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.7

The structure of Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium (pdb code 2zbf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium, PDB code: 2zbf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:F998 b:25.3 occ:1.00 F1 A:BEF998 0.0 25.3 1.0 BE A:BEF998 1.3 28.7 1.0 F3 A:BEF998 2.3 25.0 1.0 OD2 A:ASP351 2.3 23.4 1.0 F2 A:BEF998 2.3 23.5 1.0 NZ A:LYS684 2.9 23.9 1.0 ND2 A:ASN706 3.1 19.5 1.0 N A:GLY626 3.1 25.8 1.0 O A:HOH2105 3.4 25.5 1.0 CG A:ASP351 3.5 20.2 1.0 CA A:GLY182 3.5 25.9 1.0 OG1 A:THR625 3.6 27.1 1.0 CA A:THR625 3.6 22.9 1.0 C A:THR625 3.8 23.9 1.0 CE A:LYS684 3.9 29.2 1.0 MG A:MG997 3.9 21.7 1.0 OD1 A:ASP351 4.0 17.7 1.0 CG A:ASN706 4.1 25.1 1.0 CA A:GLY626 4.1 28.3 1.0 CB A:THR625 4.1 22.5 1.0 N A:GLY182 4.2 28.7 1.0 O A:THR181 4.2 25.6 1.0 OD1 A:ASN706 4.3 25.2 1.0 O A:ILE624 4.3 19.0 1.0 C A:THR181 4.5 27.7 1.0 OD1 A:ASP707 4.5 23.1 1.0 C A:GLY182 4.6 27.8 1.0 CB A:ASP351 4.6 20.8 1.0 N A:LYS352 4.7 17.7 1.0 O A:GLY182 4.7 29.4 1.0 O A:HOH2131 4.8 30.5 1.0 N A:THR625 4.8 19.6 1.0 N A:ASP627 4.9 27.9 1.0 C A:ILE624 5.0 21.1 1.0 C A:GLY626 5.0 27.5 1.0

Fluorine binding site 2 out of 3 in the Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:F998 b:23.5 occ:1.00 F2 A:BEF998 0.0 23.5 1.0 BE A:BEF998 1.3 28.7 1.0 MG A:MG997 1.9 21.7 1.0 F3 A:BEF998 2.3 25.0 1.0 F1 A:BEF998 2.3 25.3 1.0 OD2 A:ASP351 2.5 23.4 1.0 O A:HOH2105 2.7 25.5 1.0 OD1 A:ASP351 2.8 17.7 1.0 CG A:ASP351 3.0 20.2 1.0 CA A:GLY182 3.1 25.9 1.0 O A:HOH2114 3.3 19.1 1.0 O A:THR353 3.3 22.6 1.0 CB A:THR353 3.5 14.5 1.0 N A:THR353 3.7 19.1 1.0 CA A:THR353 3.9 18.4 1.0 OG1 A:THR353 4.0 18.5 1.0 C A:THR353 4.0 20.2 1.0 O A:GLY182 4.0 29.4 1.0 N A:GLY182 4.1 28.7 1.0 C A:GLY182 4.1 27.8 1.0 OD1 A:ASP703 4.1 24.5 1.0 O A:SER178 4.2 35.3 1.0 ND2 A:ASN706 4.2 19.5 1.0 OD1 A:ASN706 4.5 25.2 1.0 CB A:ASP351 4.5 20.8 1.0 N A:LYS352 4.6 17.7 1.0 OG1 A:THR625 4.6 27.1 1.0 CG2 A:THR353 4.6 15.1 1.0 NZ A:LYS684 4.6 23.9 1.0 C A:LYS352 4.6 20.8 1.0 CG A:ASN706 4.8 25.1 1.0 OD2 A:ASP707 4.9 25.4 1.0 C A:THR181 5.0 27.7 1.0

Fluorine binding site 3 out of 3 in the Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Calcium Pump Crystal Structure with Bound BEF3 and Tg in the Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:F998 b:25.0 occ:1.00 F3 A:BEF998 0.0 25.0 1.0 BE A:BEF998 1.5 28.7 1.0 F1 A:BEF998 2.3 25.3 1.0 F2 A:BEF998 2.3 23.5 1.0 OD2 A:ASP351 2.4 23.4 1.0 OG1 A:THR625 2.6 27.1 1.0 N A:THR353 2.9 19.1 1.0 N A:LYS352 3.1 17.7 1.0 CG A:ASP351 3.2 20.2 1.0 CB A:THR625 3.2 22.5 1.0 OD1 A:ASP351 3.4 17.7 1.0 OG1 A:THR353 3.5 18.5 1.0 CB A:LYS352 3.5 15.6 1.0 CA A:LYS352 3.6 18.9 1.0 C A:LYS352 3.6 20.8 1.0 CA A:THR625 3.7 22.9 1.0 CB A:THR353 3.7 14.5 1.0 CA A:THR353 3.8 18.4 1.0 MG A:MG997 3.9 21.7 1.0 N A:GLY626 4.0 25.8 1.0 CA A:GLY182 4.1 25.9 1.0 O A:GLY182 4.1 29.4 1.0 C A:ASP351 4.2 18.6 1.0 C A:THR625 4.4 23.9 1.0 CB A:ASP351 4.4 20.8 1.0 O A:THR353 4.4 22.6 1.0 CA A:ASP351 4.5 22.3 1.0 O A:HOH2105 4.5 25.5 1.0 C A:GLY182 4.6 27.8 1.0 O A:ILE624 4.6 19.0 1.0 NZ A:LYS684 4.6 23.9 1.0 C A:THR353 4.6 20.2 1.0 CG A:LYS352 4.6 22.1 1.0 CG2 A:THR625 4.7 17.0 1.0 NZ A:LYS352 4.7 24.4 1.0 CE A:LYS352 4.8 26.1 1.0 O A:LYS352 4.8 22.6 1.0 N A:THR625 4.8 19.6 1.0 N A:ASP627 4.9 27.9 1.0

C.Toyoshima, Y.Norimatsu, S.Iwasawa, T.Tsuda, H.Ogawa. How Processing of Aspartylphosphate Is Coupled to Lumenal Gating of the Ion Pathway in the Calcium Pump Proc.Natl.Acad.Sci.Usa V. 104 19831 2007.
ISSN: ISSN 0027-8424
PubMed: 18077416
DOI: 10.1073/PNAS.0709978104