Fluorine in PDB 5mpm: SERCA2A From Pig Heart

All present enzymatic activity of SERCA2A From Pig Heart:
3.6.3.8;

The structure of SERCA2A From Pig Heart, PDB code: 5mpm was solved by N.D.Drachmann, A.Sitsel, J.L.Andersen, P.Nissen, C.Olesen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.32 / 3.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.349, 253.287, 64.981, 90.00, 100.86, 90.00
R / Rfree (%)	20.4 / 25.8

The structure of SERCA2A From Pig Heart also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Potassium	(K)	1 atom

The binding sites of Fluorine atom in the SERCA2A From Pig Heart (pdb code 5mpm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the SERCA2A From Pig Heart, PDB code: 5mpm:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the SERCA2A From Pig Heart


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of SERCA2A From Pig Heart within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:0.5 occ:1.00 F1 A:MGF1001 0.0 0.5 1.0 MG A:MG1004 1.7 0.6 1.0 MG A:MGF1001 1.8 81.9 1.0 O A:HOH1104 2.3 31.8 1.0 OD2 A:ASP351 2.4 80.2 1.0 O A:GLY182 2.9 79.0 1.0 OD1 A:ASP351 3.0 95.4 1.0 CG A:ASP351 3.0 82.2 1.0 O A:HOH1101 3.0 81.2 1.0 O A:THR353 3.1 63.0 1.0 F3 A:MGF1001 3.1 68.6 1.0 F2 A:MGF1001 3.1 45.7 1.0 O A:HOH1105 3.1 68.4 1.0 CB A:THR353 3.4 0.3 1.0 CA A:GLY182 3.4 72.6 1.0 C A:GLY182 3.5 81.4 1.0 OD1 A:ASP702 3.7 0.1 1.0 CG2 A:THR353 3.8 92.4 1.0 C A:THR353 3.8 81.0 1.0 CA A:THR353 3.9 0.7 1.0 N A:THR353 4.1 0.2 1.0 ND2 A:ASN705 4.3 43.4 1.0 OG1 A:THR353 4.5 94.8 1.0 OD2 A:ASP706 4.5 0.8 1.0 CB A:ASP351 4.5 54.6 1.0 OD1 A:ASN705 4.6 98.6 1.0 N A:GLU183 4.6 0.6 1.0 CG A:ASP702 4.7 0.7 1.0 N A:GLY182 4.7 69.5 1.0 O A:THR181 4.8 0.3 1.0 NZ A:LYS683 4.8 0.5 1.0 OD2 A:ASP702 4.9 0.7 1.0 CG A:ASN705 5.0 69.0 1.0

Fluorine binding site 2 out of 3 in the SERCA2A From Pig Heart


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of SERCA2A From Pig Heart within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:45.7 occ:1.00 F2 A:MGF1001 0.0 45.7 1.0 MG A:MGF1001 1.8 81.9 1.0 NZ A:LYS683 2.2 0.5 1.0 ND2 A:ASN705 2.6 43.4 1.0 OD1 A:ASP351 2.8 95.4 1.0 O A:HOH1101 2.9 81.2 1.0 F3 A:MGF1001 3.1 68.6 1.0 F1 A:MGF1001 3.1 0.5 1.0 CE A:LYS683 3.3 0.4 1.0 CG A:ASP351 3.4 82.2 1.0 N A:GLY625 3.6 79.2 1.0 O A:HOH1104 3.7 31.8 1.0 CG A:ASN705 3.8 69.0 1.0 OD2 A:ASP351 3.8 80.2 1.0 O A:THR181 4.0 0.3 1.0 OD1 A:ASP706 4.0 0.1 1.0 CA A:THR624 4.0 73.7 1.0 C A:THR624 4.0 62.6 1.0 CA A:GLY182 4.1 72.6 1.0 OD1 A:ASN705 4.2 98.6 1.0 CB A:ASP351 4.4 54.6 1.0 CA A:GLY625 4.4 93.0 1.0 OD2 A:ASP706 4.4 0.8 1.0 O A:ILE623 4.4 0.8 1.0 OG1 A:THR624 4.5 1.0 1.0 MG A:MG1004 4.5 0.6 1.0 CD A:LYS683 4.6 99.0 1.0 CG A:ASP706 4.6 89.5 1.0 C A:THR181 4.6 92.9 1.0 N A:GLY182 4.7 69.5 1.0 CB A:THR624 4.9 83.9 1.0 O A:THR624 4.9 66.4 1.0 C A:GLY182 4.9 81.4 1.0 CB A:ASN705 4.9 62.5 1.0 N A:THR624 5.0 92.3 1.0

Fluorine binding site 3 out of 3 in the SERCA2A From Pig Heart


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of SERCA2A From Pig Heart within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:68.6 occ:1.00 F3 A:MGF1001 0.0 68.6 1.0 MG A:MGF1001 1.8 81.9 1.0 OD1 A:ASP351 1.9 95.4 1.0 OG1 A:THR624 2.4 1.0 1.0 O A:HOH1101 2.8 81.2 1.0 N A:THR353 3.0 0.2 1.0 CG A:ASP351 3.0 82.2 1.0 F2 A:MGF1001 3.1 45.7 1.0 F1 A:MGF1001 3.1 0.5 1.0 CB A:THR624 3.1 83.9 1.0 N A:LYS352 3.3 86.9 1.0 CA A:THR624 3.4 73.7 1.0 CB A:THR353 3.5 0.3 1.0 OD2 A:ASP351 3.5 80.2 1.0 N A:GLY625 3.6 79.2 1.0 CA A:THR353 3.8 0.7 1.0 OG1 A:THR353 3.8 94.8 1.0 CA A:LYS352 3.9 89.3 1.0 CB A:LYS352 3.9 92.4 1.0 C A:LYS352 3.9 95.4 1.0 C A:THR624 4.0 62.6 1.0 C A:ASP351 4.2 90.6 1.0 CB A:ASP351 4.2 54.6 1.0 O A:THR353 4.4 63.0 1.0 MG A:MG1004 4.4 0.6 1.0 CA A:ASP351 4.4 63.8 1.0 O A:ILE623 4.5 0.8 1.0 CG2 A:THR624 4.6 45.1 1.0 C A:THR353 4.6 81.0 1.0 CE A:LYS352 4.6 96.0 1.0 NZ A:LYS352 4.6 96.7 1.0 N A:THR624 4.6 92.3 1.0 NZ A:LYS683 4.7 0.5 1.0 CA A:GLY625 4.8 93.0 1.0 N A:ASP626 4.8 86.3 1.0 CG2 A:THR353 4.9 92.4 1.0 O A:HOH1104 5.0 31.8 1.0

A.Sitsel, J.De Raeymaecker, N.D.Drachmann, R.Derua, S.Smaardijk, J.L.Andersen, I.Vandecaetsbeek, J.Chen, M.De Maeyer, E.Waelkens, C.Olesen, P.Vangheluwe, P.Nissen. Structures of the Heart Specific SERCA2A CA2+-Atpase. Embo J. V. 38 2019.
ISSN: ESSN 1460-2075
PubMed: 30777856
DOI: 10.15252/EMBJ.2018100020