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

The structure of Crystal Structure Cadmium Translocating P-Type Atpase, PDB code: 7qbz 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)	45.57 / 3.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.642, 93.665, 128.258, 90, 90, 90
R / Rfree (%)	21.8 / 25.5

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

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

The binding sites of Fluorine atom in the Crystal Structure Cadmium Translocating P-Type Atpase (pdb code 7qbz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure Cadmium Translocating P-Type Atpase, PDB code: 7qbz:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure 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 Cadmium Translocating P-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:82.8 occ:1.00 F1 A:ALF701 0.0 82.8 1.0 AL A:ALF701 1.8 84.5 1.0 F4 A:ALF701 2.5 100.5 1.0 F3 A:ALF701 2.6 89.0 1.0 OD1 A:ASP369 2.6 92.8 1.0 CA A:GLY207 3.1 85.5 1.0 OD1 A:ASN574 3.1 78.4 1.0 MG A:MG702 3.2 80.9 1.0 ND2 A:ASN574 3.3 104.5 1.0 CG A:ASP369 3.3 96.1 1.0 NZ A:LYS553 3.5 88.7 1.0 OD2 A:ASP369 3.5 90.7 1.0 O A:THR206 3.5 74.5 1.0 F2 A:ALF701 3.6 81.2 1.0 CG A:ASN574 3.6 100.2 1.0 N A:GLY207 3.8 57.4 1.0 OD2 A:ASP575 3.9 96.9 1.0 C A:GLY207 4.0 85.0 1.0 OD1 A:ASP575 4.0 91.2 1.0 C A:THR206 4.0 74.0 1.0 O A:GLY207 4.2 79.3 1.0 CG A:ASP575 4.3 99.0 1.0 CB A:ASP369 4.6 91.0 1.0 CE A:LYS553 4.7 102.4 1.0 N A:GLY526 4.8 76.5 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure 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 Cadmium Translocating P-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:81.2 occ:1.00 F2 A:ALF701 0.0 81.2 1.0 AL A:ALF701 1.8 84.5 1.0 OD1 A:ASP369 2.4 92.8 1.0 OG A:SER525 2.5 78.6 1.0 F3 A:ALF701 2.5 89.0 1.0 F4 A:ALF701 2.5 100.5 1.0 N A:LYS370 2.9 101.8 1.0 N A:THR371 3.0 80.0 1.0 CG A:ASP369 3.1 96.1 1.0 CB A:LYS370 3.3 69.5 1.0 CA A:LYS370 3.4 88.8 1.0 CB A:SER525 3.4 72.3 1.0 OD2 A:ASP369 3.4 90.7 1.0 F1 A:ALF701 3.6 82.8 1.0 C A:LYS370 3.6 75.1 1.0 CA A:SER525 3.9 82.5 1.0 C A:ASP369 4.0 104.1 1.0 OE2 A:GLU208 4.0 90.2 1.0 CA A:THR371 4.0 76.3 1.0 CB A:THR371 4.0 74.9 1.0 N A:GLY526 4.2 76.5 1.0 OG1 A:THR371 4.2 90.9 1.0 CB A:ASP369 4.2 91.0 1.0 CA A:ASP369 4.3 92.0 1.0 CE A:LYS370 4.5 73.8 1.0 O A:THR371 4.5 92.5 1.0 CG A:LYS370 4.5 72.0 1.0 C A:SER525 4.6 70.5 1.0 NZ A:LYS370 4.6 94.8 1.0 NZ A:LYS553 4.7 88.7 1.0 MG A:MG702 4.8 80.9 1.0 C A:THR371 4.8 81.9 1.0 O A:LYS370 4.8 81.6 1.0 N A:ASP527 4.8 92.2 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure 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 Cadmium Translocating P-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:89.0 occ:1.00 F3 A:ALF701 0.0 89.0 1.0 AL A:ALF701 1.8 84.5 1.0 OD2 A:ASP369 2.3 90.7 1.0 MG A:MG702 2.3 80.9 1.0 F2 A:ALF701 2.5 81.2 1.0 F1 A:ALF701 2.6 82.8 1.0 OD1 A:ASP369 2.6 92.8 1.0 O A:THR371 2.7 92.5 1.0 CG A:ASP369 2.8 96.1 1.0 N A:THR371 3.2 80.0 1.0 CB A:THR371 3.3 74.9 1.0 CA A:THR371 3.5 76.3 1.0 C A:THR371 3.5 81.9 1.0 F4 A:ALF701 3.6 100.5 1.0 O A:GLY207 3.7 79.3 1.0 OD1 A:ASP571 4.1 95.7 1.0 C A:LYS370 4.2 75.1 1.0 C A:GLY207 4.2 85.0 1.0 CA A:GLY207 4.2 85.5 1.0 CG2 A:THR371 4.2 79.4 1.0 OG1 A:THR371 4.2 90.9 1.0 N A:LYS370 4.2 101.8 1.0 OE2 A:GLU208 4.2 90.2 1.0 CB A:ASP369 4.3 91.0 1.0 CA A:LYS370 4.7 88.8 1.0 N A:GLY372 4.8 83.6 1.0 OD2 A:ASP575 4.8 96.9 1.0 OG A:SER525 4.9 78.6 1.0 O A:THR206 4.9 74.5 1.0 C A:ASP369 4.9 104.1 1.0 O A:LYS370 5.0 81.6 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure 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 4 of Crystal Structure Cadmium Translocating P-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:100.5 occ:1.00 F4 A:ALF701 0.0 100.5 1.0 AL A:ALF701 1.8 84.5 1.0 OD1 A:ASP369 2.3 92.8 1.0 F1 A:ALF701 2.5 82.8 1.0 F2 A:ALF701 2.5 81.2 1.0 N A:GLY526 2.6 76.5 1.0 NZ A:LYS553 2.6 88.7 1.0 CA A:SER525 3.1 82.5 1.0 OG A:SER525 3.2 78.6 1.0 C A:SER525 3.3 70.5 1.0 CE A:LYS553 3.5 102.4 1.0 F3 A:ALF701 3.6 89.0 1.0 CG A:ASP369 3.6 96.1 1.0 CA A:GLY526 3.6 80.3 1.0 CB A:SER525 3.7 72.3 1.0 O A:THR206 3.8 74.5 1.0 ND2 A:ASN574 4.1 104.5 1.0 O A:ILE524 4.2 82.5 1.0 OD2 A:ASP369 4.4 90.7 1.0 N A:SER525 4.4 75.0 1.0 N A:ASP527 4.4 92.2 1.0 O A:SER525 4.5 85.1 1.0 C A:GLY526 4.5 77.3 1.0 OD1 A:ASP575 4.5 91.2 1.0 CB A:ASP369 4.6 91.0 1.0 N A:LYS370 4.7 101.8 1.0 C A:ILE524 4.7 72.8 1.0 C A:THR206 4.7 74.0 1.0 CA A:ASP369 4.9 92.0 1.0 CG A:ASN574 4.9 100.2 1.0 CA A:GLY207 4.9 85.5 1.0 CD A:LYS553 4.9 102.6 1.0 OD1 A:ASN574 5.0 78.4 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