Fluorine in PDB 3rfu: Crystal Structure of A Copper-Transporting Pib-Type Atpase

The structure of Crystal Structure of A Copper-Transporting Pib-Type Atpase, PDB code: 3rfu was solved by P.Gourdon, X.Liu, T.Skjorringe, J.P.Morth, L.Birk Moller, B.Panyellapedersen, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.150, 72.980, 329.950, 89.96, 90.04, 90.22
R / Rfree (%)	23.5 / 26.1

The structure of Crystal Structure of A Copper-Transporting Pib-Type Atpase also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Aluminium	(Al)	4 atoms
Potassium	(K)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of A Copper-Transporting Pib-Type Atpase (pdb code 3rfu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Crystal Structure of A Copper-Transporting Pib-Type Atpase, PDB code: 3rfu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in the Crystal Structure of A Copper-Transporting Pib-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 A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F995 b:51.0 occ:1.00 F1 A:ALF995 0.0 51.0 1.0 AL A:ALF995 1.8 0.4 1.0 F4 A:ALF995 2.5 37.0 1.0 F3 A:ALF995 2.6 52.0 1.0 O A:THR277 2.6 0.4 1.0 ND2 A:ASN627 2.7 0.0 1.0 OD1 A:ASP426 3.1 0.5 1.0 C A:THR277 3.3 0.8 1.0 N A:GLY578 3.5 58.9 1.0 F2 A:ALF995 3.6 60.1 1.0 CA A:THR277 3.7 0.6 1.0 CG A:ASN627 3.8 0.4 1.0 OG1 A:THR577 4.0 92.4 1.0 CG A:ASP426 4.2 86.3 1.0 N A:GLY278 4.2 0.9 1.0 CA A:THR577 4.2 98.2 1.0 OD1 A:ASN627 4.2 1.0 1.0 O A:GLY578 4.3 94.4 1.0 CA A:GLY578 4.4 81.6 1.0 C A:THR577 4.4 78.2 1.0 N A:THR277 4.4 0.8 1.0 CB A:THR577 4.6 89.3 1.0 OD2 A:ASP426 4.7 74.4 1.0 CA A:GLY278 4.7 0.2 1.0 NZ A:LYS605 4.7 0.8 1.0 OD2 A:ASP628 4.7 53.1 1.0 C A:GLY578 4.8 94.1 1.0 OG1 A:THR428 4.9 87.8 1.0 CB A:THR277 4.9 0.3 1.0 CG2 A:THR277 5.0 0.3 1.0 MG A:MG996 5.0 68.2 1.0

Fluorine binding site 2 out of 16 in the Crystal Structure of A Copper-Transporting Pib-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 A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F995 b:60.1 occ:1.00 F2 A:ALF995 0.0 60.1 1.0 AL A:ALF995 1.8 0.4 1.0 O A:THR428 2.2 87.2 1.0 OD2 A:ASP426 2.2 74.4 1.0 F3 A:ALF995 2.5 52.0 1.0 F4 A:ALF995 2.5 37.0 1.0 MG A:MG996 2.6 68.2 1.0 OD1 A:ASP426 2.7 0.5 1.0 N A:THR428 2.7 90.3 1.0 CG A:ASP426 2.8 86.3 1.0 C A:THR428 2.9 0.0 1.0 CA A:THR428 2.9 99.1 1.0 CB A:THR428 3.1 98.5 1.0 F1 A:ALF995 3.6 51.0 1.0 C A:LYS427 3.7 87.6 1.0 OG1 A:THR428 3.7 87.8 1.0 N A:LYS427 3.9 92.6 1.0 OD1 A:ASP624 3.9 0.5 1.0 N A:GLY429 4.2 0.6 1.0 CB A:ASP426 4.3 61.1 1.0 CG2 A:THR428 4.3 0.7 1.0 CA A:LYS427 4.3 92.9 1.0 O A:THR277 4.4 0.4 1.0 O A:LYS427 4.5 84.4 1.0 C A:ASP426 4.7 88.1 1.0 CG2 A:THR430 4.7 79.4 1.0 O A:GLY278 4.7 0.7 1.0 OD2 A:ASP628 4.9 53.1 1.0 CG A:LYS427 4.9 0.7 1.0 O A:ASP624 4.9 59.1 1.0 CA A:GLY429 4.9 0.3 1.0 N A:THR430 5.0 86.0 1.0 OG1 A:THR430 5.0 68.8 1.0

