Calcium in PDB 8toi: NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State)

The binding sites of Calcium atom in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State) (pdb code 8toi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State), PDB code: 8toi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:55.2 occ:1.00 OD2 A:ASP539 2.5 55.0 1.0 OE2 A:GLU452 2.6 70.9 1.0 OE2 A:GLU535 2.6 53.3 1.0 OE1 A:GLU506 2.6 56.2 1.0 OD1 A:ASP503 2.7 55.1 1.0 OD1 A:ASP539 2.8 55.0 1.0 CG A:ASP539 3.0 55.0 1.0 CG A:ASP503 3.4 55.1 1.0 CD A:GLU452 3.4 70.9 1.0 OE1 A:GLU452 3.6 70.9 1.0 CD A:GLU506 3.6 56.2 1.0 CD A:GLU535 3.6 53.3 1.0 CB A:ASP503 3.8 55.1 1.0 NZ A:LYS542 3.9 57.9 1.0 OH A:TYR188 4.0 50.1 1.0 CG A:GLU535 4.0 53.3 1.0 CA A:ASP503 4.0 55.1 1.0 OE2 A:GLU506 4.1 56.2 1.0 OD2 A:ASP503 4.3 55.1 1.0 CB A:ASP539 4.5 55.0 1.0 CA A:CA802 4.5 60.9 1.0 CB A:GLU506 4.7 56.2 1.0 OE1 A:GLU535 4.7 53.3 1.0 CG A:GLU506 4.7 56.2 1.0 CE A:LYS542 4.9 57.9 1.0 CG A:GLU452 4.9 70.9 1.0 O A:ASP503 4.9 55.1 1.0 CE A:MET507 4.9 52.8 1.0 N A:ASP503 5.0 55.1 1.0 C A:ASP503 5.0 55.1 1.0

Calcium binding site 2 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:60.9 occ:1.00 OE2 A:GLU535 2.5 53.3 1.0 OD1 A:ASN448 2.5 71.5 1.0 OE1 A:GLU535 2.6 53.3 1.0 OE1 A:GLU452 2.7 70.9 1.0 OE2 A:GLU506 2.8 56.2 1.0 CD A:GLU535 2.9 53.3 1.0 CD A:GLU506 3.6 56.2 1.0 CG A:ASN448 3.7 71.5 1.0 OE1 A:GLU506 3.8 56.2 1.0 CD A:GLU452 3.9 70.9 1.0 O A:ASN448 4.0 71.5 1.0 OD1 A:ASN531 4.2 52.2 1.0 CG A:GLU535 4.4 53.3 1.0 CA A:CA801 4.5 55.2 1.0 OE2 A:GLU452 4.5 70.9 1.0 C A:ASN448 4.5 71.5 1.0 CB A:ASN448 4.6 71.5 1.0 ND2 A:ASN448 4.7 71.5 1.0 ND2 A:ASN531 4.8 52.2 1.0 CB A:GLU452 4.9 70.9 1.0 CG A:ASN531 4.9 52.2 1.0

Calcium binding site 3 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:55.2 occ:1.00 OD2 B:ASP539 2.5 55.0 1.0 OE2 B:GLU452 2.6 70.9 1.0 OE2 B:GLU535 2.6 53.3 1.0 OE1 B:GLU506 2.6 56.2 1.0 OD1 B:ASP503 2.7 55.1 1.0 OD1 B:ASP539 2.8 55.0 1.0 CG B:ASP539 3.0 55.0 1.0 CG B:ASP503 3.4 55.1 1.0 CD B:GLU452 3.4 70.9 1.0 OE1 B:GLU452 3.6 70.9 1.0 CD B:GLU506 3.6 56.2 1.0 CD B:GLU535 3.6 53.3 1.0 CB B:ASP503 3.8 55.1 1.0 NZ B:LYS542 3.9 57.9 1.0 OH B:TYR188 4.0 50.1 1.0 CG B:GLU535 4.0 53.3 1.0 CA B:ASP503 4.0 55.1 1.0 OE2 B:GLU506 4.1 56.2 1.0 OD2 B:ASP503 4.3 55.1 1.0 CB B:ASP539 4.5 55.0 1.0 CA B:CA802 4.5 60.9 1.0 CB B:GLU506 4.7 56.2 1.0 OE1 B:GLU535 4.7 53.3 1.0 CG B:GLU506 4.7 56.2 1.0 CE B:LYS542 4.9 57.9 1.0 CG B:GLU452 4.9 70.9 1.0 O B:ASP503 4.9 55.1 1.0 CE B:MET507 4.9 52.8 1.0 N B:ASP503 5.0 55.1 1.0 C B:ASP503 5.0 55.1 1.0

Calcium binding site 4 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP1E3 Scaffold Protein in the Presence of CA2+ (Closed State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:60.9 occ:1.00 OE2 B:GLU535 2.5 53.3 1.0 OD1 B:ASN448 2.6 71.5 1.0 OE1 B:GLU535 2.6 53.3 1.0 OE1 B:GLU452 2.7 70.9 1.0 OE2 B:GLU506 2.8 56.2 1.0 CD B:GLU535 2.9 53.3 1.0 CD B:GLU506 3.6 56.2 1.0 CG B:ASN448 3.8 71.5 1.0 OE1 B:GLU506 3.8 56.2 1.0 CD B:GLU452 3.9 70.9 1.0 O B:ASN448 4.0 71.5 1.0 OD1 B:ASN531 4.2 52.2 1.0 CG B:GLU535 4.4 53.3 1.0 CA B:CA801 4.5 55.2 1.0 OE2 B:GLU452 4.5 70.9 1.0 C B:ASN448 4.5 71.5 1.0 CB B:ASN448 4.6 71.5 1.0 ND2 B:ASN448 4.7 71.5 1.0 ND2 B:ASN531 4.8 52.2 1.0 CB B:GLU452 4.9 70.9 1.0 CG B:ASN531 4.9 52.2 1.0

Z.Feng, O.E.Alvarenga, A.Accardi. Structural Basis of Closed Groove Scrambling By A TMEM16 Protein. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
PubMed: 38684930
DOI: 10.1038/S41594-024-01284-9