Fluorine in PDB 3ar8: Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg

All present enzymatic activity of Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg:
3.6.3.8;

The structure of Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg, PDB code: 3ar8 was solved by C.Toyoshima, S.Yonekura, J.Tsueda, S.Iwasawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.99 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.864, 69.873, 141.813, 90.00, 106.71, 90.00
R / Rfree (%)	22.6 / 25.3

The structure of Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Aluminium	(Al)	1 atom
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg (pdb code 3ar8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg, PDB code: 3ar8:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg


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 ALF4, Tnp-Amp and Tg within 5.0Å range: probe atom residue distance (Å) B Occ A:F998 b:37.6 occ:1.00 F1 A:ALF998 0.0 37.6 1.0 AL A:ALF998 1.8 36.2 1.0 F4 A:ALF998 2.4 35.8 1.0 O A:HOH4002 2.4 37.8 1.0 O A:HOH4003 2.6 26.9 1.0 OD2 A:ASP351 2.6 43.3 1.0 F3 A:ALF998 2.6 34.3 1.0 ND2 A:ASN706 2.8 33.1 1.0 O A:THR181 3.3 43.8 1.0 CA A:GLY182 3.3 40.4 1.0 CG A:ASP351 3.5 45.3 1.0 OD1 A:ASN706 3.5 44.0 1.0 F2 A:ALF998 3.5 34.5 1.0 CG A:ASN706 3.5 43.6 1.0 NZ A:LYS684 3.7 39.0 1.0 OD1 A:ASP351 3.7 45.7 1.0 MG A:MG995 3.7 37.3 1.0 C A:THR181 3.8 43.9 1.0 N A:GLY182 3.9 46.4 1.0 O A:HOH4001 4.0 36.1 1.0 OD1 A:ASP707 4.0 52.0 1.0 OD2 A:ASP707 4.0 55.9 1.0 C A:GLY182 4.2 42.6 1.0 CG A:ASP707 4.4 49.2 1.0 O A:GLY182 4.4 41.9 1.0 N A:GLY626 4.6 38.3 1.0 CE A:LYS684 4.7 41.6 1.0 CB A:ASP351 4.8 45.0 1.0 OE2 A:GLU183 4.9 50.7 1.0

Fluorine binding site 2 out of 4 in the Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg


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 ALF4, Tnp-Amp and Tg within 5.0Å range: probe atom residue distance (Å) B Occ A:F998 b:34.5 occ:1.00 F2 A:ALF998 0.0 34.5 1.0 AL A:ALF998 1.8 36.2 1.0 OG1 A:THR625 2.5 44.2 1.0 F3 A:ALF998 2.5 34.3 1.0 O A:HOH4003 2.6 26.9 1.0 F4 A:ALF998 2.6 35.8 1.0 OD2 A:ASP351 2.7 43.3 1.0 N A:THR353 2.7 43.9 1.0 N A:LYS352 2.9 41.2 1.0 CB A:LYS352 3.2 38.2 1.0 CA A:LYS352 3.3 41.4 1.0 CB A:THR625 3.3 41.6 1.0 CG A:ASP351 3.3 45.3 1.0 C A:LYS352 3.4 45.3 1.0 F1 A:ALF998 3.5 37.6 1.0 OD1 A:ASP351 3.6 45.7 1.0 OE2 A:GLU183 3.7 50.7 1.0 CB A:THR353 3.7 42.7 1.0 OG1 A:THR353 3.7 36.5 1.0 CA A:THR353 3.7 42.9 1.0 CA A:THR625 3.8 42.6 1.0 C A:ASP351 4.0 42.3 1.0 CG A:LYS352 4.1 40.0 1.0 N A:GLY626 4.2 38.3 1.0 O A:THR353 4.4 45.9 1.0 CA A:ASP351 4.4 43.6 1.0 MG A:MG995 4.5 37.3 1.0 CB A:ASP351 4.5 45.0 1.0 C A:THR353 4.6 44.5 1.0 CD A:LYS352 4.6 43.7 1.0 C A:THR625 4.6 44.2 1.0 NZ A:LYS352 4.6 40.0 1.0 O A:LYS352 4.6 44.4 1.0 O A:ILE624 4.6 44.9 1.0 CG2 A:THR625 4.7 43.0 1.0 NZ A:LYS684 4.7 39.0 1.0 O A:HOH4002 4.9 37.8 1.0 N A:THR625 4.9 44.5 1.0 CD A:GLU183 5.0 51.8 1.0

