Calcium in PDB 8tok: NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP2N2 Scaffold Protein in the Presence of CA2+ (Open State)

The binding sites of Calcium atom in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP2N2 Scaffold Protein in the Presence of CA2+ (Open State) (pdb code 8tok). 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 MSP2N2 Scaffold Protein in the Presence of CA2+ (Open State), PDB code: 8tok:
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 MSP2N2 Scaffold Protein in the Presence of CA2+ (Open 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 MSP2N2 Scaffold Protein in the Presence of CA2+ (Open State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:8.9 occ:1.00 OD1 A:ASP503 2.3 13.7 1.0 OE2 A:GLU535 2.3 6.2 1.0 OD2 A:ASP539 2.6 8.1 1.0 OD1 A:ASP539 2.8 8.1 1.0 OE2 A:GLU452 2.9 17.3 1.0 OE1 A:GLU506 2.9 8.6 1.0 CG A:ASP539 3.0 8.1 1.0 CD A:GLU535 3.3 6.2 1.0 CG A:ASP503 3.4 13.7 1.0 CG A:GLU535 3.6 6.2 1.0 CD A:GLU452 3.7 17.3 1.0 OE1 A:GLU452 3.7 17.3 1.0 OH A:TYR188 3.9 12.3 1.0 CB A:ASP503 3.9 13.7 1.0 CD A:GLU506 4.0 8.6 1.0 CA A:ASP503 4.2 13.7 1.0 OE2 A:GLU506 4.4 8.6 1.0 OE1 A:GLU535 4.4 6.2 1.0 OD2 A:ASP503 4.4 13.7 1.0 CB A:ASP539 4.5 8.1 1.0 NZ A:LYS542 4.7 8.9 1.0 CE A:MET507 4.9 8.8 1.0 CA A:CA802 5.0 11.4 1.0

Calcium binding site 2 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP2N2 Scaffold Protein in the Presence of CA2+ (Open 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 MSP2N2 Scaffold Protein in the Presence of CA2+ (Open State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:11.4 occ:1.00 OE1 A:GLU535 2.4 6.2 1.0 OD1 A:ASN448 2.4 8.0 1.0 OE2 A:GLU535 3.0 6.2 1.0 CD A:GLU535 3.0 6.2 1.0 OE2 A:GLU506 3.3 8.6 1.0 OE1 A:GLU452 3.4 17.3 1.0 CG A:ASN448 3.6 8.0 1.0 OD1 A:ASN531 3.8 4.1 1.0 N A:PHE449 4.1 10.7 1.0 CA A:PHE449 4.1 10.7 1.0 CD A:GLU506 4.1 8.6 1.0 CB A:PHE449 4.2 10.7 1.0 OE1 A:GLU506 4.3 8.6 1.0 C A:ASN448 4.5 8.0 1.0 CB A:ASN448 4.5 8.0 1.0 CG A:GLU535 4.5 6.2 1.0 ND2 A:ASN448 4.6 8.0 1.0 CD A:GLU452 4.6 17.3 1.0 O A:GLN445 4.7 1.7 1.0 O A:ASN448 4.7 8.0 1.0 CG A:ASN531 4.8 4.1 1.0 ND2 A:ASN531 4.8 4.1 1.0 CA A:CA801 5.0 8.9 1.0

Calcium binding site 3 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP2N2 Scaffold Protein in the Presence of CA2+ (Open 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 MSP2N2 Scaffold Protein in the Presence of CA2+ (Open State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:8.9 occ:1.00 OD1 B:ASP503 2.3 13.7 1.0 OE2 B:GLU535 2.3 6.2 1.0 OD2 B:ASP539 2.6 8.1 1.0 OD1 B:ASP539 2.8 8.1 1.0 OE2 B:GLU452 2.9 17.3 1.0 OE1 B:GLU506 2.9 8.6 1.0 CG B:ASP539 3.0 8.1 1.0 CD B:GLU535 3.3 6.2 1.0 CG B:ASP503 3.4 13.7 1.0 CG B:GLU535 3.6 6.2 1.0 CD B:GLU452 3.7 17.3 1.0 OE1 B:GLU452 3.7 17.3 1.0 OH B:TYR188 3.9 12.3 1.0 CB B:ASP503 3.9 13.7 1.0 CD B:GLU506 4.0 8.6 1.0 CA B:ASP503 4.2 13.7 1.0 OE2 B:GLU506 4.4 8.6 1.0 OE1 B:GLU535 4.4 6.2 1.0 OD2 B:ASP503 4.4 13.7 1.0 CB B:ASP539 4.5 8.1 1.0 NZ B:LYS542 4.7 8.9 1.0 CE B:MET507 4.9 8.8 1.0 CA B:CA802 5.0 11.4 1.0

Calcium binding site 4 out of 4 in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP2N2 Scaffold Protein in the Presence of CA2+ (Open 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 MSP2N2 Scaffold Protein in the Presence of CA2+ (Open State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:11.4 occ:1.00 OE1 B:GLU535 2.4 6.2 1.0 OD1 B:ASN448 2.4 8.0 1.0 OE2 B:GLU535 3.0 6.2 1.0 CD B:GLU535 3.0 6.2 1.0 OE2 B:GLU506 3.3 8.6 1.0 OE1 B:GLU452 3.4 17.3 1.0 CG B:ASN448 3.6 8.0 1.0 OD1 B:ASN531 3.8 4.1 1.0 N B:PHE449 4.1 10.7 1.0 CA B:PHE449 4.1 10.7 1.0 CD B:GLU506 4.1 8.6 1.0 CB B:PHE449 4.2 10.7 1.0 OE1 B:GLU506 4.3 8.6 1.0 C B:ASN448 4.5 8.0 1.0 CB B:ASN448 4.5 8.0 1.0 CG B:GLU535 4.5 6.2 1.0 ND2 B:ASN448 4.6 8.0 1.0 CD B:GLU452 4.6 17.3 1.0 O B:GLN445 4.7 1.7 1.0 O B:ASN448 4.7 8.0 1.0 CG B:ASN531 4.8 4.1 1.0 ND2 B:ASN531 4.8 4.1 1.0 CA B:CA801 5.0 8.9 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