Fluorine binding site 3 out of 16 in the Crystal Structure of A Copper-Transporting Pib-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 A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F995 b:52.0 occ:1.00 F3 A:ALF995 0.0 52.0 1.0 AL A:ALF995 1.8 0.4 1.0 F2 A:ALF995 2.5 60.1 1.0 F1 A:ALF995 2.6 51.0 1.0 OD1 A:ASN627 2.8 1.0 1.0 MG A:MG996 2.8 68.2 1.0 ND2 A:ASN627 2.9 0.0 1.0 OD1 A:ASP426 3.0 0.5 1.0 CG A:ASN627 3.2 0.4 1.0 OD2 A:ASP628 3.3 53.1 1.0 OD2 A:ASP426 3.4 74.4 1.0 CG A:ASP426 3.5 86.3 1.0 O A:THR277 3.5 0.4 1.0 F4 A:ALF995 3.6 37.0 1.0 O A:ASP624 3.6 59.1 1.0 CA A:GLY278 4.0 0.2 1.0 C A:THR277 4.0 0.8 1.0 N A:GLY278 4.2 0.9 1.0 O A:THR428 4.2 87.2 1.0 OD1 A:ASP624 4.4 0.5 1.0 CG A:ASP628 4.5 95.3 1.0 O A:GLY278 4.6 0.7 1.0 CB A:ASN627 4.7 0.0 1.0 C A:GLY278 4.7 0.4 1.0 CB A:ASP426 4.8 61.1 1.0 C A:ASP624 4.8 91.8 1.0 CB A:THR428 4.9 98.5 1.0

Fluorine binding site 4 out of 16 in the Crystal Structure of A Copper-Transporting Pib-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 of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:F995 b:37.0 occ:1.00 F4 A:ALF995 0.0 37.0 1.0 AL A:ALF995 1.8 0.4 1.0 F1 A:ALF995 2.5 51.0 1.0 F2 A:ALF995 2.5 60.1 1.0 OD1 A:ASP426 2.7 0.5 1.0 N A:THR428 2.9 90.3 1.0 OG1 A:THR577 3.0 92.4 1.0 OG1 A:THR428 3.0 87.8 1.0 CG A:LYS427 3.2 0.7 1.0 CB A:THR428 3.4 98.5 1.0 F3 A:ALF995 3.6 52.0 1.0 N A:LYS427 3.6 92.6 1.0 CG A:ASP426 3.6 86.3 1.0 CB A:THR577 3.6 89.3 1.0 CA A:THR428 3.7 99.1 1.0 O A:THR277 3.7 0.4 1.0 OD2 A:ASP426 3.9 74.4 1.0 C A:LYS427 3.9 87.6 1.0 CA A:LYS427 4.0 92.9 1.0 CB A:LYS427 4.1 0.9 1.0 CA A:THR577 4.2 98.2 1.0 N A:GLY578 4.3 58.9 1.0 CD A:LYS427 4.4 1.0 1.0 O A:THR428 4.4 87.2 1.0 O A:GLY578 4.5 94.4 1.0 C A:THR428 4.6 0.0 1.0 OE2 A:GLU279 4.7 0.0 1.0 C A:ASP426 4.7 88.1 1.0 C A:THR577 4.8 78.2 1.0 O A:LEU576 4.8 0.2 1.0 C A:THR277 4.9 0.8 1.0 CB A:ASP426 4.9 61.1 1.0 MG A:MG996 4.9 68.2 1.0 CG2 A:THR428 4.9 0.7 1.0

Fluorine binding site 5 out of 16 in the Crystal Structure of A Copper-Transporting Pib-Type Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:F995 b:60.1 occ:1.00 F1 B:ALF995 0.0 60.1 1.0 AL B:ALF995 1.8 0.1 1.0 F4 B:ALF995 2.5 48.9 1.0 F3 B:ALF995 2.5 63.5 1.0 ND2 B:ASN627 2.7 0.2 1.0 O B:THR277 2.9 0.2 1.0 OD1 B:ASP426 3.0 0.8 1.0 N B:GLY578 3.4 57.6 1.0 C B:THR277 3.5 0.5 1.0 F2 B:ALF995 3.6 80.2 1.0 CA B:THR277 3.8 1.0 1.0 CG B:ASN627 3.8 1.0 1.0 OG1 B:THR577 4.0 92.0 1.0 CA B:THR577 4.0 98.2 1.0 CG B:ASP426 4.1 86.9 1.0 C B:THR577 4.2 78.7 1.0 OD1 B:ASN627 4.2 0.3 1.0 CA B:GLY578 4.3 82.9 1.0 O B:GLY578 4.4 93.1 1.0 N B:GLY278 4.4 0.5 1.0 NZ B:LYS605 4.4 0.6 1.0 CB B:THR577 4.4 90.1 1.0 N B:THR277 4.5 0.1 1.0 OD2 B:ASP628 4.6 57.5 1.0 OD2 B:ASP426 4.7 77.1 1.0 C B:GLY578 4.8 93.6 1.0 CA B:GLY278 4.9 0.0 1.0