Fluorine binding site 3 out of 4 in the Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg


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 ALF4, Tnp-Amp and Tg within 5.0Å range: probe atom residue distance (Å) B Occ A:F998 b:34.3 occ:1.00 F3 A:ALF998 0.0 34.3 1.0 AL A:ALF998 1.8 36.2 1.0 MG A:MG995 2.2 37.3 1.0 F2 A:ALF998 2.5 34.5 1.0 OD1 A:ASP351 2.5 45.7 1.0 F1 A:ALF998 2.6 37.6 1.0 O A:HOH4003 2.6 26.9 1.0 O A:HOH4001 2.7 36.1 1.0 O A:THR353 2.7 45.9 1.0 OD2 A:ASP351 2.8 43.3 1.0 O A:HOH4002 2.9 37.8 1.0 CG A:ASP351 3.0 45.3 1.0 CB A:THR353 3.1 42.7 1.0 N A:THR353 3.2 43.9 1.0 CA A:THR353 3.3 42.9 1.0 C A:THR353 3.4 44.5 1.0 F4 A:ALF998 3.6 35.8 1.0 O A:GLY182 3.6 41.9 1.0 OG1 A:THR353 3.9 36.5 1.0 OE2 A:GLU183 4.0 50.7 1.0 CA A:GLY182 4.1 40.4 1.0 OD1 A:ASP703 4.1 50.9 1.0 CG2 A:THR353 4.1 36.6 1.0 C A:GLY182 4.1 42.6 1.0 C A:LYS352 4.1 45.3 1.0 N A:LYS352 4.3 41.2 1.0 CB A:ASP351 4.5 45.0 1.0 O A:THR181 4.7 43.8 1.0 N A:GLY354 4.7 44.7 1.0 CA A:LYS352 4.8 41.4 1.0 OG1 A:THR625 4.8 44.2 1.0 OD2 A:ASP707 4.9 55.9 1.0 O A:LYS352 4.9 44.4 1.0 CD A:GLU183 5.0 51.8 1.0

Fluorine binding site 4 out of 4 in the Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Calcium Pump Crystal Structure with Bound ALF4, Tnp-Amp and Tg within 5.0Å range: probe atom residue distance (Å) B Occ A:F998 b:35.8 occ:1.00 F4 A:ALF998 0.0 35.8 1.0 AL A:ALF998 1.8 36.2 1.0 F1 A:ALF998 2.4 37.6 1.0 OD2 A:ASP351 2.5 43.3 1.0 O A:HOH4003 2.5 26.9 1.0 F2 A:ALF998 2.6 34.5 1.0 N A:GLY626 2.7 38.3 1.0 NZ A:LYS684 2.8 39.0 1.0 CA A:THR625 2.9 42.6 1.0 OG1 A:THR625 3.1 44.2 1.0 C A:THR625 3.2 44.2 1.0 CB A:THR625 3.5 41.6 1.0 F3 A:ALF998 3.6 34.3 1.0 CE A:LYS684 3.7 41.6 1.0 O A:ILE624 3.7 44.9 1.0 CG A:ASP351 3.7 45.3 1.0 O A:THR181 3.8 43.8 1.0 CA A:GLY626 3.8 36.8 1.0 ND2 A:ASN706 3.9 33.1 1.0 N A:THR625 4.0 44.5 1.0 C A:ILE624 4.3 45.5 1.0 O A:THR625 4.4 44.5 1.0 OD1 A:ASP351 4.5 45.7 1.0 N A:LYS352 4.5 41.2 1.0 O A:HOH4002 4.5 37.8 1.0 OD1 A:ASP707 4.6 52.0 1.0 N A:ASP627 4.7 39.3 1.0 OE2 A:GLU183 4.7 50.7 1.0 CB A:ASP351 4.8 45.0 1.0 C A:THR181 4.8 43.9 1.0 C A:GLY626 4.8 38.9 1.0 CA A:ASP351 4.8 43.6 1.0 CG2 A:THR625 4.9 43.0 1.0

C.Toyoshima, S.Yonekura, J.Tsueda, S.Iwasawa. Trinitrophenyl Derivatives Bind Differently From Parent Adenine Nucleotides to CA2+-Atpase in the Absence of CA2+ Proc.Natl.Acad.Sci.Usa V. 108 1833 2011.
ISSN: ISSN 0027-8424
PubMed: 21239683
DOI: 10.1073/PNAS.1017659108