Calcium in PDB 6qm5: Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm

The binding sites of Calcium atom in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm (pdb code 6qm5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm, PDB code: 6qm5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:28.1 occ:1.00 OD1 A:ASP503 2.5 29.0 1.0 OE2 A:GLU535 2.5 28.7 1.0 OD2 A:ASP539 2.5 31.0 1.0 OE2 A:GLU452 2.5 37.2 1.0 OE1 A:GLU506 2.7 29.5 1.0 CG A:ASP503 3.0 29.0 1.0 OD1 A:ASP539 3.2 31.0 1.0 CG A:ASP539 3.2 31.0 1.0 CB A:ASP503 3.4 29.0 1.0 OH A:TYR188 3.4 25.4 1.0 CD A:GLU535 3.6 28.7 1.0 CD A:GLU452 3.6 37.2 1.0 CD A:GLU506 3.8 29.5 1.0 CA A:ASP503 3.8 29.0 1.0 OD2 A:ASP503 3.9 29.0 1.0 O A:ASP503 4.0 29.0 1.0 OE1 A:GLU452 4.1 37.2 1.0 CG A:GLU535 4.1 28.7 1.0 CB A:GLU506 4.2 29.5 1.0 C A:ASP503 4.4 29.0 1.0 CZ A:TYR188 4.4 25.4 1.0 OE2 A:GLU506 4.5 29.5 1.0 CG A:GLU506 4.6 29.5 1.0 NZ A:LYS542 4.6 33.7 1.0 OE1 A:GLU535 4.6 28.7 1.0 CE A:MET507 4.7 26.0 1.0 CB A:ASP539 4.7 31.0 1.0 CG A:GLU452 4.9 37.2 1.0 N A:ASP503 5.0 29.0 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:39.3 occ:1.00 OE1 A:GLU535 2.5 28.7 1.0 OD1 A:ASN448 2.5 34.3 1.0 OE2 A:GLU506 2.6 29.5 1.0 OE1 A:GLU452 3.0 37.2 1.0 CD A:GLU535 3.3 28.7 1.0 OE2 A:GLU535 3.4 28.7 1.0 CG A:ASN448 3.5 34.3 1.0 CD A:GLU506 3.5 29.5 1.0 OE1 A:GLU506 3.8 29.5 1.0 CB A:ASN448 3.8 34.3 1.0 N A:PHE449 4.0 36.3 1.0 C A:ASN448 4.0 34.3 1.0 CD A:GLU452 4.1 37.2 1.0 O A:ASN448 4.2 34.3 1.0 O A:GLN445 4.2 32.1 1.0 ND2 A:ASN531 4.3 29.6 1.0 CA A:PHE449 4.3 36.3 1.0 OE1 A:GLN445 4.4 32.1 1.0 OD1 A:ASN531 4.6 29.6 1.0 CA A:ASN448 4.6 34.3 1.0 CB A:PHE449 4.6 36.3 1.0 ND2 A:ASN448 4.6 34.3 1.0 OE2 A:GLU452 4.7 37.2 1.0 CG A:GLU535 4.7 28.7 1.0 CG A:ASN531 4.9 29.6 1.0 CG A:GLU506 4.9 29.5 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:28.1 occ:1.00 OD1 B:ASP503 2.5 29.0 1.0 OE2 B:GLU535 2.5 28.7 1.0 OD2 B:ASP539 2.5 31.0 1.0 OE2 B:GLU452 2.5 37.2 1.0 OE1 B:GLU506 2.7 29.5 1.0 CG B:ASP503 3.0 29.0 1.0 OD1 B:ASP539 3.2 31.0 1.0 CG B:ASP539 3.2 31.0 1.0 CB B:ASP503 3.4 29.0 1.0 OH B:TYR188 3.4 25.4 1.0 CD B:GLU535 3.6 28.7 1.0 CD B:GLU452 3.6 37.2 1.0 CD B:GLU506 3.8 29.5 1.0 CA B:ASP503 3.8 29.0 1.0 OD2 B:ASP503 3.9 29.0 1.0 O B:ASP503 4.0 29.0 1.0 OE1 B:GLU452 4.1 37.2 1.0 CG B:GLU535 4.1 28.7 1.0 CB B:GLU506 4.2 29.5 1.0 C B:ASP503 4.4 29.0 1.0 CZ B:TYR188 4.4 25.4 1.0 OE2 B:GLU506 4.5 29.5 1.0 CG B:GLU506 4.6 29.5 1.0 NZ B:LYS542 4.6 33.7 1.0 OE1 B:GLU535 4.6 28.7 1.0 CE B:MET507 4.7 26.0 1.0 CB B:ASP539 4.7 31.0 1.0 CG B:GLU452 4.9 37.2 1.0 N B:ASP503 5.0 29.0 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Ddm within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:39.3 occ:1.00 OE1 B:GLU535 2.5 28.7 1.0 OD1 B:ASN448 2.5 34.3 1.0 OE2 B:GLU506 2.6 29.5 1.0 OE1 B:GLU452 3.0 37.2 1.0 CD B:GLU535 3.3 28.7 1.0 OE2 B:GLU535 3.4 28.7 1.0 CG B:ASN448 3.5 34.3 1.0 CD B:GLU506 3.5 29.5 1.0 OE1 B:GLU506 3.8 29.5 1.0 CB B:ASN448 3.8 34.3 1.0 N B:PHE449 4.0 36.3 1.0 C B:ASN448 4.0 34.3 1.0 CD B:GLU452 4.1 37.2 1.0 O B:ASN448 4.2 34.3 1.0 O B:GLN445 4.2 32.1 1.0 ND2 B:ASN531 4.3 29.6 1.0 CA B:PHE449 4.3 36.3 1.0 OE1 B:GLN445 4.4 32.1 1.0 OD1 B:ASN531 4.6 29.6 1.0 CA B:ASN448 4.6 34.3 1.0 CB B:PHE449 4.6 36.3 1.0 ND2 B:ASN448 4.6 34.3 1.0 OE2 B:GLU452 4.7 37.2 1.0 CG B:GLU535 4.7 28.7 1.0 CG B:ASN531 4.9 29.6 1.0 CG B:GLU506 4.9 29.5 1.0

V.Kalienkova, V.Clerico Mosina, L.Bryner, G.T.Oostergetel, R.Dutzler, C.Paulino. Stepwise Activation Mechanism of the Scramblase NHTMEM16 Revealed By Cryo-Em. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 30785398
DOI: 10.7554/ELIFE.44364