Fluorine binding site 6 out of 16 in the Crystal Structure of A Copper-Transporting Pib-Type Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:F995 b:80.2 occ:1.00 F2 B:ALF995 0.0 80.2 1.0 AL B:ALF995 1.8 0.1 1.0 O B:THR428 2.3 86.3 1.0 OD2 B:ASP426 2.3 77.1 1.0 F3 B:ALF995 2.5 63.5 1.0 F4 B:ALF995 2.5 48.9 1.0 MG B:MG996 2.6 67.2 1.0 N B:THR428 2.7 91.6 1.0 OD1 B:ASP426 2.7 0.8 1.0 CG B:ASP426 2.9 86.9 1.0 CA B:THR428 2.9 99.4 1.0 CB B:THR428 3.0 98.7 1.0 C B:THR428 3.0 0.8 1.0 F1 B:ALF995 3.6 60.1 1.0 OG1 B:THR428 3.6 84.6 1.0 C B:LYS427 3.8 87.8 1.0 N B:LYS427 4.0 92.5 1.0 OD1 B:ASP624 4.1 0.5 1.0 O B:THR277 4.2 0.2 1.0 N B:GLY429 4.3 0.8 1.0 CG2 B:THR428 4.3 0.6 1.0 CB B:ASP426 4.4 59.9 1.0 CA B:LYS427 4.4 92.0 1.0 O B:GLY278 4.6 0.5 1.0 O B:LYS427 4.6 86.4 1.0 C B:ASP426 4.8 89.0 1.0 CG B:LYS427 4.8 0.5 1.0 CG2 B:THR430 4.9 79.9 1.0 OD2 B:ASP628 4.9 57.5 1.0 O B:ASP624 5.0 66.1 1.0

Fluorine binding site 7 out of 16 in the Crystal Structure of A Copper-Transporting Pib-Type Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:F995 b:63.5 occ:1.00 F3 B:ALF995 0.0 63.5 1.0 AL B:ALF995 1.8 0.1 1.0 F2 B:ALF995 2.5 80.2 1.0 F1 B:ALF995 2.5 60.1 1.0 OD1 B:ASN627 2.7 0.3 1.0 ND2 B:ASN627 2.8 0.2 1.0 MG B:MG996 2.9 67.2 1.0 OD1 B:ASP426 3.1 0.8 1.0 CG B:ASN627 3.1 1.0 1.0 O B:THR277 3.4 0.2 1.0 OD2 B:ASP628 3.4 57.5 1.0 OD2 B:ASP426 3.5 77.1 1.0 CG B:ASP426 3.5 86.9 1.0 F4 B:ALF995 3.6 48.9 1.0 O B:ASP624 3.7 66.1 1.0 C B:THR277 3.9 0.5 1.0 CA B:GLY278 3.9 0.0 1.0 N B:GLY278 4.1 0.5 1.0 O B:THR428 4.3 86.3 1.0 OD1 B:ASP624 4.5 0.5 1.0 CG B:ASP628 4.5 99.0 1.0 O B:GLY278 4.6 0.5 1.0 CB B:ASN627 4.6 0.2 1.0 C B:GLY278 4.7 0.6 1.0 CB B:ASP426 4.8 59.9 1.0 C B:ASP624 4.9 92.2 1.0 CA B:THR277 4.9 1.0 1.0 CB B:THR428 4.9 98.7 1.0

Fluorine binding site 8 out of 16 in the Crystal Structure of A Copper-Transporting Pib-Type Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:F995 b:48.9 occ:1.00 F4 B:ALF995 0.0 48.9 1.0 AL B:ALF995 1.8 0.1 1.0 F1 B:ALF995 2.5 60.1 1.0 F2 B:ALF995 2.5 80.2 1.0 OD1 B:ASP426 2.7 0.8 1.0 OG1 B:THR577 2.8 92.0 1.0 N B:THR428 3.1 91.6 1.0 OG1 B:THR428 3.1 84.6 1.0 CG B:LYS427 3.2 0.5 1.0 CB B:THR577 3.5 90.1 1.0 F3 B:ALF995 3.6 63.5 1.0 N B:LYS427 3.6 92.5 1.0 CG B:ASP426 3.6 86.9 1.0 CB B:THR428 3.6 98.7 1.0 O B:THR277 3.8 0.2 1.0 CA B:THR428 3.9 99.4 1.0 OD2 B:ASP426 3.9 77.1 1.0 CA B:THR577 4.0 98.2 1.0 C B:LYS427 4.0 87.8 1.0 CA B:LYS427 4.0 92.0 1.0 N B:GLY578 4.1 57.6 1.0 CB B:LYS427 4.1 0.2 1.0 CD B:LYS427 4.3 0.5 1.0 O B:GLY578 4.4 93.1 1.0 C B:THR577 4.6 78.7 1.0 O B:THR428 4.6 86.3 1.0 O B:LEU576 4.7 0.2 1.0 C B:ASP426 4.7 89.0 1.0 OE2 B:GLU279 4.7 0.8 1.0 C B:THR428 4.8 0.8 1.0 CB B:ASP426 4.9 59.9 1.0 CG2 B:THR577 4.9 54.3 1.0 C B:THR277 4.9 0.5 1.0 MG B:MG996 5.0 67.2 1.0

