Fluorine in PDB 7qc0: Crystal Structure of Cadmium Translocating P-Type Atpase

The structure of Crystal Structure of Cadmium Translocating P-Type Atpase, PDB code: 7qc0 was solved by C.Groenberg, Q.Hu, K.Wang, P.Gourdon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.27 / 3.11
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.028, 94.532, 128.774, 90, 90, 90
R / Rfree (%)	24.5 / 26.8

The structure of Crystal Structure of Cadmium Translocating P-Type Atpase also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Cadmium Translocating P-Type Atpase (pdb code 7qc0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Cadmium Translocating P-Type Atpase, PDB code: 7qc0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Cadmium Translocating P-Type Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Cadmium Translocating P-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:83.1 occ:1.00 F1 A:BEF701 0.0 83.1 1.0 BE A:BEF701 1.5 86.3 1.0 OD1 A:ASP369 2.2 93.4 1.0 OG A:SER525 2.5 84.7 1.0 F3 A:BEF701 2.5 88.0 1.0 F2 A:BEF701 2.6 80.1 1.0 N A:THR371 2.6 86.7 1.0 N A:LYS370 3.0 84.7 1.0 CG A:ASP369 3.2 92.8 1.0 CB A:SER525 3.3 80.2 1.0 CB A:LYS370 3.3 80.2 1.0 CA A:LYS370 3.4 84.8 1.0 C A:LYS370 3.4 83.3 1.0 CB A:THR371 3.6 85.7 1.0 OG1 A:THR371 3.6 96.5 1.0 CA A:SER525 3.6 81.5 1.0 OD2 A:ASP369 3.6 92.1 1.0 CA A:THR371 3.7 80.6 1.0 N A:GLY526 4.0 76.9 1.0 C A:ASP369 4.1 92.3 1.0 MG A:MG702 4.1 83.2 1.0 C A:SER525 4.3 80.1 1.0 CB A:ASP369 4.4 92.7 1.0 CA A:ASP369 4.4 90.8 1.0 O A:THR371 4.4 90.3 1.0 NZ A:LYS553 4.5 81.0 1.0 CG A:LYS370 4.5 75.2 1.0 C A:THR371 4.5 85.7 1.0 CE A:LYS370 4.6 83.7 1.0 O A:LYS370 4.6 84.7 1.0 NZ A:LYS370 4.6 94.7 1.0 O A:ILE524 4.7 86.7 1.0 N A:ASP527 4.8 81.4 1.0 N A:SER525 4.8 80.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Cadmium Translocating P-Type Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Cadmium Translocating P-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:80.1 occ:1.00 F2 A:BEF701 0.0 80.1 1.0 BE A:BEF701 1.6 86.3 1.0 F3 A:BEF701 2.5 88.0 1.0 OD1 A:ASP369 2.5 93.4 1.0 F1 A:BEF701 2.6 83.1 1.0 NZ A:LYS553 2.8 81.0 1.0 N A:GLY526 2.9 76.9 1.0 ND2 A:ASN574 3.1 89.2 1.0 CG A:ASP369 3.6 92.8 1.0 CA A:SER525 3.7 81.5 1.0 OG A:SER525 3.7 84.7 1.0 C A:SER525 3.7 80.1 1.0 CE A:LYS553 3.7 79.6 1.0 CA A:GLY526 3.7 81.6 1.0 O A:THR206 3.8 74.2 1.0 MG A:MG702 4.0 83.2 1.0 OD2 A:ASP369 4.1 92.1 1.0 CG A:ASN574 4.1 85.3 1.0 CB A:SER525 4.3 80.2 1.0 OD1 A:ASN574 4.3 88.7 1.0 CA A:GLY207 4.4 78.5 1.0 OD1 A:ASP575 4.4 88.9 1.0 O A:ILE524 4.5 86.7 1.0 N A:ASP527 4.6 81.4 1.0 C A:THR206 4.6 78.4 1.0 C A:GLY526 4.6 80.0 1.0 N A:GLY207 4.8 78.9 1.0 CB A:ASP369 4.8 92.7 1.0 N A:SER525 4.9 80.1 1.0 O A:SER525 4.9 91.3 1.0 N A:THR371 4.9 86.7 1.0 N A:LYS370 4.9 84.7 1.0 O A:HOH805 5.0 87.0 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Cadmium Translocating P-Type Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Cadmium Translocating P-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:88.0 occ:1.00 F3 A:BEF701 0.0 88.0 1.0 BE A:BEF701 1.5 86.3 1.0 MG A:MG702 1.9 83.2 1.0 F2 A:BEF701 2.5 80.1 1.0 F1 A:BEF701 2.5 83.1 1.0 OD1 A:ASP369 2.5 93.4 1.0 OD2 A:ASP369 2.6 92.1 1.0 O A:HOH805 2.9 87.0 1.0 CG A:ASP369 2.9 92.8 1.0 O A:THR371 3.2 90.3 1.0 CB A:THR371 3.3 85.7 1.0 N A:THR371 3.4 86.7 1.0 CA A:THR371 3.7 80.6 1.0 C A:THR371 3.9 85.7 1.0 OD1 A:ASP571 3.9 92.4 1.0 O A:GLY207 3.9 91.5 1.0 CA A:GLY207 4.0 78.5 1.0 OG1 A:THR371 4.1 96.5 1.0 CG2 A:THR371 4.3 85.2 1.0 C A:GLY207 4.3 80.2 1.0 ND2 A:ASN574 4.4 89.2 1.0 CB A:ASP369 4.4 92.7 1.0 C A:LYS370 4.5 83.3 1.0 OD1 A:ASN574 4.6 88.7 1.0 NZ A:LYS553 4.6 81.0 1.0 OD2 A:ASP575 4.6 97.8 1.0 N A:LYS370 4.6 84.7 1.0 OG A:SER525 4.7 84.7 1.0 O A:THR206 4.8 74.2 1.0 CG A:ASP571 4.9 94.1 1.0 CG A:ASN574 4.9 85.3 1.0

C.Gronberg, Q.Hu, D.R.Mahato, E.Longhin, N.Salustros, A.Duelli, P.Lyu, V.Bagenholm, J.Eriksson, K.U.Rao, D.I.Henderson, G.Meloni, M.Andersson, T.Croll, G.Godaly, K.Wang, P.Gourdon. Structure and Ion-Release Mechanism of P Ib-4 -Type Atpases. Elife V. 10 2021.
ISSN: ESSN 2050-084X
PubMed: 34951590
DOI: 10.7554/ELIFE.73124