Calcium in PDB 4wit: TMEM16 Lipid Scramblase in Crystal Form 2

The structure of TMEM16 Lipid Scramblase in Crystal Form 2, PDB code: 4wit was solved by R.Dutzler, J.D.Brunner, N.K.Lim, S.Schenck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 3.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.940, 127.240, 180.110, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 29.2

The binding sites of Calcium atom in the TMEM16 Lipid Scramblase in Crystal Form 2 (pdb code 4wit). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the TMEM16 Lipid Scramblase in Crystal Form 2, PDB code: 4wit:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the TMEM16 Lipid Scramblase in Crystal Form 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of TMEM16 Lipid Scramblase in Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:0.7 occ:1.00 OE2 A:GLU506 2.5 0.1 1.0 OD2 A:ASP539 2.5 0.1 1.0 OE1 A:GLU452 2.5 0.7 1.0 OE2 A:GLU535 2.5 0.9 1.0 OD1 A:ASP503 2.6 0.5 1.0 OD1 A:ASP539 2.6 0.6 1.0 CG A:ASP539 2.9 0.2 1.0 CG A:ASP503 3.3 0.1 1.0 CD A:GLU506 3.3 0.1 1.0 CD A:GLU452 3.4 0.8 1.0 OE2 A:GLU452 3.5 0.9 1.0 CD A:GLU535 3.6 0.4 1.0 OH A:TYR188 3.6 0.5 1.0 OE1 A:GLU506 3.8 0.3 1.0 CB A:ASP503 3.8 0.4 1.0 CA A:ASP503 3.8 0.8 1.0 CG A:GLU535 4.0 0.5 1.0 OD2 A:ASP503 4.2 0.1 1.0 O A:ASP503 4.3 96.8 1.0 CB A:ASP539 4.4 0.6 1.0 CG A:GLU506 4.4 0.6 1.0 CB A:GLU506 4.4 0.0 1.0 NZ A:LYS542 4.5 0.3 1.0 CA A:CA802 4.6 0.8 1.0 OE1 A:GLU535 4.6 0.1 1.0 C A:ASP503 4.6 0.2 1.0 CZ A:TYR188 4.7 0.9 1.0 CG A:GLU452 4.8 0.1 1.0 N A:ASP503 4.9 0.9 1.0 SD A:MET507 5.0 0.0 1.0 CE A:LYS542 5.0 0.5 1.0

Calcium binding site 2 out of 4 in the TMEM16 Lipid Scramblase in Crystal Form 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of TMEM16 Lipid Scramblase in Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:0.8 occ:1.00 OE1 A:GLU535 2.5 0.1 1.0 OE1 A:GLU506 2.5 0.3 1.0 OE2 A:GLU452 2.6 0.9 1.0 OE2 A:GLU535 2.7 0.9 1.0 CD A:GLU535 3.0 0.4 1.0 OD1 A:ASN448 3.2 0.0 1.0 CG A:ASN448 3.3 0.2 1.0 CD A:GLU506 3.6 0.1 1.0 ND2 A:ASN448 3.6 0.5 1.0 CD1 A:PHE449 3.6 0.7 1.0 CE1 A:PHE449 3.6 0.5 1.0 CD A:GLU452 3.8 0.8 1.0 OE2 A:GLU506 3.9 0.1 1.0 CB A:ASN448 4.1 0.5 1.0 C A:ASN448 4.4 0.9 1.0 OE1 A:GLU452 4.5 0.7 1.0 CG A:GLU535 4.5 0.5 1.0 N A:PHE449 4.5 1.0 1.0 O A:ASN448 4.6 0.2 1.0 CA A:CA801 4.6 0.7 1.0 OD1 A:ASN531 4.6 0.8 1.0 ND2 A:ASN531 4.6 0.3 1.0 OG A:SER538 4.6 1.0 1.0 CB A:GLU452 4.7 0.3 1.0 CA A:PHE449 4.8 0.6 1.0 CG A:GLU452 4.8 0.1 1.0 CG A:PHE449 4.9 0.5 1.0 CZ A:PHE449 4.9 0.9 1.0 CG A:GLU506 4.9 0.6 1.0 CA A:ASN448 4.9 0.4 1.0

