Fluorine in PDB 6zhf: Calcium Atpase-1 From Listeria Monocytogenes in Complex with Bef

The structure of Calcium Atpase-1 From Listeria Monocytogenes in Complex with Bef, PDB code: 6zhf was solved by S.Basse Hansen, M.Dyla, C.Neumann, E.M.H.Quistgaard, J.Lauwring Andersen, M.Kjaergaard, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.39 / 4.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.05, 143.857, 153.856, 90, 90, 90
R / Rfree (%)	23.2 / 28

The structure of Calcium Atpase-1 From Listeria Monocytogenes in Complex with Bef also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Calcium Atpase-1 From Listeria Monocytogenes in Complex with Bef (pdb code 6zhf). 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 Atpase-1 From Listeria Monocytogenes in Complex with Bef, PDB code: 6zhf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Calcium Atpase-1 From Listeria Monocytogenes in Complex with Bef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Calcium Atpase-1 From Listeria Monocytogenes in Complex with Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:131.5 occ:1.00 F1 A:BEF902 0.0 131.5 1.0 BE A:BEF902 1.5 127.7 1.0 MG A:MG901 1.7 136.7 1.0 OD2 A:ASP334 2.5 219.1 1.0 F3 A:BEF902 2.5 151.7 1.0 F2 A:BEF902 2.6 122.2 1.0 O A:HOH1001 2.6 129.1 1.0 OD1 A:ASP334 2.7 221.0 1.0 O A:THR336 2.8 186.5 1.0 CG A:ASP334 2.9 208.4 1.0 O A:HOH1002 3.0 115.7 1.0 CB A:THR336 3.3 107.8 1.0 N A:THR336 3.3 126.6 1.0 CA A:THR336 3.5 104.2 1.0 C A:THR336 3.6 141.7 1.0 O A:GLY166 3.7 114.6 1.0 OD1 A:ASP623 3.9 206.2 1.0 CA A:GLY166 4.0 140.8 1.0 OG1 A:THR336 4.1 109.0 1.0 CG2 A:THR336 4.3 139.4 1.0 C A:GLY166 4.3 114.8 1.0 N A:LYS335 4.4 128.0 1.0 CB A:ASP334 4.4 151.9 1.0 C A:LYS335 4.5 154.9 1.0 ND2 A:ASN626 4.8 107.4 1.0 N A:GLY337 4.9 150.1 1.0 CA A:LYS335 4.9 149.1 1.0 OD1 A:ASN626 4.9 145.2 1.0 CG A:ASP623 4.9 194.8 1.0 C A:ASP334 5.0 124.9 1.0

Fluorine binding site 2 out of 3 in the Calcium Atpase-1 From Listeria Monocytogenes in Complex with Bef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Calcium Atpase-1 From Listeria Monocytogenes in Complex with Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:122.2 occ:1.00 F2 A:BEF902 0.0 122.2 1.0 BE A:BEF902 1.6 127.7 1.0 OD1 A:ASP334 2.0 221.0 1.0 F3 A:BEF902 2.5 151.7 1.0 F1 A:BEF902 2.6 131.5 1.0 ND2 A:ASN626 2.9 107.4 1.0 O A:HOH1001 2.9 129.1 1.0 CG A:ASP334 3.1 208.4 1.0 OD2 A:ASP334 3.6 219.1 1.0 MG A:MG901 3.7 136.7 1.0 CG A:ASN626 3.7 114.8 1.0 OD1 A:ASN626 3.8 145.2 1.0 CE A:LYS604 3.9 143.6 1.0 NZ A:LYS604 4.0 134.4 1.0 CA A:GLY166 4.2 140.8 1.0 OD2 A:ASP627 4.2 192.8 1.0 N A:GLY550 4.2 124.8 1.0 CB A:ASP334 4.3 151.9 1.0 OD1 A:ASP627 4.4 156.6 1.0 O A:THR165 4.6 122.7 1.0 CA A:THR549 4.6 133.2 1.0 CG A:ASP627 4.7 170.4 1.0 O A:ILE548 4.7 181.3 1.0 N A:LYS335 4.8 128.0 1.0 C A:THR549 4.9 153.7 1.0 O A:HOH1002 4.9 115.7 1.0 N A:GLY166 4.9 157.8 1.0 CA A:ASP334 4.9 112.7 1.0

Fluorine binding site 3 out of 3 in the Calcium Atpase-1 From Listeria Monocytogenes in Complex with Bef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Calcium Atpase-1 From Listeria Monocytogenes in Complex with Bef within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:151.7 occ:1.00 F3 A:BEF902 0.0 151.7 1.0 BE A:BEF902 1.5 127.7 1.0 OD1 A:ASP334 2.4 221.0 1.0 F2 A:BEF902 2.5 122.2 1.0 F1 A:BEF902 2.5 131.5 1.0 N A:LYS335 2.9 128.0 1.0 CG A:ASP334 3.1 208.4 1.0 N A:THR336 3.2 126.6 1.0 OG1 A:THR549 3.3 128.9 1.0 CB A:LYS335 3.4 146.1 1.0 CA A:LYS335 3.5 149.1 1.0 OD2 A:ASP334 3.5 219.1 1.0 CB A:THR549 3.7 153.1 1.0 CA A:THR549 3.7 133.2 1.0 C A:LYS335 3.8 154.9 1.0 N A:GLY550 4.0 124.8 1.0 C A:ASP334 4.0 124.9 1.0 MG A:MG901 4.0 136.7 1.0 CB A:THR336 4.2 107.8 1.0 CA A:THR336 4.2 104.2 1.0 CA A:ASP334 4.2 112.7 1.0 OG1 A:THR336 4.2 109.0 1.0 CB A:ASP334 4.2 151.9 1.0 O A:ILE548 4.4 181.3 1.0 C A:THR549 4.4 153.7 1.0 O A:HOH1001 4.5 129.1 1.0 O A:THR336 4.6 186.5 1.0 CG A:LYS335 4.8 125.9 1.0 CE A:LYS335 4.8 125.2 1.0 N A:THR549 4.9 115.8 1.0 C A:THR336 4.9 141.7 1.0 NZ A:LYS604 5.0 134.4 1.0

S.Basse Hansen, M.Dyla, C.Neumann, E.Meldgaard Hoegh Quistgaard, J.Lauwring Andersen, M.Kjaergaard, P.Nissen. The Crystal Structure of the Ca 2+ -Atpase 1 From Listeria Monocytogenes Reveals A Pump Primed For Dephosphorylation. J.Mol.Biol. 67015 2021.
ISSN: ESSN 1089-8638
PubMed: 33933469
DOI: 10.1016/J.JMB.2021.167015