Calcium in PDB 6qma: Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Intermediate State)

The binding sites of Calcium atom in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Intermediate State) (pdb code 6qma). 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 Nanodisc (Intermediate State), PDB code: 6qma:
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 Nanodisc (Intermediate State)


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 Nanodisc (Intermediate State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:49.0 occ:1.00 OD2 A:ASP539 2.5 49.9 1.0 OE1 A:GLU506 2.5 52.1 1.0 OE2 A:GLU452 2.5 64.2 1.0 OE2 A:GLU535 2.5 51.4 1.0 OD1 A:ASP503 2.5 52.0 1.0 OD1 A:ASP539 2.8 49.9 1.0 CG A:ASP503 3.0 52.0 1.0 CG A:ASP539 3.0 49.9 1.0 CD A:GLU506 3.4 52.1 1.0 CB A:ASP503 3.4 52.0 1.0 CD A:GLU535 3.7 51.4 1.0 CD A:GLU452 3.7 64.2 1.0 CA A:ASP503 3.8 52.0 1.0 OD2 A:ASP503 3.8 52.0 1.0 OE2 A:GLU506 3.8 52.1 1.0 OH A:TYR188 3.9 44.6 1.0 OE1 A:GLU452 4.2 64.2 1.0 CG A:GLU535 4.3 51.4 1.0 CB A:GLU506 4.4 52.1 1.0 CG A:GLU506 4.5 52.1 1.0 CB A:ASP539 4.5 49.9 1.0 O A:ASP503 4.6 52.0 1.0 OE1 A:GLU535 4.6 51.4 1.0 C A:ASP503 4.7 52.0 1.0 NZ A:LYS542 4.8 51.0 1.0 N A:ASP503 4.8 52.0 1.0 CG A:GLU452 4.9 64.2 1.0 CE A:MET507 4.9 46.6 1.0 CZ A:TYR188 5.0 44.6 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Intermediate State)


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 Nanodisc (Intermediate State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:66.1 occ:1.00 OE1 A:GLU535 2.5 51.4 1.0 ND2 A:ASN448 2.6 66.4 1.0 OE1 A:GLU452 2.6 64.2 1.0 CG A:ASN448 3.3 66.4 1.0 CD A:GLU535 3.4 51.4 1.0 OE2 A:GLU535 3.5 51.4 1.0 OE2 A:GLU506 3.5 52.1 1.0 CD A:GLU452 3.7 64.2 1.0 OD1 A:ASN448 3.8 66.4 1.0 N A:PHE449 3.9 67.1 1.0 C A:ASN448 3.9 66.4 1.0 CA A:PHE449 4.0 67.1 1.0 O A:ASN448 4.0 66.4 1.0 CB A:ASN448 4.1 66.4 1.0 OE2 A:GLU452 4.2 64.2 1.0 CD1 A:PHE449 4.3 67.1 1.0 OD1 A:ASN531 4.3 52.7 1.0 CB A:PHE449 4.4 67.1 1.0 CD A:GLU506 4.5 52.1 1.0 CB A:GLU452 4.6 64.2 1.0 OG A:SER538 4.7 50.0 1.0 CA A:ASN448 4.7 66.4 1.0 CG A:GLU452 4.7 64.2 1.0 CG A:GLU535 4.7 51.4 1.0 O A:GLN445 4.8 67.2 1.0 ND2 A:ASN531 4.8 52.7 1.0 CG A:PHE449 4.8 67.1 1.0 OE1 A:GLU506 4.8 52.1 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Intermediate State)


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 Nanodisc (Intermediate State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:49.0 occ:1.00 OD2 B:ASP539 2.5 49.9 1.0 OE1 B:GLU506 2.5 52.1 1.0 OE2 B:GLU452 2.5 64.2 1.0 OE2 B:GLU535 2.5 51.4 1.0 OD1 B:ASP503 2.5 52.0 1.0 OD1 B:ASP539 2.8 49.9 1.0 CG B:ASP503 3.0 52.0 1.0 CG B:ASP539 3.0 49.9 1.0 CD B:GLU506 3.4 52.1 1.0 CB B:ASP503 3.4 52.0 1.0 CD B:GLU535 3.7 51.4 1.0 CD B:GLU452 3.7 64.2 1.0 CA B:ASP503 3.8 52.0 1.0 OD2 B:ASP503 3.8 52.0 1.0 OE2 B:GLU506 3.8 52.1 1.0 OH B:TYR188 3.9 44.6 1.0 OE1 B:GLU452 4.2 64.2 1.0 CG B:GLU535 4.3 51.4 1.0 CB B:GLU506 4.4 52.1 1.0 CG B:GLU506 4.5 52.1 1.0 CB B:ASP539 4.5 49.9 1.0 O B:ASP503 4.6 52.0 1.0 OE1 B:GLU535 4.6 51.4 1.0 C B:ASP503 4.7 52.0 1.0 NZ B:LYS542 4.8 51.0 1.0 N B:ASP503 4.8 52.0 1.0 CG B:GLU452 4.9 64.2 1.0 CE B:MET507 4.9 46.6 1.0 CZ B:TYR188 5.0 44.6 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Calcium-Bound NHTMEM16 Lipid Scramblase in Nanodisc (Intermediate State)


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 Nanodisc (Intermediate State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:66.1 occ:1.00 OE1 B:GLU535 2.5 51.4 1.0 ND2 B:ASN448 2.6 66.4 1.0 OE1 B:GLU452 2.6 64.2 1.0 CG B:ASN448 3.3 66.4 1.0 CD B:GLU535 3.4 51.4 1.0 OE2 B:GLU535 3.5 51.4 1.0 OE2 B:GLU506 3.5 52.1 1.0 CD B:GLU452 3.7 64.2 1.0 OD1 B:ASN448 3.8 66.4 1.0 N B:PHE449 3.9 67.1 1.0 C B:ASN448 3.9 66.4 1.0 CA B:PHE449 4.0 67.1 1.0 O B:ASN448 4.0 66.4 1.0 CB B:ASN448 4.1 66.4 1.0 OE2 B:GLU452 4.2 64.2 1.0 CD1 B:PHE449 4.3 67.1 1.0 OD1 B:ASN531 4.3 52.7 1.0 CB B:PHE449 4.4 67.1 1.0 CD B:GLU506 4.5 52.1 1.0 CB B:GLU452 4.6 64.2 1.0 OG B:SER538 4.7 50.0 1.0 CA B:ASN448 4.7 66.4 1.0 CG B:GLU452 4.7 64.2 1.0 CG B:GLU535 4.7 51.4 1.0 O B:GLN445 4.8 67.2 1.0 ND2 B:ASN531 4.8 52.7 1.0 CG B:PHE449 4.8 67.1 1.0 OE1 B:GLU506 4.8 52.1 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