Calcium binding site 3 out of 4 in the TMEM16 Lipid Scramblase in Crystal Form 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of TMEM16 Lipid Scramblase in Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:0.8 occ:1.00 OE2 B:GLU506 2.5 0.6 1.0 OD2 B:ASP539 2.5 0.2 1.0 OD1 B:ASP503 2.6 0.2 1.0 OE2 B:GLU535 2.6 0.4 1.0 OE1 B:GLU452 2.6 0.9 1.0 OD1 B:ASP539 2.7 0.6 1.0 CG B:ASP539 2.9 0.6 1.0 CG B:ASP503 3.3 0.6 1.0 CD B:GLU506 3.3 0.9 1.0 CD B:GLU452 3.5 0.5 1.0 OH B:TYR188 3.6 0.4 1.0 CD B:GLU535 3.6 0.9 1.0 OE2 B:GLU452 3.6 0.4 1.0 CB B:ASP503 3.7 0.9 1.0 CA B:ASP503 3.8 0.7 1.0 OE1 B:GLU506 3.8 0.8 1.0 CG B:GLU535 4.0 1.0 1.0 OD2 B:ASP503 4.1 0.2 1.0 O B:ASP503 4.3 0.4 1.0 CB B:GLU506 4.4 0.1 1.0 CG B:GLU506 4.4 1.0 1.0 CB B:ASP539 4.4 0.8 1.0 NZ B:LYS542 4.5 0.3 1.0 C B:ASP503 4.5 0.8 1.0 CA B:CA802 4.6 0.7 1.0 OE1 B:GLU535 4.6 0.4 1.0 CZ B:TYR188 4.6 0.8 1.0 N B:ASP503 4.8 0.8 1.0 CG B:GLU452 4.9 0.8 1.0 SD B:MET507 4.9 0.4 1.0 CE B:LYS542 5.0 0.2 1.0

Calcium binding site 4 out of 4 in the TMEM16 Lipid Scramblase in Crystal Form 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of TMEM16 Lipid Scramblase in Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:0.7 occ:1.00 OE1 B:GLU535 2.5 0.4 1.0 OE2 B:GLU452 2.5 0.4 1.0 OE2 B:GLU535 2.6 0.4 1.0 OE1 B:GLU506 2.8 0.8 1.0 CD B:GLU535 2.9 0.9 1.0 OD1 B:ASN448 3.4 0.8 1.0 CD1 B:PHE449 3.4 0.6 1.0 CE1 B:PHE449 3.5 0.9 1.0 CG B:ASN448 3.6 0.7 1.0 CD B:GLU452 3.7 0.5 1.0 CD B:GLU506 3.8 0.9 1.0 ND2 B:ASN448 3.9 0.6 1.0 OE2 B:GLU506 4.1 0.6 1.0 CB B:ASN448 4.3 1.0 1.0 OG B:SER538 4.3 0.7 1.0 CG B:GLU535 4.4 1.0 1.0 OE1 B:GLU452 4.4 0.9 1.0 N B:PHE449 4.5 0.9 1.0 C B:ASN448 4.5 0.6 1.0 CB B:GLU452 4.6 1.0 1.0 O B:ASN448 4.6 0.8 1.0 CA B:CA801 4.6 0.8 1.0 CA B:PHE449 4.7 0.1 1.0 CG B:PHE449 4.7 0.8 1.0 OD1 B:ASN531 4.7 0.5 1.0 CG B:GLU452 4.7 0.8 1.0 CZ B:PHE449 4.8 0.8 1.0 ND2 B:ASN531 4.8 0.5 1.0

J.D.Brunner, N.K.Lim, S.Schenck, A.Duerst, R.Dutzler. X-Ray Structure of A Calcium-Activated TMEM16 Lipid Scramblase. Nature 2014.
ISSN: ESSN 1476-4687
PubMed: 25383531
DOI: 10.1038/NATURE13984