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

The binding sites of Calcium atom in the NHTMEM16 Lipid Scramblase in Lipid Nanodiscs with MSP2N2 Scaffold Protein in the Presence of CA2+ (Intermediate State) (pdb code 8tpn). 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+ (Intermediate State), PDB code: 8tpn:
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+ (Intermediate 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+ (Intermediate State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:32.4 occ:1.00 OE2 A:GLU535 2.3 17.6 1.0 OD1 A:ASP503 2.4 15.7 1.0 OE1 A:GLU452 2.5 30.9 1.0 OD1 A:ASP539 2.6 19.2 1.0 OE2 A:GLU452 2.8 30.9 1.0 CD A:GLU452 2.9 30.9 1.0 NZ A:LYS542 3.2 21.7 1.0 CG A:ASP539 3.3 19.2 1.0 OD2 A:ASP539 3.3 19.2 1.0 CD A:GLU535 3.5 17.6 1.0 CG A:ASP503 3.6 15.7 1.0 OE1 A:GLU506 3.6 14.7 1.0 CG A:GLU452 4.2 30.9 1.0 OE1 A:GLU535 4.3 17.6 1.0 CD A:GLU506 4.3 14.7 1.0 OD2 A:ASP503 4.3 15.7 1.0 CE A:LYS542 4.4 21.7 1.0 CG A:GLU535 4.6 17.6 1.0 OE2 A:GLU506 4.6 14.7 1.0 CB A:ASP503 4.7 15.7 1.0 CB A:ASP539 4.8 19.2 1.0 CA A:ASP503 4.9 15.7 1.0 OD1 A:ASN448 4.9 29.3 1.0 OH A:TYR188 5.0 11.9 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+ (Intermediate 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+ (Intermediate State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:20.8 occ:1.00 OE1 A:GLU535 2.3 17.6 1.0 ND2 A:ASN448 2.4 29.3 1.0 CG A:ASN448 2.8 29.3 1.0 CD A:GLU535 3.4 17.6 1.0 OD1 A:ASN448 3.4 29.3 1.0 CB A:ASN448 3.5 29.3 1.0 OD1 A:ASN531 3.6 18.4 1.0 O A:ASN448 3.7 29.3 1.0 OE2 A:GLU535 3.8 17.6 1.0 OE1 A:GLU452 3.9 30.9 1.0 ND2 A:ASN531 4.1 18.4 1.0 C A:ASN448 4.2 29.3 1.0 CG A:ASN531 4.3 18.4 1.0 OE1 A:GLU506 4.4 14.7 1.0 CA A:ASN448 4.4 29.3 1.0 CG A:GLU535 4.6 17.6 1.0 CB A:GLU535 4.8 17.6 1.0 CD A:GLU452 4.9 30.9 1.0 N A:PHE449 5.0 31.0 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+ (Intermediate 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+ (Intermediate State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:32.4 occ:1.00 OE2 B:GLU535 2.3 17.6 1.0 OD1 B:ASP503 2.4 15.7 1.0 OE1 B:GLU452 2.5 30.9 1.0 OD1 B:ASP539 2.6 19.2 1.0 OE2 B:GLU452 2.8 30.9 1.0 CD B:GLU452 2.9 30.9 1.0 NZ B:LYS542 3.2 21.7 1.0 CG B:ASP539 3.3 19.2 1.0 OD2 B:ASP539 3.3 19.2 1.0 CD B:GLU535 3.5 17.6 1.0 CG B:ASP503 3.6 15.7 1.0 OE1 B:GLU506 3.6 14.7 1.0 CG B:GLU452 4.2 30.9 1.0 OE1 B:GLU535 4.3 17.6 1.0 CD B:GLU506 4.3 14.7 1.0 OD2 B:ASP503 4.3 15.7 1.0 CE B:LYS542 4.4 21.7 1.0 CG B:GLU535 4.6 17.6 1.0 OE2 B:GLU506 4.6 14.7 1.0 CB B:ASP503 4.7 15.7 1.0 CB B:ASP539 4.8 19.2 1.0 CA B:ASP503 4.9 15.7 1.0 OD1 B:ASN448 4.9 29.3 1.0 OH B:TYR188 5.0 11.9 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+ (Intermediate 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+ (Intermediate State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:20.8 occ:1.00 OE1 B:GLU535 2.3 17.6 1.0 ND2 B:ASN448 2.4 29.3 1.0 CG B:ASN448 2.8 29.3 1.0 CD B:GLU535 3.4 17.6 1.0 OD1 B:ASN448 3.4 29.3 1.0 CB B:ASN448 3.5 29.3 1.0 OD1 B:ASN531 3.6 18.4 1.0 O B:ASN448 3.7 29.3 1.0 OE2 B:GLU535 3.8 17.6 1.0 OE1 B:GLU452 3.9 30.9 1.0 ND2 B:ASN531 4.1 18.4 1.0 C B:ASN448 4.2 29.3 1.0 CG B:ASN531 4.3 18.4 1.0 OE1 B:GLU506 4.4 14.7 1.0 CA B:ASN448 4.4 29.3 1.0 CG B:GLU535 4.6 17.6 1.0 CB B:GLU535 4.8 17.6 1.0 CD B:GLU452 4.9 30.9 1.0 N B:PHE449 5.0 31.0 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