Fluorine binding site 9 out of 16 in the Crystal Structure of A Copper-Transporting Pib-Type Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ C:F995 b:62.0 occ:1.00 F1 C:ALF995 0.0 62.0 1.0 AL C:ALF995 1.8 0.9 1.0 F4 C:ALF995 2.5 45.2 1.0 F3 C:ALF995 2.5 57.9 1.0 O C:THR277 2.8 0.6 1.0 ND2 C:ASN627 2.8 0.5 1.0 OD1 C:ASP426 3.0 0.1 1.0 N C:GLY578 3.3 58.3 1.0 C C:THR277 3.4 0.1 1.0 F2 C:ALF995 3.6 61.7 1.0 CA C:THR277 3.8 0.7 1.0 OG1 C:THR577 3.8 96.4 1.0 CA C:THR577 3.9 96.1 1.0 CG C:ASN627 4.0 0.3 1.0 C C:THR577 4.1 76.8 1.0 CG C:ASP426 4.2 86.8 1.0 CA C:GLY578 4.2 81.1 1.0 O C:GLY578 4.2 94.3 1.0 CB C:THR577 4.3 88.9 1.0 OD1 C:ASN627 4.4 0.0 1.0 N C:GLY278 4.4 0.6 1.0 N C:THR277 4.5 0.6 1.0 NZ C:LYS605 4.5 0.7 1.0 C C:GLY578 4.7 92.0 1.0 OD2 C:ASP426 4.7 80.3 1.0 OD2 C:ASP628 4.8 56.8 1.0 CA C:GLY278 4.9 0.1 1.0 OG1 C:THR428 5.0 83.9 1.0 CG2 C:THR277 5.0 0.2 1.0

Fluorine binding site 10 out of 16 in the Crystal Structure of A Copper-Transporting Pib-Type Atpase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ C:F995 b:61.7 occ:1.00 F2 C:ALF995 0.0 61.7 1.0 AL C:ALF995 1.8 0.9 1.0 O C:THR428 2.3 83.0 1.0 OD2 C:ASP426 2.3 80.3 1.0 F3 C:ALF995 2.5 57.9 1.0 F4 C:ALF995 2.5 45.2 1.0 MG C:MG996 2.6 58.3 1.0 OD1 C:ASP426 2.7 0.1 1.0 N C:THR428 2.7 93.1 1.0 CG C:ASP426 2.8 86.8 1.0 C C:THR428 2.9 0.5 1.0 CA C:THR428 3.0 99.3 1.0 CB C:THR428 3.0 98.0 1.0 F1 C:ALF995 3.6 62.0 1.0 OG1 C:THR428 3.6 83.9 1.0 C C:LYS427 3.7 88.0 1.0 N C:LYS427 3.9 93.2 1.0 OD1 C:ASP624 4.1 0.1 1.0 O C:THR277 4.2 0.6 1.0 N C:GLY429 4.2 0.4 1.0 CB C:ASP426 4.3 58.2 1.0 CG2 C:THR428 4.3 0.9 1.0 CA C:LYS427 4.4 93.5 1.0 O C:LYS427 4.6 86.0 1.0 O C:GLY278 4.6 0.5 1.0 C C:ASP426 4.7 88.9 1.0 CG C:LYS427 4.8 0.5 1.0 CG2 C:THR430 4.8 80.1 1.0 OD2 C:ASP628 4.9 56.8 1.0 O C:ASP624 4.9 63.4 1.0

P.Gourdon, X.Y.Liu, T.Skjorringe, J.P.Morth, L.B.Moller, B.P.Pedersen, P.Nissen. Crystal Structure of A Copper-Transporting Pib-Type Atpase. Nature V. 475 59 2011.
ISSN: ISSN 0028-0836
PubMed: 21716286
DOI: 10.1038/NATURE10191